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GitLab

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<h3>

Andrius Merkys pushed to branch upstream

at <a href="https://salsa.debian.org/java-team/openchemlib">Debian Java Maintainers / openchemlib</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb">f63e99bf</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2021-10-04T02:16:25-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.10.0+dfsg</pre>

</li>

</ul>

<h4>29 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">

pom.xml

</a>

</li>

<li class="file-stats">

<a href="#67800693fa8bb7e226e47f0411ca790ea518c656">

src/main/java/com/actelion/research/chem/Canonizer.java

</a>

</li>

<li class="file-stats">

<a href="#a366ae93c6b2697647f789b85e058d12270016b2">

src/main/java/com/actelion/research/chem/ExtendedMolecule.java

</a>

</li>

<li class="file-stats">

<a href="#3357d4852d9e2d697d79a0b5c96ed0a78ce44afb">

src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java

</a>

</li>

<li class="file-stats">

<a href="#ba44c1f7e56c2598decf65ca012c856547ff2f0f">

src/main/java/com/actelion/research/chem/SmilesParser.java

</a>

</li>

<li class="file-stats">

<a href="#b3f92c9221147b0b87192f33311736c1b323a29c">

src/main/java/com/actelion/research/chem/StereoIsomerEnumerator.java

</a>

</li>

<li class="file-stats">

<a href="#297bbf96bfa984fd860791b0f081b476f79d916b">

src/main/java/com/actelion/research/chem/TautomerHelper.java

</a>

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<li class="file-stats">

<a href="#2324bbf7db1501a1bb2aaae4a1db707a20b5f9b1">

src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java

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<li class="file-stats">

<a href="#42976117f38fa37d60dd738b507feb19719d5616">

src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java

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</li>

<li class="file-stats">

<a href="#ec05b3badbc5071521d94ee516cf51235293f843">

src/main/java/com/actelion/research/chem/docking/DockingEngine.java

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<li class="file-stats">

<a href="#819430bd4feb0962132eaba56931cbec7c761fd8">

src/main/java/com/actelion/research/chem/docking/LigandPose.java

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<li class="file-stats">

<a href="#6bf6bc0e867dc60438664fa7e2197883ae9a4053">

src/main/java/com/actelion/research/chem/docking/scoring/AbstractScoringEngine.java

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<li class="file-stats">

<a href="#35842adf3930ed08842a9c3177f4efd0161d8603">

src/main/java/com/actelion/research/chem/docking/scoring/ChemPLP.java

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<li class="file-stats">

<a href="#1e236c5e43c30a02fbeea4e900a0c284f6fa34a8">

src/main/java/com/actelion/research/chem/docking/scoring/IdoScore.java

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<li class="file-stats">

<a href="#b913e9301eb349935afa9f9053995d0205bb3b8e">

src/main/java/com/actelion/research/chem/io/Mol2FileParser.java

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</li>

<li class="file-stats">

<a href="#262e1a444c63ad8c6f38e8d5341f3605e1f567ee">

src/main/java/com/actelion/research/chem/properties/complexity/ContainerFragBondsSolutions.java

</a>

</li>

<li class="file-stats">

<a href="#45e84a8050acd058a0497af42eacc0972aec8aa0">

src/main/java/com/actelion/research/chem/properties/complexity/ExhaustiveFragmentsStatistics.java

</a>

</li>

<li class="file-stats">

<a href="#cb31a3eb9ce056b7b6950e3c00e22e6ea9374b65">

src/main/java/com/actelion/research/chem/reaction/mapping/MappingScorer.java

</a>

</li>

<li class="file-stats">

<a href="#60ccb435ab9538009a24ad8c50dfe7583b481728">

src/main/java/com/actelion/research/chem/reaction/mapping/RootAtomPairSource.java

</a>

</li>

<li class="file-stats">

<a href="#fd828ea16dfc40dd5d8d20957d2ed4a3e324497c">

src/main/java/com/actelion/research/chem/reaction/mapping/SimilarityGraphBasedReactionMapper.java

</a>

</li>

<li class="file-stats">

<a href="#e4a461ea6c1e83c20f9aecaffed9344cdcbe8a19">

src/main/java/com/actelion/research/gui/JDrawDialog.java

</a>

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<li class="file-stats">

<a href="#4c2a41d526b7b14792efa22a7224c243662939f7">

src/main/java/com/actelion/research/gui/JEditableChemistryView.java

</a>

</li>

<li class="file-stats">

<a href="#0286e69308a5dc8f38cd96a6e642e56ef8ffa0e1">

src/main/java/com/actelion/research/gui/clipboard/ClipboardHandler.java

</a>

</li>

<li class="file-stats">

<a href="#6e2078f60f1fd5ba17658e0850d34a9a27b9ae38">

<span class="new-file">

+

src/main/java/com/actelion/research/gui/dock/DividerChangeListener.java

</span>

</a>

</li>

<li class="file-stats">

<a href="#e0ad42de8a1873c3f3f3a7e6771a49e8e3a1ddcb">

src/main/java/com/actelion/research/gui/dock/JDockingPanel.java

</a>

</li>

<li class="file-stats">

<a href="#eb4ec2cc0ab826869c0310cdf4b423f1e8123cb9">

src/main/java/com/actelion/research/gui/dock/TreeFork.java

</a>

</li>

<li class="file-stats">

<a href="#473d383df3e59af9a3f20234b3ff116ee7ffe896">

src/main/java/com/actelion/research/gui/dock/TreeLeaf.java

</a>

</li>

<li class="file-stats">

<a href="#844f2796cb8822367a2a6bc3ad00b9d56d5e18b3">

src/main/java/com/actelion/research/gui/dock/TreeRoot.java

</a>

</li>

<li class="file-stats">

<a href="#ec1e7f260c5e341b5b4551f820f746b392a3e2e8">

src/main/java/com/actelion/research/util/ConstantsDWAR.java

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="442292b8a7efeabbe4cc176709b833b1792140ec">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">    Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">    (eg. 2016.4.1 for second release in Apr 2016)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">    --></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="xml">    <span class="nt" style="color: #000080;"><version></span>2021.<span class="idiff left right">9</span>.0<span class="nt" style="color: #000080;"></version></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="xml">    <span class="nt" style="color: #000080;"><version></span>2021.<span class="idiff left right">10</span>.0<span class="nt" style="color: #000080;"></version></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="xml">    <span class="nt" style="color: #000080;"><name></span>OpenChemLib<span class="nt" style="color: #000080;"></name></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="xml">    <span class="nt" style="color: #000080;"><description></span>Open Source Chemistry Library<span class="nt" style="color: #000080;"></description></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,7 +195,7 @@</td>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="xml">        <span class="nt" style="color: #000080;"><connection></span>scm:git:git@github.com:Actelion/openchemlib.git<span class="nt" style="color: #000080;"></connection></span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="xml">        <span class="nt" style="color: #000080;"><developerConnection></span>scm:git:git@github.com:Actelion/openchemlib.git<span class="nt" style="color: #000080;"></developerConnection></span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="xml">        <span class="nt" style="color: #000080;"><url></span>https://github.com/Actelion/openchemlib<span class="nt" style="color: #000080;"></url></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="xml">      <span class="nt" style="color: #000080;"><tag></span>openchemlib-2021.<span class="idiff left right">9</span>.0<span class="nt" style="color: #000080;"></tag></span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="xml">      <span class="nt" style="color: #000080;"><tag></span>openchemlib-2021.<span class="idiff left right">10</span>.0<span class="nt" style="color: #000080;"></tag></span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="xml">  <span class="nt" style="color: #000080;"></scm></span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="xml"></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="xml">    <span class="nt" style="color: #000080;"><distributionManagement></span></span>

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<br>

</li>

<li id="67800693fa8bb7e226e47f0411ca790ea518c656">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#67800693fa8bb7e226e47f0411ca790ea518c656"><strong>src/main/java/com/actelion/research/chem/Canonizer.java</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -245,9 +245,10 @@ public class Canonizer {</td>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Locate those tetrahedral nitrogen atoms with at least 3 neighbors that</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * qualify for tetrahedral parity calculation because:<br></span></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * - they are quarternary nitrogen atoms<br></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * or - their configuration inversion is hindered in a polycyclic structure<br></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * or - flag ASSIGN_PARITIES_TO_TETRAHEDRAL_N is set</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * - being a quarternary nitrogen atom<br></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * - being an aziridin nitrogen atom<br></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * - the configuration inversion is hindered in a polycyclic structure<br></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * - flag ASSIGN_PARITIES_TO_TETRAHEDRAL_N is set</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">canFindNitrogenQualifyingForParity</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="java">         <span class="n" style="color: #333;">mNitrogenQualifiesForParity</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -258,6 +259,11 @@ public class Canonizer {</td>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomRingSize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="java">                                         <span class="n" style="color: #333;">mNitrogenQualifiesForParity</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="java">                                         <span class="n" style="color: #333;">mNitrogenQualifiesForParity</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

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<br>

</li>

<li id="a366ae93c6b2697647f789b85e058d12270016b2">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#a366ae93c6b2697647f789b85e058d12270016b2"><strong>src/main/java/com/actelion/research/chem/ExtendedMolecule.java</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,7 +232,7 @@ public class ExtendedMolecule extends Molecule implements Serializable {</td>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * The neighbours (connected atoms) of any atom are sorted by their relevance:<br></span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * 1. non-hydrogen atoms (bond order 1 and above) and unusual hydrogen atoms (non natural abundance isotops, custom labelled hydrogen, etc.)<br></span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * 2. plain-hydrogen atoms (natural abundance, bond order 1)<br></span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * 3. loosely connected atoms (bond order 0, i.e. metal<span class="idiff left right">l</span> ligand bond)<br></span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * 3. loosely connected atoms (bond order 0, i.e. metal ligand bond)<br></span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Only valid after calling ensureHelperArrays(cHelperNeighbours or higher);</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param atom</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return count of category 1 & 2 neighbour atoms (excludes neighbours connected with zero bond order)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3141,13 +3141,13 @@ public class ExtendedMolecule extends Molecule implements Serializable {</td>

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<pre style="margin: 0;"> <span id="LC3141" class="line" lang="java">                <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">getHandleHydrogenAtomMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">findSimpleHydrogens</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC3142" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC3143" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC3144" class="line" lang="java"><span class="idiff left right"> </span>   <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">-<span id="LC3145" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">     </span>    * If ensureHelperArrays() (and with it handleHydrogens()) was not called yet</span></span>

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<pre style="margin: 0;">-<span id="LC3146" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">     </span>    * on a fresh molecule and if the molecule contains simple hydrogen atoms within</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3147" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">     </span>    * non-hydrogens atoms, then this function returns a map from current atom indexes</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="3144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3148" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">     </span>    * to those new atom indexes that would result from a call to handleHydrogens.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3149" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">     </span>    * @return</span></span>

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<pre style="margin: 0;">-<span id="LC3150" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">     </span>    */</span></span>

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<pre style="margin: 0;">+<span id="LC3144" class="line" lang="java">        <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">+<span id="LC3145" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * If ensureHelperArrays() (and with it handleHydrogens()) was not called yet</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3146" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * on a fresh molecule and if the molecule contains simple hydrogen atoms within</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3147" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * non-hydrogens atoms, then this function returns a map from current atom indexes</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3148" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * to those new atom indexes that would result from a call to handleHydrogens.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3149

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<pre style="margin: 0;">+<span id="LC3149" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @return</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3150

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<pre style="margin: 0;">+<span id="LC3150" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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3151

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3151

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<pre style="margin: 0;"> <span id="LC3151" class="line" lang="java">        <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">getHandleHydrogenAtomMap</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3152

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3152

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<pre style="margin: 0;"> <span id="LC3152" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mAllAtoms</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3153

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3153

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<pre style="margin: 0;"> <span id="LC3153" class="line" lang="java">                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mAllAtoms</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3163,6 +3163,11 @@ public class ExtendedMolecule extends Molecule implements Serializable {</td>

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3163

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3163

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<pre style="margin: 0;"> <span id="LC3163" class="line" lang="java">                                <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lastNonHAtom</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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3164

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<td class="new_line diff-line-num" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3164

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<pre style="margin: 0;"> <span id="LC3164" class="line" lang="java">                                <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lastNonHAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempIndex</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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3165

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<td class="new_line diff-line-num" data-linenumber="3165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3165

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<pre style="margin: 0;"> <span id="LC3165" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3166

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<pre style="margin: 0;">+<span id="LC3166" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// swap simple H flags also</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3167

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<pre style="margin: 0;">+<span id="LC3167" class="line" lang="java">                                <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">temp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3168

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<pre style="margin: 0;">+<span id="LC3168" class="line" lang="java">                                <span class="n" style="color: #333;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lastNonHAtom</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3169

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<pre style="margin: 0;">+<span id="LC3169" class="line" lang="java">                                <span class="n" style="color: #333;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lastNonHAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3170

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<pre style="margin: 0;">+<span id="LC3170" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3166

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<td class="new_line diff-line-num" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3171

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<pre style="margin: 0;"> <span id="LC3171" class="line" lang="java">                                <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">lastNonHAtom</span><span class="o" style="font-weight: 600;">--;</span></span>

</pre>

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3167

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<td class="new_line diff-line-num" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3172

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<pre style="margin: 0;"> <span id="LC3172" class="line" lang="java">                                <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lastNonHAtom</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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3168

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<td class="new_line diff-line-num" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3173

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<pre style="margin: 0;"> <span id="LC3173" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<br>

</li>

<li id="3357d4852d9e2d697d79a0b5c96ed0a78ce44afb">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#3357d4852d9e2d697d79a0b5c96ed0a78ce44afb"><strong>src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,12 +50,10 @@ public class IsomericSmilesCreator {</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAtomRank</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mSmilesIndex</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mClosureBuffer</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">mKnownTHCountInESRGroup</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mGraphAtomList</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAtomUsed</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mClosureOpened</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mPseudoStereoGroupInversion</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mPseudoStereoGroupInitialized</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">findRingClosures</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">closureNumberUsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">()];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java">         <span class="n" style="color: #333;">mClosureNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">()];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// find closure neighbours of every atom and put them in canonical order. i.e. order of appearance in SMILES</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span> <span class="nl">smilesAtom:</span><span class="n" style="color: #333;">mGraphAtomList</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java">                         <span class="n" style="color: #333;">closureNumberUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getUnusedConnBondIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java">                 <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">closureBond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java">                         <span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureBond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">closureNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java">                         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">closureNumberUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureNumber</span><span class="o" style="font-weight: 600;">])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java">                                 <span class="n" style="color: #333;">closureNumber</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

225

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<td class="new_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

226

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java">                         <span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureBond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">closureNumber</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

227

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<td class="new_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="java">                         <span class="n" style="color: #333;">closureNumberUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureNumber</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">closureCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)])</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java">                                 <span class="n" style="color: #333;">closureCount</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">closureCount</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="java">                         <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureCount</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java">                         <span class="n" style="color: #333;">closureCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java">                         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)])</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighbour</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java">                                         <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureCount</span><span class="o" style="font-weight: 600;">++]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mSmilesIndex</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">neighbour</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">neighbour</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java">                         <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getUnusedConnBondIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java">                         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java">                                 <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x0000FFFF</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="java">         <span class="n" style="color: #333;">mClosureOpened</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">()];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="java">         <span class="n" style="color: #333;">mClosureBuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// assign closure digits to closure bonds</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">closureNumberUsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">()];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java">         <span class="n" style="color: #333;">mClosureNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">()];</span></span>

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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span> <span class="nl">smilesAtom:</span><span class="n" style="color: #333;">mGraphAtomList</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java">                         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nl">neighbour:</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">neighbour</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">// opening closure bond</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="java">                                                         <span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="java">                                                         <span class="c1" style="color: #998; font-style: italic;">// assign and allocation closure digit</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="java">                                                         <span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">closureNumberUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]])</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java">                                                                 <span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]++;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java">                                                         <span class="n" style="color: #333;">closureNumberUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java">                                                 <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span>  <span class="c1" style="color: #998; font-style: italic;">// closing closure bond: release closure digit</span></span>

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<td class="old_line diff-line-num new" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="java">                                                         <span class="n" style="color: #333;">closureNumberUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java">                                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">calculateEZBonds</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -391,16 +412,6 @@ public class IsomericSmilesCreator {</td>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestIndex</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getUnusedConnBondIndex</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

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397

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mBondUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

398

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bestIndex</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mAtomRank</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bestIndex</span><span class="o" style="font-weight: 600;">)]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mAtomRank</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)]))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

399

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="java">                         <span class="n" style="color: #333;">bestIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestIndex</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC403" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addToGraph</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">listIndex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="java">         <span class="n" style="color: #333;">mGraphAtomList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">listIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="java">         <span class="n" style="color: #333;">mAtomUsed</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -444,7 +455,7 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

444

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<td class="new_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

455

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isotop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMass</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

445

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<td class="new_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

456

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_INCLUDE_MAPPING</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

446

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<td class="new_line diff-line-num" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

457

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">smartsFeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_CREATE_SMARTS</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">getAtomSMARTSFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">smartsFeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_CREATE_SMARTS</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">getAtomSMARTSFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="kc" style="font-weight: 600;"><span class="idiff left right">null</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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448

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="java"></span>

</pre>

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449

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useBrackets</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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450

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="java">                         <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">isAnyAtom</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isOrganic</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -456,7 +467,7 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

456

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="old_line diff-line-num" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

457

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<td class="new_line diff-line-num" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomAbnormalValence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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458

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<td class="new_line diff-line-num" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomRadical</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomRadicalStateNone</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

459

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<td class="new_line diff-line-num old" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">smartsFeatures</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">length</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">smartsFeatures</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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460

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<td class="new_line diff-line-num" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

471

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

461

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<td class="new_line diff-line-num" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

472

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">useBrackets</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

462

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<td class="new_line diff-line-num" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="java">                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'['</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -483,6 +494,9 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

483

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<td class="new_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="java">                         <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">charge</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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484

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<td class="new_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

485

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<td class="new_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

496

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smartsFeatures</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="java">                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smartsFeatures</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC499" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="java">                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">':'</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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<td class="new_line diff-line-num" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

502

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="java">                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapNo</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -589,7 +603,8 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

589

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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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<td class="new_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC604" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

591

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<td class="new_line diff-line-num" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ringSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">queryFeatures</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingSize</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingSizeShift</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

592

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<td class="new_line diff-line-num old" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC592" class="line" lang="java">         <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";r"</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">ringSize</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ringSize</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC606" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringSize</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="java">                 <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";r"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ringSize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

593

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<td class="new_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC608" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<td class="new_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC609" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighbourFeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryFeatures</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNeighbours</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<td class="new_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC610" class="line" lang="java">         <span class="k" style="font-weight: 600;">switch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">neighbourFeatures</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -625,7 +640,7 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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<td class="new_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

640

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">queryFeatures</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFMoreNeighbours</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

626

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<td class="new_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="java">                 <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";!D"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">));</span>  <span class="c1" style="color: #998; font-style: italic;">// Convert into exact explicit neighbour count 'D'</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

628

</td>

<td class="new_line diff-line-num old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC628" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">buffer</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">length</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff">null</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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629

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644

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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630

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<td class="new_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

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<pre style="margin: 0;"> <span id="LC645" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<td class="new_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

646

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -647,31 +662,47 @@ public class IsomericSmilesCreator {</td>

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647

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<td class="new_line diff-line-num" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

662

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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<td class="new_line diff-line-num" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

663

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

649

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<td class="new_line diff-line-num" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

664

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">appendClosureBonds</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

650

</td>

<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC650" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">closureCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

651

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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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652

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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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653

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<pre style="margin: 0;">-<span id="LC653" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC654" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isOpenFlag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mClosureOpened</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="mh" style="color: #099;">0x40000000</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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655

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<pre style="margin: 0;">-<span id="LC655" class="line" lang="java">                         <span class="n" style="color: #333;">mClosureBuffer</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">closureCount</span><span class="o" style="font-weight: 600;">++]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isOpenFlag</span> <span class="o" style="font-weight: 600;">|</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">;</span></span>

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656

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<pre style="margin: 0;">-<span id="LC656" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC657" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC658" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">closureCount</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC659" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// when sorting, then put and handle open closures first</span></span>

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660

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<pre style="margin: 0;">-<span id="LC660" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mClosureBuffer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">closureCount</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// we must sort to be canonical</span></span>

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">closureCount</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC662" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mClosureBuffer</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x0003FFFF</span><span class="o" style="font-weight: 600;">;</span></span>

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663

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">closureNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">mClosureBuffer</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x3FFC0000</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC664" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mClosureOpened</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="java">                                 <span class="n" style="color: #333;">mClosureOpened</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="java">                                 <span class="n" style="color: #333;">appendBondOrderSymbol</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nl">neighbour:</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">closureNeighbour</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="java">                         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

668

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">neighbour</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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</td>

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<pre style="margin: 0;">+<span id="LC669" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</td>

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670

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="java">                                         <span class="n" style="color: #333;">appendBondOrderSymbol</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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</td>

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672

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="java">                                                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'%'</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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673

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<pre style="margin: 0;">+<span id="LC673" class="line" lang="java">                                         <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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674

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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667

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<td class="new_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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668

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<td class="new_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">closureNumber</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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669

</td>

<td class="new_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="java">                                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'%'</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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670

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<td class="new_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC670" class="line" lang="java">                         <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">closureNumber</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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671

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<td class="new_line diff-line-num" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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672

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<td class="new_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC677" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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673

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<pre style="margin: 0;"> <span id="LC678" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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674

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679

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC679" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//   private void appendClosureBonds(SmilesAtom smilesAtom, StringBuilder builder) {</span></span>

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//           int closureCount = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//           for (int i=0; i<mMol.getConnAtoms(smilesAtom.atom); i++) {</span></span>

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   int bond = mMol.getConnBond(smilesAtom.atom, i);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   if (mClosureNumber[bond] != 0) {</span></span>

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           int isOpenFlag = mClosureOpened[bond] ? 0 : 0x40000000;</span></span>

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           mClosureBuffer[closureCount++] = isOpenFlag | (mClosureNumber[bond] << 20) | bond;</span></span>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   }</span></span>

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//           }</span></span>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//           if (closureCount != 0) {</span></span>

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   // when sorting, then put and handle open closures first</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   Arrays.sort(mClosureBuffer, 0, closureCount); // we must sort to be canonical</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   for (int i=0; i<closureCount; i++) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           int bond = mClosureBuffer[i] & 0x0003FFFF;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           int closureNumber = ((mClosureBuffer[i] & 0x3FFC0000) >> 20);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           if (!mClosureOpened[bond]) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                                   mClosureOpened[bond] = true;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                                   appendBondOrderSymbol(bond, smilesAtom.atom, builder);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           }</span></span>

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           if (closureNumber > 9)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                                   builder.append('%');</span></span>

</pre>

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</td>

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                           builder.append(closureNumber);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                   }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC703" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//           }</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC704" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//   }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="java"></span>

</pre>

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675

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">appendBondOrderSymbol</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span> <span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

676

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<td class="new_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ezHalfParity</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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677

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<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="java">                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smilesAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ezHalfParity</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;">:</span> <span class="sc" style="color: #d14;">'\\'</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -814,23 +845,24 @@ public class IsomericSmilesCreator {</td>

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814

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<pre style="margin: 0;"> <span id="LC845" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC846" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC847" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param atom for which to return a neighbor's smiles rank</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC817" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param neighborIndex index for getConnAtoms() to get neighbor atom and bond</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC848" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param neighbo<span class="idiff left right">u</span>rIndex index for getConnAtoms() to get neighbor atom and bond</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

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<td class="new_line diff-line-num" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

849

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<pre style="margin: 0;"> <span id="LC849" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return neighbor's position rank in smiles from a perspective of atom using closure digit positions for closure neighbors</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

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<td class="new_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

850

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<pre style="margin: 0;"> <span id="LC850" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

820

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<td class="new_line diff-line-num old" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC820" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getSmilesRank</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighborIndex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC821" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">neighborIndex</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

851

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getSmilesRank</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighbourIndex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

852

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">neighbourIndex</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

853

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC853" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighbour</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">neighbourIndex</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

822

</td>

<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

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<pre style="margin: 0;"> <span id="LC854" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mClosureNumber</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

823

</td>

<td class="new_line diff-line-num old" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC823" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// if neighbor is attached via a closure digit, then the rank is based primarily on atom's position</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

855

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<pre style="margin: 0;">+<span id="LC855" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// if neighbo<span class="idiff left right">u</span>r is attached via a closure digit, then the rank is based primarily on atom's position</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

</td>

<td class="new_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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<pre style="margin: 0;"> <span id="LC856" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// in the smiles and secondary on the count of other closures at atom that precede this closure</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

</td>

<td class="new_line diff-line-num" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

857

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<pre style="margin: 0;"> <span id="LC857" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mSmilesIndex</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

826

</td>

<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC826" class="line" lang="java">                 <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">neighborIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++)</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

827

</td>

<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC827" class="line" lang="java">                 <span class="idiff left">       </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mClosureNumber</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">mMol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">getConnAtom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

828

</td>

<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC828" class="line" lang="java">                         <span class="idiff left right"> </span><span class="n" style="color: #333;">rank</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

858

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC858" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">closureNeighbour</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mGraphAtomList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">get</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mSmilesIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]).</span></span><span class="na" style="color: #008080;"><span class="idiff">closureNeighbour</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">;</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

859

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC859" class="line" lang="java">                 <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">closureNeighbour</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">neighbour</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">closureNeighbour</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

860

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<pre style="margin: 0;">+<span id="LC860" class="line" lang="java">                         <span class="n" style="color: #333;">rank</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

</td>

<td class="new_line diff-line-num" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

861

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<pre style="margin: 0;"> <span id="LC861" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rank</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

830

</td>

<td class="new_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

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<pre style="margin: 0;"> <span id="LC862" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

831

</td>

<td class="new_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

863

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<pre style="margin: 0;"> <span id="LC863" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

832

</td>

<td class="new_line diff-line-num old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC832" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// if the neighbor is not a closure return a rank based on its atom index in the smiles</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

833

</td>

<td class="new_line diff-line-num old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC833" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mSmilesIndex</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;"><span class="idiff left">mMol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">getConnAtom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">neighborIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>];</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

864

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<pre style="margin: 0;">+<span id="LC864" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// if the neighbo<span class="idiff left right">u</span>r is not a closure return a rank based on its atom index in the smiles</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

865

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<pre style="margin: 0;">+<span id="LC865" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mSmilesIndex</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;"><span class="idiff left right">neighbour</span></span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

</td>

<td class="new_line diff-line-num" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

866

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC866" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="new_line diff-line-num" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

867

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC867" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="new_line diff-line-num" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

868

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<pre style="margin: 0;"> <span id="LC868" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isOrganic</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atomicNo</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -844,6 +876,7 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

844

</td>

<td class="new_line diff-line-num" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

876

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC876" class="line" lang="java"><span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SmilesAtom</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

845

</td>

<td class="new_line diff-line-num" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

877

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC877" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ezHalfParity</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

</td>

<td class="new_line diff-line-num" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

878

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC878" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isSideChainStart</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">isSideChainEnd</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

879

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<pre style="margin: 0;">+<span id="LC879" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">closureNeighbour</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

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880

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<pre style="margin: 0;"> <span id="LC880" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

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<td class="new_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

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<pre style="margin: 0;"> <span id="LC881" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SmilesAtom</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isSideChainStart</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isSideChainEnd</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

849

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<td class="new_line diff-line-num" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

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<pre style="margin: 0;"> <span id="LC882" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<br>

</li>

<li id="ba44c1f7e56c2598decf65ca012c856547ff2f0f">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#ba44c1f7e56c2598decf65ca012c856547ff2f0f"><strong>src/main/java/com/actelion/research/chem/SmilesParser.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,16 +38,22 @@ import com.actelion.research.chem.reaction.Reaction;</td>

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38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.ArrayUtils</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.SortedList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.TreeMap</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SmilesParser</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">SMARTS_MODE_MASK</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">SMARTS_MODE_IS_SMILES</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">SMARTS_MODE_GUESS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC50" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">SMARTS_MODE_IS_SMARTS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_SKIP_COORDINATE_TEMPLATES</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">INITIAL_CONNECTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_CONNECTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// largest allowed one in SMILES is 99</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_BRACKET_LEVELS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_RE_CONNECTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_AROMATIC_RING_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">HYDROGEN_ANY</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,8 +64,8 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mIsAromaticBond</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mAromaticAtoms</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mAromaticBonds</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mSmartsMode</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mCreateSmartsWarnings</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mAromaticAtoms</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mAromaticBonds</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mSmartsMode</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">mCoordinateMode</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mCreateSmartsWarnings</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">mSkipTemplates</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">mSmartsWarningBuffer</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,12 +85,39 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * single bond and without any implicit hydrogen atoms. If smartsMode is SMARTS_MODE_IS_GUESS,</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * then</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * molecules is never set.</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param <span class="idiff left right">smartsM</span>ode one of SMARTS_MODE...</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param <span class="idiff left">m</span>ode one of SMARTS_MODE...<span class="idiff right"> and optionally other mode flags</span></span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param createSmartsWarnings if true, then getSmartsWarning() may be used after parsing a SMILES or SMARTS</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SmilesParser</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">smartsM</span>ode</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">createSmartsWarnings</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java">          <span class="n" style="color: #333;">mSmartsMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">smartsMode</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SmilesParser</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left right">m</span>ode</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">createSmartsWarnings</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java">          <span class="n" style="color: #333;">mSmartsMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">SMARTS_MODE_MASK</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">          <span class="n" style="color: #333;">mCreateSmartsWarnings</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createSmartsWarnings</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">          <span class="n" style="color: #333;">mCoordinateMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">CoordinateInventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MODE_DEFAULT</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_SKIP_COORDINATE_TEMPLATES</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java">                  <span class="n" style="color: #333;">mCoordinateMode</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">CoordinateInventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MODE_SKIP_DEFAULT_TEMPLATES</span><span class="o" style="font-weight: 600;">;</span></span>

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97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java">          <span class="n" style="color: #333;">mSkipTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_SKIP_COORDINATE_TEMPLATES</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="nf" style="color: #900; font-weight: 600;">parseMolecule</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">smiles</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">parseMolecule</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Convenience method to quickly obtain a StereoMolecule from a SMILES string.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * If you process many SMILES, then the parse() methods are preferred, because</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * they avoid the steady instantiation new StereoMolecules.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param smiles</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="nf" style="color: #900; font-weight: 600;">parseMolecule</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java">         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java">                 <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java">         <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="nf" style="color: #900; font-weight: 600;">parseReaction</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,17 +240,17 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">baseAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;">MAX_BRACKET_LEVELS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="java">         <span class="n" style="color: #333;">baseAtom</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">MAX_RE</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosurePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">MAX_RE</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureBondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">MAX_RE</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureBondQueryFeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">MAX_RE</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="no" style="color: #008080;"><span class="idiff right">MAX_RE</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">INITIAL</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosurePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">INITIAL</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureBondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">INITIAL</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureBondQueryFeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">INITIAL</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="no" style="color: #008080;"><span class="idiff right">INITIAL</span>_CONNECTIONS</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="java">                 <span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atomMass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fromAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">squareBracketOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;"><span class="idiff left right">percentFound</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;"><span class="idiff left right">isDoubleDigit</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">smartsFeatureFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bracketLevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondTypeSingle</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -409,8 +442,11 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'D'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span>   <span class="c1" style="color: #998; font-style: italic;">// non-H-neighbours</span></span>

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<td class="old_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="java">                                                 <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC413" class="line" lang="java">                                                 <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="java">                                                         <span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="java">                                                         <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="java">                                                         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">qf</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNot0Neighbours</span></span>

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<td class="old_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="java">                                                            <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNot1Neighbour</span></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="java">                                                            <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">neighbours</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNot2Neighbours</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -432,15 +468,17 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="java">                                                 <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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435

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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437

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="java">                                                         <span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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438

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="java">                                                         <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isNot</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondQFRingState</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">~</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">else</span></span>

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<td class="new_line diff-line-num new" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="java">                                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="java">                                                 <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isNot</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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441

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<td class="new_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

442

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<td class="new_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingState</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">~</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

443

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<td class="new_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC443" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

481

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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444

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<td class="new_line diff-line-num" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

445

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<td class="new_line diff-line-num" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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446

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<td class="new_line diff-line-num" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNot2RingBonds</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -454,9 +492,7 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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492

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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455

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<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="java">                                                                 <span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

457

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<td class="new_line diff-line-num old" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC457" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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458

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<td class="new_line diff-line-num old" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

459

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<td class="new_line diff-line-num old" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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460

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<td class="new_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

496

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingState</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">~</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

461

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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingState</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">~</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNot2RingBonds</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -472,11 +508,17 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'r'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="java">                                                 <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isNot</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondQFRingState</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">~</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="java">                                                                 <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNotChain</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="java">                                                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ringSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="java">                                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ringCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringSize</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ringSize</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="java">                                                 <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

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<pre style="margin: 0;">-<span id="LC478" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">isNot</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ring<span class="idiff left right">Cod</span>e</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="java">                                                         <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ring<span class="idiff left right">Cod</span>e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingSizeShift</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">isNot</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ring<span class="idiff left">Size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ringSiz</span>e</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="java">                                                         <span class="n" style="color: #333;">atomQueryFeatures</span> <span class="o" style="font-weight: 600;">|=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ring<span class="idiff left right">Siz</span>e</span> <span class="o" style="font-weight: 600;"><<</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRingSizeShift</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="java">                                                         <span class="nf" style="color: #900; font-weight: 600;">smartsWarning</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">isNot</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"!r"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"r"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ringSize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -582,6 +624,9 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="java">                         <span class="c1" style="color: #998; font-style: italic;">// mark aromatic atoms</span></span>

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<pre style="margin: 0;"> <span id="LC626" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isLowerCase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">theChar</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atomicNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atomicNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atomicNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">7</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atomicNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atomicNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">15</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">atomicNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SmilesParser: atomicNo "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">atomicNo</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" must not be aromatic"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="java">                                 <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomMarker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="java">                                 <span class="n" style="color: #333;">mAromaticAtoms</span><span class="o" style="font-weight: 600;">++;</span></span>

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -626,7 +671,7 @@ public class SmilesParser {</td>

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626

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<td class="new_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

671

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="java"> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<td class="new_line diff-line-num" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

672

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="java">                                         <span class="c1" style="color: #998; font-style: italic;">// using position as hydrogenPosition is close enough</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

628

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<td class="new_line diff-line-num" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hydrogenCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">explicitHydrogens</span> <span class="o" style="font-weight: 600;">==</span> <span class="no" style="color: #008080;">HYDROGEN_IMPLICIT_ZERO</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">explicitHydrogens</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

629

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<td class="new_line diff-line-num old" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC629" class="line" lang="java">                                         <span class="n" style="color: #333;">parityMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">THParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fromAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hydrogenCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isClockwise</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

674

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="java">                                         <span class="n" style="color: #333;">parityMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">THParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fromAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hydrogenCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isClockwise</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

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<td class="new_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<td class="new_line diff-line-num" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

676

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<td class="new_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

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<pre style="margin: 0;"> <span id="LC677" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -739,15 +784,29 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

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<td class="new_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

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<pre style="margin: 0;"> <span id="LC784" class="line" lang="java">                                                                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

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<td class="new_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

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<pre style="margin: 0;"> <span id="LC785" class="line" lang="java">                                                                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">':'</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="new_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

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<pre style="margin: 0;"> <span id="LC786" class="line" lang="java">                                                                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

742

</td>

<td class="new_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC742" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">percentFound</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC787" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">isDoubleDigit</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC788" class="line" lang="java">                                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">endIndex</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

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<td class="new_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC789" class="line" lang="java">                                  <span class="o" style="font-weight: 600;">&&</span> <span class="nc" style="color: #458; font-weight: 600;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDigit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

<td class="new_line diff-line-num" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC790" class="line" lang="java">                                         <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'0'</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC791" class="line" lang="java">                                         <span class="n" style="color: #333;">isDoubleDigit</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

</td>

<td class="new_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

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<pre style="margin: 0;"> <span id="LC792" class="line" lang="java">                                         <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

</td>

<td class="new_line diff-line-num" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC793" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

748

</td>

<td class="new_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC748" class="line" lang="java">                                 <span class="n" style="color: #333;">percentFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

749

</td>

<td class="new_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC749" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="no" style="color: #008080;">MAX_RE_CONNECTIONS</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

750

</td>

<td class="new_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC750" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SmilesParser: ringClosureAtom number out of range"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

794

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC794" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

795

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC795" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">>=</span><span class="no" style="color: #008080;">MAX_CONNECTIONS</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

796

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC796" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SmilesParser: ringClosureAtom number out of range"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC797" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

798

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC798" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">oldSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

799

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC799" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

800

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC800" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newSize</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC801" class="line" lang="java">                                                 <span class="n" style="color: #333;">newSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MAX_CONNECTIONS</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">INITIAL_CONNECTIONS</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

802

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC802" class="line" lang="java"></span>

</pre>

</td>

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803

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="java">                                         <span class="n" style="color: #333;">ringClosureAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newSize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

804

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="java">                                         <span class="n" style="color: #333;">ringClosurePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringClosurePosition</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newSize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

805

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="java">                                         <span class="n" style="color: #333;">ringClosureBondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringClosureBondType</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newSize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

806

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="java">                                         <span class="n" style="color: #333;">ringClosureBondQueryFeatures</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringClosureBondQueryFeatures</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newSize</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">oldSize</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">newSize</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

808

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<pre style="margin: 0;">+<span id="LC808" class="line" lang="java">                                                 <span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

809

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<pre style="margin: 0;">+<span id="LC809" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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751

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<td class="new_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

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<pre style="margin: 0;"> <span id="LC810" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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752

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<td class="new_line diff-line-num" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="java">                                         <span class="n" style="color: #333;">ringClosureAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baseAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bracketLevel</span><span class="o" style="font-weight: 600;">];</span></span>

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753

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<td class="new_line diff-line-num" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

812

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<pre style="margin: 0;"> <span id="LC812" class="line" lang="java">                                         <span class="n" style="color: #333;">ringClosurePosition</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">number</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -816,7 +875,7 @@ public class SmilesParser {</td>

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816

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875

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<pre style="margin: 0;"> <span id="LC875" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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817

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876

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<pre style="margin: 0;"> <span id="LC876" class="line" lang="java"></span>

</pre>

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818

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<td class="new_line diff-line-num" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

877

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">theChar</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'%'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

819

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<td class="new_line diff-line-num old" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC819" class="line" lang="java">                         <span class="n" style="color: #333;"><span class="idiff left right">percentFound</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

878

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<pre style="margin: 0;">+<span id="LC878" class="line" lang="java">                         <span class="n" style="color: #333;"><span class="idiff left right">isDoubleDigit</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

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<td class="new_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

879

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<pre style="margin: 0;"> <span id="LC879" class="line" lang="java">                         <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

</td>

<td class="new_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

880

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<pre style="margin: 0;"> <span id="LC880" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

822

</td>

<td class="new_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC881" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -835,8 +894,8 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="new_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// Check for unsatisfied open bonds</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="new_line diff-line-num" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

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<pre style="margin: 0;"> <span id="LC895" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondTypeSingle</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

<td class="new_line diff-line-num" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

896

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<pre style="margin: 0;"> <span id="LC896" class="line" lang="java">                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SmilesParser: dangling open bond"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

838

</td>

<td class="new_line diff-line-num old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC838" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="no" style="color: #008080;"><span class="idiff">MAX_RE_CONNECTIONS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

839

</td>

<td class="new_line diff-line-num old" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC839" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r<span class="idiff left">ingClosureAtom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

897

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC897" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nl"><span class="idiff left">rca:</span></span><span class="n" style="color: #333;"><span class="idiff right">ringClosureAtom</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

898

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC898" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r<span class="idiff left right">ca</span></span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

840

</td>

<td class="new_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC899" class="line" lang="java">                         <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"SmilesParser: dangling ring closure"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

</td>

<td class="new_line diff-line-num" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC900" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

</td>

<td class="new_line diff-line-num" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC901" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">handleHydrogenAtomMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getHandleHydrogenMap</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -921,7 +980,7 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

921

</td>

<td class="new_line diff-line-num" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

980

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC980" class="line" lang="java">         <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setParitiesValid</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

922

</td>

<td class="new_line diff-line-num" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC981" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

</td>

<td class="new_line diff-line-num" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC982" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">createCoordinates</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

924

</td>

<td class="new_line diff-line-num old" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC924" class="line" lang="java">                 <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">CoordinateInventor</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">invent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

983

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC983" class="line" lang="java">                 <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">CoordinateInventor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">mCoordinateMode</span></span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">invent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

925

</td>

<td class="new_line diff-line-num" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

984

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC984" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

926

</td>

<td class="new_line diff-line-num" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

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<pre style="margin: 0;"> <span id="LC985" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readStereoFeatures</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

927

</td>

<td class="new_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC986" class="line" lang="java">                         <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setUnknownParitiesToExplicitlyUnknown</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1456,11 +1515,21 @@ public class SmilesParser {</td>

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<td class="old_line diff-line-num" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1456

</td>

<td class="new_line diff-line-num" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1515

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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="java">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">paritiesFound</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1457

</td>

<td class="new_line diff-line-num" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1516

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1516" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1458

</td>

<td class="new_line diff-line-num" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1517

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1517" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1518

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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ParityNeighbour</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1519

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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mAtom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mPosition</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1520

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1520" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mIsHydrogen</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1521

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1521" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1522

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1522" class="line" lang="java">                <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">ParityNeighbour</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isHydrogen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1523

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1523" class="line" lang="java">                        <span class="n" style="color: #333;">mAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1524

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1524" class="line" lang="java">                        <span class="n" style="color: #333;">mPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1525

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1525" class="line" lang="java">                        <span class="n" style="color: #333;">mIsHydrogen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isHydrogen</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1526

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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1527

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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1528

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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1459

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<td class="new_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1529

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<pre style="margin: 0;"> <span id="LC1529" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">THParity</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1460

</td>

<td class="new_line diff-line-num old" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1460" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mCentralAtom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mImplicitHydrogen</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mFromAtom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1461

</td>

<td class="new_line diff-line-num old" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1461" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mNeighborAtom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mNeighborPosition</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1462

</td>

<td class="new_line diff-line-num old" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1462" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mNeighborIsHydrogen</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1530

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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mCentralAtom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mImplicitHydrogen</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mFromAtom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1463

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<td class="new_line diff-line-num" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1531

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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mIsClockwise</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mError</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1532

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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="java">                <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">ParityNeighbour</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mNeighbourList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1464

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<td class="new_line diff-line-num" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1533

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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1465

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<td class="new_line diff-line-num" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="java">                <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1466

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<td class="new_line diff-line-num" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">             * Instantiates a new parity object during smiles traversal.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1472,26 +1541,23 @@ public class SmilesParser {</td>

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1472

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<td class="new_line diff-line-num" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="java">                <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">THParity</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">centralAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fromAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">implicitHydrogen</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hydrogenPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isClockwise</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1473

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<td class="new_line diff-line-num" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1542

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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">implicitHydrogen</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">implicitHydrogen</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1474

</td>

<td class="new_line diff-line-num" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1543

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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="java">                                <span class="n" style="color: #333;">mError</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1475

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<td class="new_line diff-line-num old" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1475" class="line" lang="java">                        <span class="idiff left right"> </span><span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1544

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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1476

</td>

<td class="new_line diff-line-num" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1545

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<pre style="margin: 0;"> <span id="LC1545" class="line" lang="java">                        <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1477

</td>

<td class="new_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1546

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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="java">                                <span class="n" style="color: #333;">mCentralAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">centralAtom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1478

</td>

<td class="new_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="java">                                <span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fromAtom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1479

</td>

<td class="new_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="java">                                <span class="n" style="color: #333;">mImplicitHydrogen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">implicitHydrogen</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1480

</td>

<td class="new_line diff-line-num" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1549

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<pre style="margin: 0;"> <span id="LC1549" class="line" lang="java">                                <span class="n" style="color: #333;">mIsClockwise</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isClockwise</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1481

</td>

<td class="new_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1481" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighborCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1482

</td>

<td class="new_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1482" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighborIsHydrogen</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1483

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<td class="new_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1483" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighborAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1484

</td>

<td class="new_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1484" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighborPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1550

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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighbourList</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1485

</td>

<td class="new_line diff-line-num" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1551

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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1486

</td>

<td class="new_line diff-line-num" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1552

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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// If we have a fromAtom and we have an implicit hydrogen,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1487

</td>

<td class="new_line diff-line-num old" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1487" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// then make the implicit hydrogen a normal neighbor.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1553

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<pre style="margin: 0;">+<span id="LC1553" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// then make the implicit hydrogen a normal neighbo<span class="idiff left right">u</span>r.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1488

</td>

<td class="new_line diff-line-num" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1554" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">implicitHydrogen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1489

</td>

<td class="new_line diff-line-num" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1555

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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="java">                                        <span class="c1" style="color: #998; font-style: italic;">// We put it at the end of the atom list with MAX_VALUE</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1490

</td>

<td class="new_line diff-line-num" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1556

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<pre style="margin: 0;"> <span id="LC1556" class="line" lang="java">                                        <span class="n" style="color: #333;">addNeighbor</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hydrogenPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1491

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<td class="new_line diff-line-num" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1557

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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="java">                                        <span class="n" style="color: #333;">mImplicitHydrogen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1492

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<td class="new_line diff-line-num old" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1492" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1493

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<td class="new_line diff-line-num" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1558

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<pre style="margin: 0;"> <span id="LC1558" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1494

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<td class="new_line diff-line-num" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1559

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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1560

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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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1495

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<td class="new_line diff-line-num" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1561

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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1496

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<td class="new_line diff-line-num" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1562

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<pre style="margin: 0;"> <span id="LC1562" class="line" lang="java">                <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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1497

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<td class="new_line diff-line-num" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1563" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">             * Adds a currently traversed neighbor or ring closure to parity object,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1505,19 +1571,14 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">             * @param isHydrogen</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">             */</span></span>

</pre>

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1507

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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="java">                <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addNeighbor</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isHydrogen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1508

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<td class="new_line diff-line-num old" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1508" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mError</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1509

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<td class="new_line diff-line-num old" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1509" class="line" lang="java">                                <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mError</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mNeighbourList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mNeighbourList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="java">                                        <span class="n" style="color: #333;">mError</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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1577

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1577" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1578

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1578" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1510

</td>

<td class="new_line diff-line-num" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1579

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1579" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1511

</td>

<td class="new_line diff-line-num old" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1511" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mNeighborCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1512

</td>

<td class="new_line diff-line-num old" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1512" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mNeighborCount</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1513

</td>

<td class="new_line diff-line-num old" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1513" class="line" lang="java">                                <span class="n" style="color: #333;">mError</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1514

</td>

<td class="new_line diff-line-num old" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1514" class="line" lang="java">                                <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1580

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1580" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighbourList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ParityNeighbour</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isHydrogen</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1515

</td>

<td class="new_line diff-line-num" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1581

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1581" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1516

</td>

<td class="new_line diff-line-num old" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1516" class="line" lang="java"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1517

</td>

<td class="new_line diff-line-num old" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1517" class="line" lang="java">                        <span class="n" style="color: #333;">mNeighborIsHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isHydrogen</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1518

</td>

<td class="new_line diff-line-num old" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1518" class="line" lang="java">                        <span class="n" style="color: #333;">mNeighborAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1519

</td>

<td class="new_line diff-line-num old" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1519" class="line" lang="java">                        <span class="n" style="color: #333;">mNeighborPosition</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1520

</td>

<td class="new_line diff-line-num old" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1520" class="line" lang="java">                        <span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1521

</td>

<td class="new_line diff-line-num" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1582

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1582" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1522

</td>

<td class="new_line diff-line-num" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1583

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1583" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1523

</td>

<td class="new_line diff-line-num" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1584

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1584" class="line" lang="java">                <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">calculateParity</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">handleHydrogenAtomMap</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1528,71 +1589,66 @@ public class SmilesParser {</td>

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1528

</td>

<td class="new_line diff-line-num" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1589

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<pre style="margin: 0;"> <span id="LC1589" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// uses after calling handleHydrogens, which is called from ensureHelperArrays().</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1529

</td>

<td class="new_line diff-line-num" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1590

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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1530

</td>

<td class="new_line diff-line-num" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1591

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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="java">                                <span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handleHydrogenAtomMap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mFromAtom</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1531

</td>

<td class="new_line diff-line-num old" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1531" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">mNeighborCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1532

</td>

<td class="new_line diff-line-num old" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1532" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">mN</span>eighbo<span class="idiff">r</span>Atom</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span></span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1533

</td>

<td class="new_line diff-line-num old" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1533" class="line" lang="java">                                        <span class="n" style="color: #333;"><span class="idiff left">mN</span>eighbo<span class="idiff">r</span>Atom</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handleHydrogenAtomMap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;"><span class="idiff">mN</span>eighbo<span class="idiff">r</span>Atom</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1592

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1592" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">neighbour:</span></span><span class="n" style="color: #333;"><span class="idiff right">mNeighbourList</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1593

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1593" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>Atom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1594

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1594" class="line" lang="java">                                        <span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">m</span>Atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handleHydrogenAtomMap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;"><span class="idiff">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>Atom</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

</td>

<td class="new_line diff-line-num" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1595

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1595" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

</td>

<td class="new_line diff-line-num" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1596

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1596" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mImplicitHydrogen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

</td>

<td class="new_line diff-line-num" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1597

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1597" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// If we have no implicit hydrogen and the central atom is the first atom in the smiles,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1537

</td>

<td class="new_line diff-line-num" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1598

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1598" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// then we assume that we have to take the first neighbor as from-atom (not described in Daylight theory manual).</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

</td>

<td class="new_line diff-line-num" data-linenumber="1599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1599

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1599" class="line" lang="java">                                <span class="c1" style="color: #998; font-style: italic;">// Assumption: take the first neighbor as front atom, i.e. skip it when comparing positions</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1539

</td>

<td class="new_line diff-line-num" data-linenumber="1600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1600

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1600" class="line" lang="java">                                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1540

</td>

<td class="new_line diff-line-num old" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1540" class="line" lang="java">                                <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">minIndex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1541

</td>

<td class="new_line diff-line-num old" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1541" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">mNeighborCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1542

</td>

<td class="new_line diff-line-num old" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1542" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minPosition</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left">mN</span>eighbo<span class="idiff">r</span>Position</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1543

</td>

<td class="new_line diff-line-num old" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1543" class="line" lang="java">                                                <span class="n" style="color: #333;">minPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">mN</span>eighbo<span class="idiff">r</span>Position</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1544

</td>

<td class="new_line diff-line-num old" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1544" class="line" lang="java">                                                <span class="n" style="color: #333;">min<span class="idiff left">Index</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1601

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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="java">                                <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">minNeighbour</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1602

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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">neighbour:</span></span><span class="n" style="color: #333;"><span class="idiff right">mNeighbourList</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1603

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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minPosition</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>Position</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1604

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1604" class="line" lang="java">                                                <span class="n" style="color: #333;">minPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>Position</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1605

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1605" class="line" lang="java">                                                <span class="n" style="color: #333;">min<span class="idiff left">Neighbour</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">neighbour</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1545

</td>

<td class="new_line diff-line-num" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1606

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1606" class="line" lang="java">                                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1546

</td>

<td class="new_line diff-line-num" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1607

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1607" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1547

</td>

<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1547" class="line" lang="java">                                <span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mNeighborAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">minIndex</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1548

</td>

<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1548" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">minIndex</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1549

</td>

<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1549" class="line" lang="java">                                        <span class="n" style="color: #333;">mNeighborAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mNeighborAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1550

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<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1550" class="line" lang="java">                                        <span class="n" style="color: #333;">mNeighborPosition</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mNeighborPosition</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1551

</td>

<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1551" class="line" lang="java">                                        <span class="n" style="color: #333;">mNeighborIsHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mNeighborIsHydrogen</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1552

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<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1552" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1553

</td>

<td class="new_line diff-line-num old" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1553" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighborCount</span><span class="o" style="font-weight: 600;">--;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1608

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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="java">                                <span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minNeighbour</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mAtom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1609

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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="java">                                <span class="n" style="color: #333;">mNeighbourList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minNeighbour</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

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<td class="new_line diff-line-num" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1610

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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1555

</td>

<td class="new_line diff-line-num" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1611

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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1556

</td>

<td class="new_line diff-line-num old" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1556" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">totalNeighborCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mImplicitHydrogen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mNeighbo<span class="idiff left right">rCount</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1612

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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">totalNeighborCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mImplicitHydrogen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mNeighbo<span class="idiff left">urList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">size</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1557

</td>

<td class="new_line diff-line-num" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1613

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1613" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalNeighborCount</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">totalNeighborCount</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1558

</td>

<td class="new_line diff-line-num" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1614

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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="java">                                <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParityUnknown</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1559

</td>

<td class="new_line diff-line-num" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1615

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1615" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1560

</td>

<td class="new_line diff-line-num" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1616

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1616" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// We look from the hydrogen towards the central carbon if the fromAtom is a hydrogen or</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1561

</td>

<td class="new_line diff-line-num" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1617

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1617" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// if there is no fromAtom but the central atom has an implicit hydrogen.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1562

</td>

<td class="new_line diff-line-num" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1618

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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">fromAtomIsHydrogen</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mImplicitHydrogen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1563

</td>

<td class="new_line diff-line-num old" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1563" class="line" lang="java">                                        <span class="idiff left right">                           </span><span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1619

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<pre style="margin: 0;">+<span id="LC1619" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isSimpleHydrogen</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1564

</td>

<td class="new_line diff-line-num" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1620

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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1565

</td>

<td class="new_line diff-line-num old" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1565" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span> <span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff">rIndex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1566

</td>

<td class="new_line diff-line-num old" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1566" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">mNeighborCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1567

</td>

<td class="new_line diff-line-num old" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1567" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">mN</span>eighbo<span class="idiff">r</span>IsHydrogen</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1568

</td>

<td class="new_line diff-line-num old" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1568" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff left">rIndex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fromAtomIsHydrogen</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1621

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1621" class="line" lang="java">                        <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span> <span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff">ur</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1622

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1622" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">neighbour:</span></span><span class="n" style="color: #333;"><span class="idiff right">mNeighbourList</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1623

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1623" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>IsHydrogen</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1624

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1624" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff left">ur</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fromAtomIsHydrogen</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1569

</td>

<td class="new_line diff-line-num" data-linenumber="1625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1625

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1625" class="line" lang="java">                                                <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParityUnknown</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1570

</td>

<td class="new_line diff-line-num old" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1570" class="line" lang="java">                                        <span class="n" style="color: #333;">hydrogenNeighborIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1571

</td>

<td class="new_line diff-line-num old" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1571" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1626

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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="java">                                        <span class="n" style="color: #333;">hydrogenNeighbour</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">neighbour</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1572

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<td class="new_line diff-line-num" data-linenumber="1627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1627

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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1628

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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1573

</td>

<td class="new_line diff-line-num" data-linenumber="1629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1629

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1629" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1574

</td>

<td class="new_line diff-line-num" data-linenumber="1630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1630

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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// hydrogens are moved to the end of the atom list. If the hydrogen passes an odd number of</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1575

</td>

<td class="new_line diff-line-num" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1631

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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// neighbor atoms on its way to the list end, we are effectively inverting the atom order.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1576

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<td class="new_line diff-line-num" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1632

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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isHydrogenTraversalInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1577

</td>

<td class="new_line diff-line-num old" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1577" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff left">rIndex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1578

</td>

<td class="new_line diff-line-num old" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1578" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">mNeighborCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1579

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<td class="new_line diff-line-num old" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1579" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">mN</span>eighbo<span class="idiff">rIsHydrogen</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1580

</td>

<td class="new_line diff-line-num old" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1580" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">mNeighborAtom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff">rIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff">mN</span>eighbo<span class="idiff">r</span>Atom</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1633

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1633" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff left">ur</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1634

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1634" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">neighbour:</span></span><span class="n" style="color: #333;"><span class="idiff right">mNeighbourList</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1635

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1635" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hydrogenNeighbour</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1636

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1636" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">hydrogenNeighbo<span class="idiff left">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">mAtom</span></span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>Atom</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1581

</td>

<td class="new_line diff-line-num" data-linenumber="1637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1637

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1637" class="line" lang="java">                                                <span class="n" style="color: #333;">isHydrogenTraversalInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isHydrogenTraversalInversion</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1582

</td>

<td class="new_line diff-line-num" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1638

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1638" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1583

</td>

<td class="new_line diff-line-num" data-linenumber="1639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1639

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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// If fromAtom is not a hydrogen, we consider it moved to highest atom index,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1584

</td>

<td class="new_line diff-line-num" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1640

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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// because</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1585

</td>

<td class="new_line diff-line-num" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1641

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1641" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">fromAtomTraversalInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1586

</td>

<td class="new_line diff-line-num" data-linenumber="1642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1642

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1642" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fromAtomIsHydrogen</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1587

</td>

<td class="new_line diff-line-num old" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1587" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">mNeighborCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span>)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1588

</td>

<td class="new_line diff-line-num old" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1588" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">mN</span>eighbo<span class="idiff">r</span>Atom</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1643

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1643" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ParityNeighbour</span></span><span class="idiff"> </span><span class="nl"><span class="idiff">neighbour:</span></span><span class="n" style="color: #333;"><span class="idiff right">mNeighbourList</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1644

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1644" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mFromAtom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">n</span>eighbo<span class="idiff">ur</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">m</span>Atom</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1589

</td>

<td class="new_line diff-line-num" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1645

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1645" class="line" lang="java">                                                <span class="n" style="color: #333;">fromAtomTraversalInversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fromAtomTraversalInversion</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1590

</td>

<td class="new_line diff-line-num" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1646

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1646" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1591

</td>

<td class="new_line diff-line-num" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1647

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1647" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mIsClockwise</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1592

</td>

<td class="new_line diff-line-num old" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1592" class="line" lang="java">                                        <span class="idiff left">       </span><span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">isInverseOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff">mNeighborAtom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mNeighborPosition</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mNeighborCount</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1593

</td>

<td class="new_line diff-line-num old" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1593" class="line" lang="java">                                        <span class="idiff left right"> </span><span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">fromAtomTraversalInversion</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1594

</td>

<td class="new_line diff-line-num old" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1594" class="line" lang="java">                                        <span class="idiff left right"> </span><span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">isHydrogenTraversalInversion</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1595

</td>

<td class="new_line diff-line-num old" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1595" class="line" lang="java">                                        <span class="idiff left right">                 </span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1648

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1648" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">isInverseOrder</span><span class="o" style="font-weight: 600;">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1649

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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">fromAtomTraversalInversion</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1650

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<pre style="margin: 0;">+<span id="LC1650" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">^</span> <span class="n" style="color: #333;">isHydrogenTraversalInversion</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1651

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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="java">                                        <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1596

</td>

<td class="new_line diff-line-num" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1652

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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1597

</td>

<td class="new_line diff-line-num" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1653

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1653" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">System.out.println();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1598

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<td class="new_line diff-line-num" data-linenumber="1654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1654

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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">System.out.println("central:"+mCentralAtom+(mIsClockwise?" @@":" @")+" from:"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1606,19 +1662,19 @@ System.out.println("parity:"+parity);</td>

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<td class="old_line diff-line-num" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1606

</td>

<td class="new_line diff-line-num" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1662

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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="java">                        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1607

</td>

<td class="new_line diff-line-num" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1663

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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1608

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<td class="new_line diff-line-num" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1664

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1664" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1609

</td>

<td class="new_line diff-line-num old" data-linenumber="1665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1609" class="line" lang="java">                <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isInverseOrder</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">count</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1665

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1665" class="line" lang="java">                <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isInverseOrder</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1610

</td>

<td class="new_line diff-line-num" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1666

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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="java">                        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">inversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1611

</td>

<td class="new_line diff-line-num old" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1611" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">count</span></span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1667

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1667" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">mNeighbourList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">size</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1612

</td>

<td class="new_line diff-line-num" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1668

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<pre style="margin: 0;"> <span id="LC1668" class="line" lang="java">                                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1613

</td>

<td class="new_line diff-line-num old" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1613" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1669

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1669" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">mNeighbourList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">get</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">).</span></span><span class="na" style="color: #008080;"><span class="idiff">mAtom</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mNeighbourList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">get</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">).</span></span><span class="na" style="color: #008080;"><span class="idiff right">mAtom</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1614

</td>

<td class="new_line diff-line-num" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1670

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1670" class="line" lang="java">                                                <span class="n" style="color: #333;">inversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">inversion</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1615

</td>

<td class="new_line diff-line-num old" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1615" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">position</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span>osition</span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1671

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1671" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">mNeighbourList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">get</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">).</span></span><span class="na" style="color: #008080;"><span class="idiff">mPosition</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mNeighbourList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">get</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">).</span></span><span class="na" style="color: #008080;"><span class="idiff right">mP</span>osition</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1616

</td>

<td class="new_line diff-line-num" data-linenumber="1672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1672

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1672" class="line" lang="java">                                                <span class="n" style="color: #333;">inversion</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">inversion</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1617

</td>

<td class="new_line diff-line-num old" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1617" class="line" lang="java">                                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1618

</td>

<td class="new_line diff-line-num" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1673

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1673" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1619

</td>

<td class="new_line diff-line-num old" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1619" class="line" lang="java">                        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inversion</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1620

</td>

<td class="new_line diff-line-num" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1674

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1674" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1675

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1675" class="line" lang="java">                        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inversion</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1621

</td>

<td class="new_line diff-line-num" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1676

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1676" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1677

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1677" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1622

</td>

<td class="new_line diff-line-num" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1678

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1678" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1623

</td>

<td class="new_line diff-line-num" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1679

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1679" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">testStereo</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1680" class="line" lang="java">                <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span> <span class="o" style="font-weight: 600;">{</span> <span class="s" style="color: #d14;">"F/C=C/I"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"F/C=C/I"</span> <span class="o" style="font-weight: 600;">},</span></span>

</pre>

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</li>

<li id="b3f92c9221147b0b87192f33311736c1b323a29c">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#b3f92c9221147b0b87192f33311736c1b323a29c"><strong>src/main/java/com/actelion/research/chem/StereoIsomerEnumerator.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,11 +28,11 @@ public class StereoIsomerEnumerator {</td>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">mAtomIsParity1</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mBondIsParity1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="new_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * If the passed molecule<span class="idiff left right">s</span> has stereo-chemically undefined configurations</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * If the passed molecule has stereo-chemically undefined configurations</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * (double bonds, stereo centers) or/and one or more AND/OR groups of</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * defined relative stereo configurations, then it represents multiple</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * stereo isomers. The StereoIsomerEnumerator generates all individual</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

35

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<td class="new_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * stereo isomers of the passe<span class="idiff left right">s</span> molecule. If the passed molecule does</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * stereo isomers of the passe<span class="idiff left right">d</span> molecule. If the passed molecule does</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * not include absolute stereo centers (or atrop isomeric configuration),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * but unknown stereo centers or groups with defined relative configuration,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * then we have pairs of enantiomers. In this case the StereoIsomerEnumerator</span></span>

</pre>

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<br>

</li>

<li id="297bbf96bfa984fd860791b0f081b476f79d916b">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#297bbf96bfa984fd860791b0f081b476f79d916b"><strong>src/main/java/com/actelion/research/chem/TautomerHelper.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,6 +42,8 @@ import java.util.TreeSet;</td>

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TautomerHelper</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_TAUTOMERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sMaxTautomers</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">MAX_TAUTOMERS</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">sSuppressWarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mOriginalMol</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mIsTautomerBond</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +56,14 @@ public class TautomerHelper {</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">BondOrders</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mBondOrderSet</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayDeque</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">BondOrders</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mBondOrderDeque</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setMaxTautomers</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxTautomers</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java">          <span class="n" style="color: #333;">sMaxTautomers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxTautomers</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setSuppressWarning</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">suppressWarning</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java">          <span class="n" style="color: #333;">sSuppressWarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suppressWarning</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param mol</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -284,8 +294,9 @@ public class TautomerHelper {</td>

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<td class="old_line diff-line-num" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="java">                 <span class="n" style="color: #333;">mBondOrderDeque</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">poll</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">copyToTautomer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tautomer</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="java">                 <span class="n" style="color: #333;">addAllTautomers</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tautomer</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mBondOrderSet</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="no" style="color: #008080;">MAX_TAUTOMERS</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Tautomer count exceeds maximum: "</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Canonizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mOriginalMol</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mBondOrderSet</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sMaxTautomers</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">sSuppressWarning</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="java">                                 <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Tautomer count exceeds maximum: "</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Canonizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mOriginalMol</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="java">                         <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="2324bbf7db1501a1bb2aaae4a1db707a20b5f9b1">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#2324bbf7db1501a1bb2aaae4a1db707a20b5f9b1"><strong>src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,6 +43,7 @@ public class CoordinateInventor {</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_KEEP_MARKED_ATOM_COORDS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_PREFER_MARKED_ATOM_COORDS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java">  <span class="kd" style="font-weight: 600;">protected</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_CONSIDER_MARKED_ATOMS</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">MODE_KEEP_MARKED_ATOM_COORDS</span> <span class="o" style="font-weight: 600;">|</span> <span class="no" style="color: #008080;">MODE_PREFER_MARKED_ATOM_COORDS</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_DEFAULT</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">MODE_REMOVE_HYDROGEN</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="no" style="color: #008080;">FLIP_AS_LAST_RESORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="no" style="color: #008080;">FLIP_POSSIBLE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,7 +80,7 @@ public class CoordinateInventor {</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * polycyclic structures from these templates (adamantanes, cubane, etc.).</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">CoordinateInventor</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MODE_<span class="idiff left right">REMOVE_HYDROGEN</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MODE_<span class="idiff left right">DEFAULT</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -372,7 +373,7 @@ public class CoordinateInventor {</td>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">locateInitialFragments</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// take every atom with more than 4 neighbours including first neighbour shell</span></span>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getA<span class="idiff left right">llA</span>toms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">InventorFragment</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">InventorFragment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">mMode</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="java"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -437,7 +438,7 @@ public class CoordinateInventor {</td>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">// take every large ring that has ring bonds that are not member of a fragment added already</span></span>

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<pre style="margin: 0;">-<span id="LC440" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get<span class="idiff left right">All</span>Bonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isRingBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mBondHandled</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">InventorChain</span> <span class="n" style="color: #333;">theRing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSmallestRingFromBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theRing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRingAtoms</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1183,9 +1184,7 @@ public class CoordinateInventor {</td>

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<td class="new_line diff-line-num" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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1184

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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">highest</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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1185

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<td class="new_line diff-line-num" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="java">                <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">current</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">highest</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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1186

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<td class="new_line diff-line-num old" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                  if (graphLevel[graphAtom[current]] > RingCollection.MAX_LARGE_RING_SIZE)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                          return null;            // disabled ring size limit;  TLS 20130613</span></span>

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<td class="old_line diff-line-num old" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1188

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<td class="new_line diff-line-num old" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="java">                                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">candidate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">current</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">candidate</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">atom1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="java">                                        <span class="nc" style="color: #458; font-weight: 600;">InventorChain</span> <span class="n" style="color: #333;">theRing</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">InventorChain</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphLevel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]]);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1222,9 +1221,7 @@ public class CoordinateInventor {</td>

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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="java">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">highest</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="java">                <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">current</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">highest</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                  if (graphLevel[graphAtom[current]] > RingCollection.MAX_LARGE_RING_SIZE)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1226" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//                          return 0;               // disabled ring size limit;  TLS 20130613</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1227" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="java">                        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC1225" class="line" lang="java">                                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">candidate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="java">                                <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">candidate</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">atom3</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="java">                                        <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">graphLevel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">graphAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]];</span></span>

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<br>

</li>

<li id="42976117f38fa37d60dd738b507feb19719d5616">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#42976117f38fa37d60dd738b507feb19719d5616"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@ import com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphExtract</td>

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.interactionstatistics.InteractionAtomTypeCalculator</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.openmolecules.chem.conf.gen.ConformerGenerator</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.openmolecules.chem.conf.gen.RigidFragmentCache</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Date</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,6 +61,7 @@ public class CreatorMolDistHistViz {</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java">        <span class="n" style="color: #333;">subGraphExtractor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">SubGraphExtractor</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java">        <span class="n" style="color: #333;">conformerGenerator</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ConformerGenerator</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java">        <span class="nc" style="color: #458; font-weight: 600;">RigidFragmentCache</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getDefaultInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">loadDefaultCache</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">        <span class="n" style="color: #333;">conformationMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">CONF_GEN_TS</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"></span>

</pre>

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<br>

</li>

<li id="ec05b3badbc5071521d94ee516cf51235293f843">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#ec05b3badbc5071521d94ee516cf51235293f843"><strong>src/main/java/com/actelion/research/chem/docking/DockingEngine.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +17,7 @@ import org.openmolecules.chem.conf.gen.ConformerGenerator;</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.calc.ThreadMaster</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Canonizer</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Coordinates</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.IDCodeParser</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.IDCodeParserWithoutCoordinateInvention</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Molecule</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Molecule3D</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +122,7 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java">         <span class="n" style="color: #333;">threadMaster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tm</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="java"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getStartingPositions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Conformer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">initialPos</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getStartingPositions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Conformer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">initialPos</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">throws</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">DockingFailedException</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Object</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ffOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Object</span><span class="o" style="font-weight: 600;">>();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,7 +141,14 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">conf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toMolecule</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java">                         <span class="n" style="color: #333;">conf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperParities</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span> <span class="n" style="color: #333;">mmff</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">conf</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MMFF94SPLUS</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ffOptions</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java">                         </span>

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span> <span class="n" style="color: #333;">mmff</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java">                         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java">                                 <span class="n" style="color: #333;">mmff</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">conf</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MMFF94SPLUS</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ffOptions</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java">                         <span class="k" style="font-weight: 600;">catch</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">DockingFailedException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"could not assess atom types"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">PositionConstraint</span> <span class="n" style="color: #333;">constraint</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">PositionConstraint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">conf</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">0.2</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java">                         <span class="n" style="color: #333;">mmff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addEnergyTerm</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">constraint</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="java">                         <span class="n" style="color: #333;">mmff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">minimise</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -170,6 +178,7 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ForceFieldMMFF94</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MMFF94SPLUS</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Conformer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">startPoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eMin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getStartingPositions</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">startPoints</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">contributions</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Conformer</span> <span class="n" style="color: #333;">ligConf</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">startPoints</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">transform</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">PheSAAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">initialTransform</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">Conformer</span> <span class="n" style="color: #333;">newLigConf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Conformer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ligConf</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,6 +200,7 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">energy</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bestEnergy</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java">                                 <span class="n" style="color: #333;">bestEnergy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">energy</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java">                                 <span class="n" style="color: #333;">bestPose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getLigConf</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java">                                 <span class="n" style="color: #333;">contributions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getContributions</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">threadMaster</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">threadMaster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">threadMustDie</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,8 +212,7 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Translation</span> <span class="n" style="color: #333;">translate</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Translation</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">origCOM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">origCOM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">y</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">origCOM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">});</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java">                 <span class="n" style="color: #333;">rot</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">apply</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">best</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="java">                 <span class="n" style="color: #333;">translate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">apply</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">best</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"></span>

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">best</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bestEnergy</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">best</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bestEnergy</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="java">         <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java">                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">DockingFailedException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"docking failed"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -265,7 +274,6 @@ public class DockingEngine {</td>

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<td class="old_line diff-line-num" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="java">         <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setState</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bestState</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="java">         <span class="n" style="color: #333;">engine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getScore</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestEnergy</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="java">         </span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -391,11 +399,16 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DockingResult</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Comparable</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">></span>  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">DELIMITER</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">";"</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">DELIMITER2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">DELIMITER3</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%"</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="java">         <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">NULL_CONTRIBUTION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"#"</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="java">         </span>

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<td class="new_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Map</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">String</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">contributions</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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397

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<td class="new_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="java">                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="java">                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="java">                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contributions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="java">         </span>

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<td class="new_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getScore</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -406,6 +419,11 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="java">         </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getContributions</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="java">         </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="java">         </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Encoder</span> <span class="n" style="color: #333;">encoder</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Base64</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getEncoder</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -417,6 +435,19 @@ public class DockingEngine {</td>

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<td class="old_line diff-line-num" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

417

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435

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="java">                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">idcoords</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

418

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<td class="new_line diff-line-num" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

436

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="java">                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DELIMITER</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

419

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<td class="new_line diff-line-num" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

437

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="java">                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">encoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">encodeToString</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">EncodeFunctions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">doubleToByteArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">)));</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

438

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="java">                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DELIMITER</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

439

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

440

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="java">                         <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">NULL_CONTRIBUTION</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

441

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="java">                 <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

442

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="java">                         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

443

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="java">                                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

444

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="java">                                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DELIMITER3</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

445

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="java">                                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">encoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">encodeToString</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">EncodeFunctions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">doubleToByteArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">))));</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

446

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC446" class="line" lang="java">                                 <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DELIMITER2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

447

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

448

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="java">                         <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setLength</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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450

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="java">                 </span>

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420

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="java">         </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -430,7 +461,19 @@ public class DockingEngine {</td>

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<td class="old_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="java">                 <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">idcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">idcoords</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC462" class="line" lang="java">                 <span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">EncodeFunctions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">byteArrayToDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">()));</span></span>

</pre>

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433

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<td class="new_line diff-line-num old" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">DockingResult</span> <span class="n" style="color: #333;">dockingResult</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">contributions</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">NULL_CONTRIBUTION</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="java">                         <span class="n" style="color: #333;">contributions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">>();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="java">                         <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">splitted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DELIMITER2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="java">                         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">contr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">splitted</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="java">                                 <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">splitted2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DELIMITER3</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="java">                                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splitted2</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">EncodeFunctions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">byteArrayToDouble</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitted2</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">()));</span></span>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="java">                                 <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="java">                         </span>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">DockingResult</span> <span class="n" style="color: #333;">dockingResult</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">DockingResult</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pose</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dockingResult</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -444,6 +487,8 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="java">           </span>

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="java"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="java"> </span>

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<td class="new_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="java"> </span>

</pre>

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<br>

</li>

<li id="819430bd4feb0962132eaba56931cbec7c761fd8">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#819430bd4feb0962132eaba56931cbec7c761fd8"><strong>src/main/java/com/actelion/research/chem/docking/LigandPose.java</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,6 +136,10 @@ public class LigandPose implements Evaluable{</td>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="java">                 </span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="java"> </span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getContributions</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">engine</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getContributions</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> </span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setInitialState</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">torsionHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRotatableBonds</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//3 translational, 3 rotational, 3 torsion</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java">         <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">elements</span><span class="o" style="font-weight: 600;">];</span></span>

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</li>

<li id="6bf6bc0e867dc60438664fa7e2197883ae9a4053">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#6bf6bc0e867dc60438664fa7e2197883ae9a4053"><strong>src/main/java/com/actelion/research/chem/docking/scoring/AbstractScoringEngine.java</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,8 @@ package com.actelion.research.chem.docking.scoring;</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Set</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Map</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Coordinates</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Molecule3D</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.StereoMolecule</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,6 +80,8 @@ public abstract class AbstractScoringEngine  {</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">abstract</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getFGValue</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">  </span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">abstract</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getScore</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java">  </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">abstract</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getContributions</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Conformer</span> <span class="nf" style="color: #900; font-weight: 600;">getReceptorConf</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">receptorConf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<br>

</li>

<li id="35842adf3930ed08842a9c3177f4efd0161d8603">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#35842adf3930ed08842a9c3177f4efd0161d8603"><strong>src/main/java/com/actelion/research/chem/docking/scoring/ChemPLP.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +98,7 @@ public class ChemPLP extends AbstractScoringEngine {</td>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">          <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setState</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">candidatePose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCartState</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ffEnergy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTotalEnergy</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">ffEnergy</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">e0</span><span class="o" style="font-weight: 600;">)></span><span class="no" style="color: #008080;">STRAIN_CUTOFF</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java">                 <span class="n" style="color: #333;">energy</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ffEnergy</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java">                 <span class="n" style="color: #333;">energy</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ffEnergy</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="n" style="color: #333;"><span class="idiff right">e0</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java">                 <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addGradient</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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103

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103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PotentialEnergyTerm</span> <span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">constraints</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -498,6 +498,34 @@ public class ChemPLP extends AbstractScoringEngine {</td>

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498

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498

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<td class="new_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="java"></span>

</pre>

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500

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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="java"> <span class="nd">@Override</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getContributions</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC503" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">contributions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">>();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">grad</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">candidatePose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getLigConf</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getMolecule</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAllAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

505

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">hbond</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

506

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PotentialEnergyTerm</span> <span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">chemscoreHbond</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

507

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="java">                 <span class="n" style="color: #333;">hbond</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">term</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFGValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

508

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="java">         <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"HBOND"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hbond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">metal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

510

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PotentialEnergyTerm</span> <span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">chemscoreMetal</span><span class="o" style="font-weight: 600;">)</span> </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

511

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="java">                 <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">term</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFGValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="java">         <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"METAL"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">metal</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

513

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">plpContr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

514

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PotentialEnergyTerm</span> <span class="n" style="color: #333;">term</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">plp</span><span class="o" style="font-weight: 600;">)</span> </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

515

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="java">                 <span class="n" style="color: #333;">plpContr</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">term</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFGValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

516

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="java">         <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"PLP"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">plpContr</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

517

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC517" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">strain</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

518

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="java">         <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setState</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">candidatePose</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCartState</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

519

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ffEnergy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTotalEnergy</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

520

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">ffEnergy</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">e0</span><span class="o" style="font-weight: 600;">)></span><span class="no" style="color: #008080;">STRAIN_CUTOFF</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

521

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC521" class="line" lang="java">                 <span class="n" style="color: #333;">strain</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">ffEnergy</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

522

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC522" class="line" lang="java">                 <span class="n" style="color: #333;">ff</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addGradient</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

523

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC523" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

524

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC524" class="line" lang="java">         <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"STRAIN"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">strain</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

525

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC525" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">contributions</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

526

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC526" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

527

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC527" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

528

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<td class="new_line diff-line-num" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

502

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<td class="new_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

530

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

503

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<td class="new_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

531

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC531" class="line" lang="java"></span>

</pre>

</td>

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<br>

</li>

<li id="1e236c5e43c30a02fbeea4e900a0c284f6fa34a8">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#1e236c5e43c30a02fbeea4e900a0c284f6fa34a8"><strong>src/main/java/com/actelion/research/chem/docking/scoring/IdoScore.java</strong></a>

<hr>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,6 +140,12 @@ public class IdoScore extends AbstractScoringEngine {</td>

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<td class="old_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="new_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java">                 </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<td class="new_line diff-line-num" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="nd">@Override</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getContributions</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// TODO Auto-generated method stub</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

148

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<td class="new_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC149" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

144

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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

145

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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"></span>

</pre>

</td>

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<br>

</li>

<li id="b913e9301eb349935afa9f9053995d0205bb3b8e">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#b913e9301eb349935afa9f9053995d0205bb3b8e"><strong>src/main/java/com/actelion/research/chem/io/Mol2FileParser.java</strong></a>

<hr>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -243,8 +243,9 @@ public class Mol2FileParser extends AbstractParser {</td>

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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

243

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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

243

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC243" class="line" lang="java"> </span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

244

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<td class="new_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

244

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atomicNo</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomX</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomZ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java">                                         <span class="c1" style="color: #998; font-style: italic;">//invert y and z coordinates for compatibility with Java coordinate system (analogously to Molfileparser)</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomZ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomName</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">atomName</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomChainId</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">chainId</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="java">                                         <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomAmino</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">amino</span><span class="o" style="font-weight: 600;">);</span></span>

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<br>

</li>

<li id="262e1a444c63ad8c6f38e8d5341f3605e1f567ee">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#262e1a444c63ad8c6f38e8d5341f3605e1f567ee"><strong>src/main/java/com/actelion/research/chem/properties/complexity/ContainerFragBondsSolutions.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -197,7 +197,7 @@ public class ContainerFragBondsSolutions {</td>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">ELUSIVE</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ContainerFragBondsSolutions maximum<span class="idiff left">N</span>umber<span class="idiff right">BondsInF</span>ragment "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maximumNumberBondsInFragment</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ContainerFragBondsSolutions maximum<span class="idiff left"> n</span>umber<span class="idiff"> of bonds in a single f</span>ragment "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maximumNumberBondsInFragment</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"."</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arrCapacity</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<li id="45e84a8050acd058a0497af42eacc0972aec8aa0">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#45e84a8050acd058a0497af42eacc0972aec8aa0"><strong>src/main/java/com/actelion/research/chem/properties/complexity/ExhaustiveFragmentsStatistics.java</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +115,7 @@ public class ExhaustiveFragmentsStatistics {</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java">         <span class="n" style="color: #333;">efg</span>  <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ExhaustiveFragmentGeneratorBonds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bits</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">totalCapacity</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ExhaustiveFragmentsStatistics init(...) max <span class="idiff left right">capacity</span> bonds in fragment "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">efg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMaximumCapacityBondsInFragment</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ExhaustiveFragmentsStatistics init(...) max <span class="idiff left">number of</span> bonds in <span class="idiff right">a </span>fragment "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">efg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMaximumCapacityBondsInFragment</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java">         <span class="n" style="color: #333;">minNumBondsFragment</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">MINLEN_FRAG</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java">                         </span>

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<li id="cb31a3eb9ce056b7b6950e3c00e22e6ea9374b65">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#cb31a3eb9ce056b7b6950e3c00e22e6ea9374b65"><strong>src/main/java/com/actelion/research/chem/reaction/mapping/MappingScorer.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +52,8 @@ public class MappingScorer {</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// we add/remove fractional bond orders for new/broken bonds and</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// we add fractional bond order changes of changed bonds</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// to reflect the corresponding change in implicit hydrogen bond counts.</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hydrogenBondPenalty</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hydrogenBondPenalty</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">SCORE_HYDROGEN</span> <span class="o" style="font-weight: 600;">?</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()]</span> <span class="o" style="font-weight: 600;">:</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">isAssignedProductAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java">          <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nl">atom:</span><span class="n" style="color: #333;">reactantToProductAtom</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,24 +72,32 @@ public class MappingScorer {</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pAtom1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pAtom2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java">                                  <span class="n" style="color: #333;">penalty</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getBondCreateOrBreakPenalty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mReactant</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rBond</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pAtom1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java">                                  <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pAtom2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java">                                  <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">SCORE_HYDROGEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java">                                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pAtom1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java">                                          <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java">                                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pAtom2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java">                                          <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java">                                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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78

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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">                          <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">                          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pBond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pBond</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">                          <span class="n" style="color: #333;">penalty</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getBondCreateOrBreakPenalty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mReactant</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java">                          <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java">                          <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java">                          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">SCORE_HYDROGEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java">                                  <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java">                                  <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java">                                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">                          <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java">                          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">bondOrderChange</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rBondOrder</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">getFractionalBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java">                  <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bondOrderChange</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java">                  <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bondOrderChange</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">SCORE_HYDROGEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java">                          <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">bondOrderChange</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rBondOrder</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">getFractionalBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java">                          <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bondOrderChange</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java">                          <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bondOrderChange</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="new_line diff-line-num" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java">                 <span class="n" style="color: #333;">productBondHandled</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java">                 <span class="n" style="color: #333;">penalty</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getBondChangePenalty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rBond</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,13 +106,16 @@ public class MappingScorer {</td>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">productBondHandled</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java">                         <span class="n" style="color: #333;">penalty</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getBondCreateOrBreakPenalty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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100

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pBondOrder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getFractionalBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

101

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pAtom1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pAtom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

103

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isAssignedProductAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">])</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

104

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java">                                 <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

105

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isAssignedProductAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">])</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java">                                 <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">SCORE_HYDROGEN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pBondOrder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getFractionalBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pAtom1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pAtom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pBond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC114" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isAssignedProductAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java">                                         <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isAssignedProductAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java">                                         <span class="n" style="color: #333;">hydrogenBondPenalty</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pAtom2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">pBondOrder</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,7 +147,7 @@ public class MappingScorer {</td>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isHetero2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isElectronegative</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom2</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">isHetero1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isHetero2</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="mf" style="color: #099;">1.9f</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;"><span class="idiff left right">2.1</span>f</span> <span class="o" style="font-weight: 600;">:</span> <span class="mf" style="color: #099;">1.9f</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isHetero1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isHetero2</span><span class="o" style="font-weight: 600;">)</span>    <span class="c1" style="color: #998; font-style: italic;">// e.g. m-CPBA</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">1.7f</span><span class="o" style="font-weight: 600;">;</span></span>

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<br>

</li>

<li id="60ccb435ab9538009a24ad8c50dfe7583b481728">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#60ccb435ab9538009a24ad8c50dfe7583b481728"><strong>src/main/java/com/actelion/research/chem/reaction/mapping/RootAtomPairSource.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,10 +139,6 @@ public class RootAtomPairSource {</td>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getPairSequenceCount</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mSequenceCount</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * RootAtomPairs are returned in similarity order. The first returned pair is that</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * pair of atoms that is more similar than any other mutual combination of reactant</span></span>

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<br>

</li>

<li id="fd828ea16dfc40dd5d8d20957d2ed4a3e324497c">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#fd828ea16dfc40dd5d8d20957d2ed4a3e324497c"><strong>src/main/java/com/actelion/research/chem/reaction/mapping/SimilarityGraphBasedReactionMapper.java</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,10 @@ public class SimilarityGraphBasedReactionMapper {</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">RootAtomPairSource</span> <span class="n" style="color: #333;">rootAtomPairSource</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">RootAtomPairSource</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mReactantMapNo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mProductMapNo</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java">          <span class="n" style="color: #333;">mAtomPairSequenceCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rootAtomPairSource</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNextPairSequence</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java">                  <span class="n" style="color: #333;">mAtomPairSequenceCount</span><span class="o" style="font-weight: 600;">++;</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">                  <span class="n" style="color: #333;">mMapNo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootAtomPairSource</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getManualMapCount</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java">                  <span class="n" style="color: #333;">mMappableAtomCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootAtomPairSource</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMappableAtomCount</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,8 +120,6 @@ if (DEBUG) {</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java">                                 <span class="n" style="color: #333;">productMapNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mProductMapNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java">         <span class="n" style="color: #333;">mAtomPairSequenceCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootAtomPairSource</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPairSequenceCount</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -299,16 +300,16 @@ if (DEBUG) {</td>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mSimilarityComparator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mReactantConnAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">reactantConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">],</span></span>

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<td class="new_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="java">                         <span class="n" style="color: #333;">mProductConnAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">productConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="java">                 <span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">++;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">NO_PI_PENALTY</span> <span class="o" style="font-weight: 600;"><</span> <span class="no" style="color: #008080;">MAX_ENVIRONMENT_RADIUS</span></span>

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<td class="new_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mReactantNoPiAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">reactantConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">NO_PI_PENALTY</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mSimilarityComparator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mReactantNoPiAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">reactantConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">NO_PI_PENALTY</span><span class="o" style="font-weight: 600;">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="java">                         <span class="n" style="color: #333;">mProductNoPiAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">productConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">NO_PI_PENALTY</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="java">                 <span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">SKELETON_PENALTY</span> <span class="o" style="font-weight: 600;"><</span> <span class="no" style="color: #008080;">MAX_ENVIRONMENT_RADIUS</span></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mReactantSkelAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">reactantConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">SKELETON_PENALTY</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mSimilarityComparator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mReactantSkelAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">reactantConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">SKELETON_PENALTY</span><span class="o" style="font-weight: 600;">],</span></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="java">                         <span class="n" style="color: #333;">mProductSkelAtomEnv</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">productConnIndex</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">+</span><span class="no" style="color: #008080;">SKELETON_PENALTY</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="java">                 <span class="n" style="color: #333;">radius</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>               while (radius+NO_PI_PENALTY < MAX_ENVIRONMENT_RADIUS</span></span>

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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                        && mReactantNoPiAtomEnv[reactantAtom][reactantConnIndex][radius+NO_PI_PENALTY] != null</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                        && mSimilarityComparator.compare(mReactantNoPiAtomEnv[reactantAtom][reactantConnIndex][radius+NO_PI_PENALTY],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                               mProductNoPiAtomEnv[productAtom][productConnIndex][radius+NO_PI_PENALTY]) == 0)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                       radius++;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>               while (radius+SKELETON_PENALTY < MAX_ENVIRONMENT_RADIUS</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                        && mReactantSkelAtomEnv[reactantAtom][reactantConnIndex][radius+SKELETON_PENALTY] != null</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                        && mSimilarityComparator.compare(mReactantSkelAtomEnv[reactantAtom][reactantConnIndex][radius+SKELETON_PENALTY],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                               mProductSkelAtomEnv[productAtom][productConnIndex][radius+SKELETON_PENALTY]) == 0)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                       radius++;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">radius</span> <span class="o" style="font-weight: 600;"><<</span> <span class="no" style="color: #008080;">SIMILARITY_SHIFT</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">getBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">candidateBond</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="java">                                          <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">skelSimilarity</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">passesBasicRules</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantRoot</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reactantCandidate</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">productRoot</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">productCandidate</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="java">                                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">envSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getCombinedAtomSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantRoot</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reactantCandidate</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">productRoot</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">productCandidate</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                                                               int envSimilarity = getCombinedAtomSimilarity(reactantRoot, reactantCandidate, productRoot, productCandidate);</span></span>

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="java">                                                         <span class="c1" style="color: #998; font-style: italic;">// introducing the non-pi similarity does not really seem to improve matters</span></span>

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">//</span>                                                             int envSimilarity = get<span class="idiff right">Combined</span>AtomSimilarity(reactantRoot, reactantCandidate, productRoot, productCandidate);</span></span>

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="java">                                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">envSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getAtomSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantRoot</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reactantCandidate</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">productRoot</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">productCandidate</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//System.out.println("skel:"+skelSimilarity+" conn:"+envSimilarity+" comb:"+envSimilarityCandidate);</span></span>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="java">                                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">skelSimilarity</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">envSimilarity</span><span class="o" style="font-weight: 600;">);</span></span>

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</li>

<li id="e4a461ea6c1e83c20f9aecaffed9344cdcbe8a19">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#e4a461ea6c1e83c20f9aecaffed9344cdcbe8a19"><strong>src/main/java/com/actelion/research/gui/JDrawDialog.java</strong></a>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.gui</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.StereoMolecule</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.reaction.IReactionMapper</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.reaction.MCSReactionMapper</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.reaction.Reaction</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.gui.clipboard.ClipboardHandler</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.gui.hidpi.HiDPIHelper</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.ActionEvent</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.ActionListener</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.KeyEvent</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.KeyListener</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">JDrawDialog</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">JDialog</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">ActionListener</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">KeyListener</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,6 +61,22 @@ public class JDrawDialog extends JDialog implements ActionListener,KeyListener {</td>

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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java">          <span class="n" style="color: #333;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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61

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62

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Dialog</span> <span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ModalityType</span> <span class="n" style="color: #333;">modalityType</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java">          <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">modalityType</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java">          <span class="n" style="color: #333;">mMolecule</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java">          <span class="n" style="color: #333;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">JDrawArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MODE_MULTIPLE_FRAGMENTS</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java">                  <span class="n" style="color: #333;">mArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setFragments</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Dialog</span> <span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ModalityType</span> <span class="n" style="color: #333;">modalityType</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java">          <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">modalityType</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java">          <span class="n" style="color: #333;">mMolecule</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" class="line" lang="java">          <span class="n" style="color: #333;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">JDrawArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MODE_REACTION</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java">                  <span class="n" style="color: #333;">mArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Frame</span> <span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DEFAULT_TITLE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,7 +125,7 @@ public class JDrawDialog extends JDialog implements ActionListener,KeyListener {</td>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Frame</span> <span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ModalityType</span> <span class="n" style="color: #333;">modalityType</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java">         <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">modalityType</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java">         <span class="n" style="color: #333;">mMolecule</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java">         <span class="n" style="color: #333;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">JDrawArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MODE_<span class="idiff left right">REACTION</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java">         <span class="n" style="color: #333;">initialize</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">owner</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">JDrawArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MODE_<span class="idiff left right">MULTIPLE_FRAGMENTS</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java">                 <span class="n" style="color: #333;">mArea</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setFragments</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="4c2a41d526b7b14792efa22a7224c243662939f7">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#4c2a41d526b7b14792efa22a7224c243662939f7"><strong>src/main/java/com/actelion/research/gui/JEditableChemistryView.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,7 +149,10 @@ public class JEditableChemistryView extends JChemistryView {</td>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(!(</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Frame</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java">                 <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Frame</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Edit Reaction"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ModalityType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCUMENT_MODAL</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Frame</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Frame</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Edit Reaction"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ModalityType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCUMENT_MODAL</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java">         <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Edit Reaction"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ModalityType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCUMENT_MODAL</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="nc" style="color: #458; font-weight: 600;">JDrawDialog</span> <span class="nf" style="color: #900; font-weight: 600;">createDrawDialog</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,6 +160,9 @@ public class JEditableChemistryView extends JChemistryView {</td>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="java">         <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(!(</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Frame</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java">                 <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Frame</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Edit Molecules"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ModalityType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCUMENT_MODAL</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Frame</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Frame</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Edit Molecules"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ModalityType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCUMENT_MODAL</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java">         <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">JDrawDialog</span><span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Edit Molecules"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Dialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ModalityType</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCUMENT_MODAL</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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<td class="new_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<br>

</li>

<li id="0286e69308a5dc8f38cd96a6e642e56ef8ffa0e1">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#0286e69308a5dc8f38cd96a6e642e56ef8ffa0e1"><strong>src/main/java/com/actelion/research/gui/clipboard/ClipboardHandler.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,6 +35,7 @@ package com.actelion.research.gui.clipboard;</td>

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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.*</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.coords.CoordinateInventor</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.dnd.ChemistryFlavors</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.RXNFileCreator</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.RXNFileParser</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.name.StructureNameResolver</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.reaction.Reaction</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -497,10 +498,10 @@ public class ClipboardHandler implements IClipboardHandler</td>

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<td class="old_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

498

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<td class="new_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">copyReactionToClipboard</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">ctab</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>               if (ctab == null) {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC501" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                       RXNFileCreator mc = new RXNFileCreator(rxn);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>                       ctab = mc.getRXNfile();</span></span>

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<td class="new_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>               }</span></span>

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<td class="old_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ctab</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">RXNFileCreator</span> <span class="n" style="color: #333;">mc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">RXNFileCreator</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="java">                 <span class="n" style="color: #333;">ctab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRXNfile</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="java"></span>

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<td class="new_line diff-line-num" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">ChemDrawCDX</span> <span class="n" style="color: #333;">cdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">com</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">actelion</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">research</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">gui</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clipboard</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">external</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ChemDrawCDX</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">cdxBuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cdx</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getChemDrawBuffer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -514,7 +515,7 @@ public class ClipboardHandler implements IClipboardHandler</td>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="java">         <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="java">         <span class="n" style="color: #333;">bos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="java"></span>

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<td class="new_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC517" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">NativeClipboardAccessor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copy<span class="idiff left">Molecule</span>ToClipboard</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cdxBuffer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toByteArray</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">NativeClipboardAccessor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copy<span class="idiff left">Reaction</span>ToClipboard</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff">ctab</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">getBytes</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">cdxBuffer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toByteArray</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">writeMol2Metafile</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">temp</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sketch</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<li id="6e2078f60f1fd5ba17658e0850d34a9a27b9ae38">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#6e2078f60f1fd5ba17658e0850d34a9a27b9ae38"><strong>src/main/java/com/actelion/research/gui/dock/DividerChangeListener.java</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.gui.dock</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">interface</span> <span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java">   <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dividerLocationChanged</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">fork</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<li id="e0ad42de8a1873c3f3f3a7e6771a49e8e3a1ddcb">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#e0ad42de8a1873c3f3f3a7e6771a49e8e3a1ddcb"><strong>src/main/java/com/actelion/research/gui/dock/JDockingPanel.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,7 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mTargetPosition</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mPreviousTargetPosition</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">GhostPreview</span> <span class="n" style="color: #333;">mPreview</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Dockable</span> <span class="n" style="color: #333;">mMaximizedView</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"></span>

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Creates a docking panel to which any Dockables may be added by</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,6 +86,23 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">                  <span class="o" style="font-weight: 600;">},</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addDividerChangeLister</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDividerChangeListeners</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java">                  <span class="n" style="color: #333;">mDividerChangeListeners</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><>();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java">          <span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mTreeRoot</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java">                  <span class="n" style="color: #333;">mTreeRoot</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">removeDividerChangeLister</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDividerChangeListeners</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java">                 <span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mTreeRoot</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java">                         <span class="n" style="color: #333;">mTreeRoot</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">actionPerformed</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ActionEvent</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<td class="new_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getActionCommand</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"close_"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getActionCommand</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -309,7 +327,7 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="java">         <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span> <span class="n" style="color: #333;">newLeaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isDragging</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeContainer</span> <span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">treeLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dividerPosition</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dividerPosition</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mDividerChangeListeners</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java">                 <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceChildElement</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">treeLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">treeFork</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java">                 <span class="n" style="color: #333;">mLeafMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -430,6 +448,34 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="java"></span>

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<td class="new_line diff-line-num new" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="new_line diff-line-num new" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Checks, whether a dockable with the given title exists, and whether it is visible (selected if in a JTabbedPane)</span></span>

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * and whether it is in the left or right branch (depending on parameter left) of a JSplitPane.</span></span>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param title</span></span>

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<td class="new_line diff-line-num new" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param left if true, then</span></span>

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<td class="new_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @return true the respective dockable is visible and in the left part of a JSplitPane</span></span>

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isVisibleInSplitPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">Component</span> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mDockableMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="java"></span>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">Component</span> <span class="n" style="color: #333;">pane</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">view</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pane</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">pane</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getSelectedComponent</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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466

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="java">                         <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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467

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

468

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="java">                 <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pane</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

469

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC469" class="line" lang="java">                 <span class="n" style="color: #333;">pane</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

470

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

471

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC471" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

472

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pane</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

473

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">pane</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getLeftComponent</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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474

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">pane</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getRightComponent</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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475

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="java"></span>

</pre>

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476

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC476" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

477

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

478

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

433

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<td class="new_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

479

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

434

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<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

480

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * changes a title of a docked Dockable</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

435

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<td class="new_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

481

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * @param oldTitle existing title</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -596,7 +642,7 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<td class="old_line diff-line-num" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

596

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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Dockable</span> <span class="n" style="color: #333;">dockable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dockables</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

597

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<td class="new_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="java">                 <span class="n" style="color: #333;">bottomLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

598

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<td class="new_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

644

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeContainer</span> <span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

599

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<td class="new_line diff-line-num old" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DOCK_BOTTOM</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">);</span><span class="idiff left right">   </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC645" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DOCK_BOTTOM</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mDividerChangeListeners</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="java">                 <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceChildElement</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">treeFork</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<td class="new_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="java">                 <span class="n" style="color: #333;">mLeafMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<td class="new_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="java">                 <span class="n" style="color: #333;">mDockableMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -606,7 +652,7 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<td class="old_line diff-line-num" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

606

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<td class="new_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

652

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC652" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Dockable</span> <span class="n" style="color: #333;">dockable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dockables</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

607

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<td class="new_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

653

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="java">                 <span class="n" style="color: #333;">topRight</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<td class="new_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

654

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC654" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeContainer</span> <span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

609

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<td class="new_line diff-line-num old" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC609" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">topRight</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DOCK_RIGHT</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">);</span><span class="idiff left right">      </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

655

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC655" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">topRight</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DOCK_RIGHT</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mDividerChangeListeners</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<td class="new_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="java">                 <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceChildElement</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">topLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">treeFork</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

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<td class="new_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="java">                 <span class="n" style="color: #333;">mLeafMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">topRight</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<td class="new_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="java">                 <span class="n" style="color: #333;">mDockableMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -616,7 +662,7 @@ public class JDockingPanel extends JPanel implements ActionListener {</td>

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<td class="old_line diff-line-num" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

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<td class="new_line diff-line-num" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">Dockable</span> <span class="n" style="color: #333;">dockable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dockables</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size3</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

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<td class="new_line diff-line-num" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

663

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="java">                 <span class="n" style="color: #333;">bottomRight</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

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<td class="new_line diff-line-num" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

664

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeContainer</span> <span class="n" style="color: #333;">parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParent</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

619

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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC619" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottomRight</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DOCK_RIGHT</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">);</span><span class="idiff left right">        </span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC665" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="n" style="color: #333;">treeFork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottomRight</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">DOCK_RIGHT</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">.</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mDividerChangeListeners</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

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<td class="new_line diff-line-num" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

666

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="java">                 <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceChildElement</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bottomLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">treeFork</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<td class="new_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="java">                 <span class="n" style="color: #333;">mLeafMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">bottomRight</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<td class="new_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

668

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="java">                 <span class="n" style="color: #333;">mDockableMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<br>

</li>

<li id="eb4ec2cc0ab826869c0310cdf4b423f1e8123cb9">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#eb4ec2cc0ab826869c0310cdf4b423f1e8123cb9"><strong>src/main/java/com/actelion/research/gui/dock/TreeFork.java</strong></a>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.gui.dock</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>

</pre>

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3

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.plaf.SplitPaneUI</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.plaf.basic.BasicSplitPaneUI</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.MouseAdapter</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.event.MouseEvent</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">TreeContainer</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">TreeElement</span> <span class="n" style="color: #333;">mLeftChildElement</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">TreeElement</span> <span class="n" style="color: #333;">mRightChildElement</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * Constructor to create a fork element that is inserted between the specified</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,42 +20,55 @@ public class TreeFork extends TreeContainer {</td>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param oldLeaf</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param newLeaf</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param newLeafPosition</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param <span class="idiff left right">proportionalD</span>ividerLocation</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       * @param <span class="idiff left right">d</span>ividerLocation</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newLeafPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left right">proportionalDividerLocation</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newLeafPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;"><span class="idiff left">dividerLocation</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">DividerChangeListener</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">listeners</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="java">          <span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span> <span class="n" style="color: #333;">splitPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java">          <span class="k" style="font-weight: 600;">switch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newLeafPosition</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java">          <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">JDockingPanel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCK_TOP</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java">                  <span class="n" style="color: #333;">splitPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MySplitPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">VERTICAL_SPLIT</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java">                                  <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">proportionalD</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java">                                  <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">d</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="java">                  <span class="n" style="color: #333;">mLeftChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java">                  <span class="n" style="color: #333;">mRightChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java">                  <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="java">          <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">JDockingPanel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCK_LEFT</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="java">                  <span class="n" style="color: #333;">splitPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MySplitPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">HORIZONTAL_SPLIT</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java">                                  <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">proportionalD</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java">                                  <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">d</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java">                  <span class="n" style="color: #333;">mLeftChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java">                  <span class="n" style="color: #333;">mRightChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java">                  <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java">          <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">JDockingPanel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCK_BOTTOM</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java">                  <span class="n" style="color: #333;">splitPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MySplitPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">VERTICAL_SPLIT</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="java">                                  <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">proportionalD</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="java">                                  <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">d</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java">                  <span class="n" style="color: #333;">mLeftChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="java">                  <span class="n" style="color: #333;">mRightChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="java">                  <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC46" class="line" lang="java">          <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">JDockingPanel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DOCK_RIGHT</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC47" class="line" lang="java">                  <span class="n" style="color: #333;">splitPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MySplitPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">HORIZONTAL_SPLIT</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="java">                                  <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">proportionalD</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="java">                                  <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComponent</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;"><span class="idiff left right">d</span>ividerLocation</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java">                  <span class="n" style="color: #333;">mLeftChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java">                  <span class="n" style="color: #333;">mRightChildElement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java">                  <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="new_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//            splitPane.addPropertyChangeListener(JSplitPane.DIVIDER_LOCATION_PROPERTY, pce -> {} );</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java">          <span class="n" style="color: #333;">splitPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addPropertyChangeListener</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JSplitPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DIVIDER_LOCATION_PROPERTY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDividerChangeListeners</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">MySplitPane</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mComponent</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">isDragged</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java">                          <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span> <span class="nl">l:</span><span class="n" style="color: #333;">mDividerChangeListeners</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java">                                  <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">dividerLocationChanged</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java">          <span class="n" style="color: #333;">mDividerChangeListeners</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java">          <span class="n" style="color: #333;">mComponent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splitPane</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java">          <span class="n" style="color: #333;">oldLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setParent</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java">          <span class="n" style="color: #333;">newLeaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setParent</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">updateDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java">          <span class="n" style="color: #333;">mDividerChangeListeners</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mLeftChildElement</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java">                  <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mLeftChildElement</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">updateDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mLeftChildElement</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java">                  <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mRightChildElement</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">updateDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">removeWithLeaf</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">TreeLeaf</span> <span class="n" style="color: #333;">leaf</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java">          <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">leaf</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mLeftChildElement</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">leaf</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mRightChildElement</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">leaf</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mLeftChildElement</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,6 +175,7 @@ class MySplitPane extends JSplitPane {</td>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">serialVersionUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x20070726</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mProportionalLocation</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mMouseDown</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MySplitPane</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newOrientation</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Component</span> <span class="n" style="color: #333;">newLeftComponent</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Component</span> <span class="n" style="color: #333;">newRightComponent</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">proportionalLocation</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="java">         <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newOrientation</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newLeftComponent</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newRightComponent</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,6 +183,22 @@ class MySplitPane extends JSplitPane {</td>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java">         <span class="n" style="color: #333;">setResizeWeight</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">proportionalLocation</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java">         <span class="n" style="color: #333;">setBorder</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java">         <span class="n" style="color: #333;">mProportionalLocation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proportionalLocation</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"></span>

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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">SplitPaneUI</span> <span class="n" style="color: #333;">spui</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getUI</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">spui</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">BasicSplitPaneUI</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java">                 <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">BasicSplitPaneUI</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">spui</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getDivider</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">addMouseListener</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MouseAdapter</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java">                         <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mousePressed</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MouseEvent</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java">                                 <span class="n" style="color: #333;">mMouseDown</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="java">                         <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mouseReleased</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MouseEvent</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java">                                 <span class="n" style="color: #333;">mMouseDown</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

199

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

200

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isDragged</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mMouseDown</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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166

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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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<td class="new_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="java"> <span class="nd">@Override</span></span>

</pre>

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<br>

</li>

<li id="473d383df3e59af9a3f20234b3ff116ee7ffe896">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#473d383df3e59af9a3f20234b3ff116ee7ffe896"><strong>src/main/java/com/actelion/research/gui/dock/TreeLeaf.java</strong></a>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.gui.dock</span><span class="o" style="font-weight: 600;">;</span></span>

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2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.gui.hidpi.HiDPIHelper</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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4

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.event.ChangeEvent</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.event.ChangeListener</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +82,13 @@ public class TreeLeaf extends TreeElement implements ChangeListener {</td>

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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addContent</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Dockable</span> <span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isDragging</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mComponent</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">Dockable</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">Dockable</span> <span class="n" style="color: #333;">existingDockable</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Dockable</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mComponent</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span> <span class="n" style="color: #333;">tabbedPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">BOTTOM</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC85" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span> <span class="n" style="color: #333;">tabbedPane</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JTabbedPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">BOTTOM</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC86" class="line" lang="java">                          <span class="nd">@Override</span> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Dimension</span> <span class="nf" style="color: #900; font-weight: 600;">getMinimumSize</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java">                                  <span class="c1" style="color: #998; font-style: italic;">// of not modified, the minimum size == preferred size.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java">                                  <span class="c1" style="color: #998; font-style: italic;">// Then width is at least the width of the longest tab name.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java">                                  <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Dimension</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">HiDPIHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">scale</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">),</span><span class="nc" style="color: #458; font-weight: 600;">HiDPIHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">scale</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC90" class="line" lang="java">                                  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java">                          <span class="o" style="font-weight: 600;">};</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java">                  <span class="n" style="color: #333;">tabbedPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">putClientProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Quaqua.TabbedPane.contentBorderPainted"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FALSE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

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<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">                  <span class="n" style="color: #333;">tabbedPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">existingDockable</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">existingDockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

</td>

<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC94" class="line" lang="java">                  <span class="n" style="color: #333;">tabbedPane</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dockable</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getTitle</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<br>

</li>

<li id="844f2796cb8822367a2a6bc3ad00b9d56d5e18b3">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#844f2796cb8822367a2a6bc3ad00b9d56d5e18b3"><strong>src/main/java/com/actelion/research/gui/dock/TreeRoot.java</strong></a>

<hr>

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<td class="old_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.gui.dock</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.BorderLayout</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.Component</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TreeRoot</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">TreeContainer</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">TreeElement</span> <span class="n" style="color: #333;">mChildElement</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Constructor to create a root element to which the first leaf should be connected.</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param <span class="idiff left right">par</span>ent</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param <span class="idiff left right">rootCompon</span>ent</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">TreeRoot</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">JComponent</span> <span class="n" style="color: #333;">rootComponent</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">TreeElement</span> <span class="n" style="color: #333;">child</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="java">        <span class="n" style="color: #333;">mComponent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootComponent</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,6 +19,11 @@ public class TreeRoot extends TreeContainer {</td>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java">        <span class="n" style="color: #333;">mChildElement</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setParent</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">DividerChangeListener</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mChildElement</span> <span class="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java">            <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">TreeFork</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">mChildElement</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">updateDividerChangeListeners</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

</td>

<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">TreeElement</span> <span class="nf" style="color: #900; font-weight: 600;">getChild</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

</td>

<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mChildElement</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC29" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="ec1e7f260c5e341b5b4551f820f746b392a3e2e8">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/f63e99bffb2f96ef45a8e4d1d087acd1dd99a4fb#ec1e7f260c5e341b5b4551f820f746b392a3e2e8"><strong>src/main/java/com/actelion/research/util/ConstantsDWAR.java</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,6 +115,10 @@ public class ConstantsDWAR {</td>

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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">TAG_COOR2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"idcoordinates2D"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">IDCODE_EMPTY</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"dH"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC122" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

123

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      * Can be one or multiple sets of 3D coordinates.</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC124" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">      */</span></span>

</pre>

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