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GitLab

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<h3>

Andrius Merkys pushed to branch master

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/70529c8336f232014c918042675800457beae710">70529c83</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-04-14T02:53:42-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Exclude mvnw.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad">b7b04036</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-04-14T02:54:07-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2022.4.2+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/bf2a7d86a53e3b28033ce6f2956c22ff6ecd18aa">bf2a7d86</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-04-14T02:54:14-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2022.4.2+dfsg'

Update to upstream version '2022.4.2+dfsg'

with Debian dir bc9af82ed9d624a1f9c1616a5486b482f8ac59af</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/4a0fef140038d8ad05d7df3a2e2abf8fd097c25e">4a0fef14</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-04-14T02:56:02-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/c520e82c5c7fd14332840598114d7bea96ea5ebb">c520e82c</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2022-04-14T02:56:19-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog for 2022.4.2+dfsg-1 release

</pre>

</li>

</ul>

<h4>20 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

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<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

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<li class="file-stats">

<a href="#86f5ff6c6075c2da045f28d3e5f76380f5c1292e">

debian/patches/javafx.patch

</a>

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<li class="file-stats">

<a href="#f28e061bd04986660d21d2f6096ef23b697bd93e">

debian/patches/libtablelayout-java.patch

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<li class="file-stats">

<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">

pom.xml

</a>

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<li class="file-stats">

<a href="#ba44c1f7e56c2598decf65ca012c856547ff2f0f">

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

</a>

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<li class="file-stats">

<a href="#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3">

src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java

</a>

</li>

<li class="file-stats">

<a href="#f678d35a688802dfd7e0cbfc6c14290a34944abc">

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

</a>

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<li class="file-stats">

<a href="#f9cb63e80b748296a596a354aa485682819c7904">

<span class="new-file">

+

src/main/java/com/actelion/research/chem/hyperspace/SimpleCombinatorialHit.java

</span>

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<li class="file-stats">

<a href="#2d0bffca02cf955165915399414eb28114819627">

<span class="new-file">

+

src/main/java/com/actelion/research/chem/hyperspace/SimpleSynthon.java

</span>

</a>

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<li class="file-stats">

<a href="#57834476cf2f3a0474fee1ce1fbff3ada6845cfb">

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

</a>

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<li class="file-stats">

<a href="#d0922db37ba2d4e1c4162276b7b27af29aeca835">

src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java

</a>

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<li class="file-stats">

<a href="#7e9910936f51c5883dc0e383abac0f0720181e30">

src/main/java/com/actelion/research/chem/phesa/pharmacophore/PPTriangle.java

</a>

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<li class="file-stats">

<a href="#1a2948d1808e5bf4b5ae448818a4c444d9b4870a">

src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java

</a>

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<li class="file-stats">

<a href="#86999a714d04156d77451e9ca14c33aff8a98a76">

src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/PPGaussian.java

</a>

</li>

<li class="file-stats">

<a href="#3dbbe7b950b7f9e3cf1fa45df59255c90fc56046">

src/main/java/com/actelion/research/chem/phesaflex/EvaluableFlexibleOverlap.java

</a>

</li>

<li class="file-stats">

<a href="#88f7248516cf1351766ec9d506223745b62982c0">

src/main/java/com/actelion/research/chem/reaction/Reactor.java

</a>

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<li class="file-stats">

<a href="#b23ac1794ae5ae3ca39c5fd7604dd429cdcd2393">

src/main/java/com/actelion/research/gui/editor/AtomQueryFeatureDialogBuilder.java

</a>

</li>

<li class="file-stats">

<a href="#98ac8c26d9087ed4dfec10db567462ed5ca7be22">

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

</a>

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</ul>

<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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

</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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OpenChemLib</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(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="LC2" class="line" lang="markdown"></span>

</pre></td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*OpenChemLib*</span> is Java based framework providing cheminformatics core functionality and user interface components. Its main focus is on organics chemistry and small molecules. It is built around a StereoMolecule class, which represents a molecule using atom and bond tables, provides atom neighbours, ring and aromaticity information, and supports MDL's concept of enhanced stereo representation. Additional classes provide, 2D-depiction, descriptor calculation, molecular similarity and substructure search, reaction search, property prediction, conformer generation, support for molfile and SMILES formats, energy minimization, ligand-protein interactions, and more. <span class="ge" style="font-style: italic;">*OpenChemLib's idcode*</span> represents molecules, fragments or reactions as canonical, very compact string that includes stereo and query features.</span>

</pre></td>

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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">

4

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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="markdown">Different to other cheminformatics frameworks, <span class="ge" style="font-style: italic;">*OpenChemLib*</span> also provides user interface components that allow to easily embed chemical functionality into Java applications, e.g. to display or edit chemical structures or reactions.</span>

</pre></td>

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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="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">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>

</pre></td>

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

<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,8 +6,15 @@ Different to other cheminformatics frameworks, *OpenChemLib* also provides user</td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*OpenChemLib*</span> requires JRE 8 or newer including JavaFX. Otherwise, there are no dependencies.</span>

</pre></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">

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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="markdown"></span>

</pre></td>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### How to download the project</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(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="LC10" class="line" lang="markdown"></span>

</pre></td>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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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="LC9" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre></td>

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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="markdown">git clone https://github.com/Actelion/openchemlib.git</span>

</pre></td>

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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="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="markdown"><span class="p">```</span></span>

</pre></td>

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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="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">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>

</pre></td>

</tr>

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

<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="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">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Build the project</span></span>

</pre></td>

</tr>

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

<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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">To build the project run the following from within the project directory.</span>

</pre></td>

</tr>

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

<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="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">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>

</pre></td>

</tr>

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

<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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">./mvnw package</span>

</pre></td>

</tr>

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

<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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">```</span></span>

</pre></td>

</tr>

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

<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

</td>

<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">

18

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>

</pre></td>

</tr>

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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">

13

</td>

<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">

19

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Folder 'examples'</span></span>

</pre></td>

</tr>

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

<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">

14

</td>

<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">

20

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">Contains examples for working with the <span class="ge" style="font-style: italic;">*OpenChemLib*</span> library.</span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">openchemlib (2022.4.2+dfsg-1) unstable; urgency=medium</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version 2022.4.2+dfsg</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(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

</td>

<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="plaintext">  * Exclude mvnw.</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(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

</td>

<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="plaintext"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(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

</td>

<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="plaintext"> -- Andrius Merkys <merkys@debian.org>  Thu, 14 Apr 2022 02:56:11 -0400</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre></td>

</tr>

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

<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="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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">openchemlib (2022.3.2+dfsg-1) unstable; urgency=medium</span>

</pre></td>

</tr>

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

<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

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre></td>

</tr>

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

<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

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * New upstream version 2022.3.2+dfsg</span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,9 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</td>

</tr>

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

<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

</td>

<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="plaintext">Upstream-Name: OpenChemLib</span>

</pre></td>

</tr>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/Actelion/openchemlib</span>

</pre></td>

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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">

4

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<td class="new_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">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded:</span>

</pre></td>

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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">

</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="plaintext"> .mvn</span>

</pre></td>

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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">

</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="plaintext"> mvnw</span>

</pre></td>

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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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> mvnw.cmd</span>

</pre></td>

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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

</td>

<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="plaintext"> src/main/java/com/actelion/research/chem/descriptor/flexophore/MDHFeature.java</span>

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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">

6

</td>

<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="plaintext"> src/main/java/info</span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

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<br>

</li>

<li id="86f5ff6c6075c2da045f28d3e5f76380f5c1292e">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#86f5ff6c6075c2da045f28d3e5f76380f5c1292e"><strong>debian/patches/javafx.patch</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Author: Andrius Merkys <merkys@debian.org></td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

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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">

6

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pom.xml</span></span>

</pre></td>

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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="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>

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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(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="LC8" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left deletion">07</span>,6 +1<span class="idiff right deletion">07</span>,21 @@</span></span>

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<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(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="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="diff"><span class="p">@@ -1<span class="idiff left addition">11</span>,6 +1<span class="idiff right addition">11</span>,21 @@</span></span>

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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="diff">             <version>4.13.1</version></span>

</pre></td>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="diff">             <scope>test</scope></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">         </dependency></span>

</pre></td>

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<br>

</li>

<li id="f28e061bd04986660d21d2f6096ef23b697bd93e">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#f28e061bd04986660d21d2f6096ef23b697bd93e"><strong>debian/patches/libtablelayout-java.patch</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Author: Andrius Merkys <merkys@debian.org></td>

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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">

4

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<td class="new_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">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

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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="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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pom.xml</span></span>

</pre></td>

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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">

6

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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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>

</pre></td>

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7

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<td class="new_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left deletion">2</span>,6 +12<span class="idiff right deletion">2</span>,10 @@</span></span>

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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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left addition">6</span>,6 +12<span class="idiff right addition">6</span>,10 @@</span></span>

</pre></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="diff">             <artifactId>javafx-graphics</artifactId></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="diff">             <version>11</version></span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="diff">         </dependency></span>

</pre></td>

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</table>

<br>

</li>

<li id="442292b8a7efeabbe4cc176709b833b1792140ec">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<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>

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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></td>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;">    --></span></span>

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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>2022.<span class="idiff left right deletion">3</span>.2<span class="nt" style="color: #000080;"></version></span></span>

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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="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>2022.<span class="idiff left right addition">4</span>.2<span class="nt" style="color: #000080;"></version></span></span>

</pre></td>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"></span>

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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">

13

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

14

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

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,6 +47,10 @@</td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="xml"></span>

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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">

48

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="xml">    <span class="nt" style="color: #000080;"><packaging></span>jar<span class="nt" style="color: #000080;"></packaging></span></span>

</pre></td>

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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">

49

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="xml"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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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="LC50" class="line" lang="xml">    <span class="nt" style="color: #000080;"><properties></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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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="LC51" class="line" lang="xml">        <span class="nt" style="color: #000080;"><project.build.sourceEncoding></span>UTF-8<span class="nt" style="color: #000080;"></project.build.sourceEncoding></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

52

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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="LC52" class="line" lang="xml">    <span class="nt" style="color: #000080;"></properties></span></span>

</pre></td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC198" class="line" lang="xml">      <span class="nt" style="color: #000080;"><tag></span>openchemlib-2022.<span class="idiff left right deletion">3</span>.2<span class="nt" style="color: #000080;"></tag></span></span>

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="xml">      <span class="nt" style="color: #000080;"><tag></span>openchemlib-2022.<span class="idiff left right addition">4</span>.2<span class="nt" style="color: #000080;"></tag></span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC205" class="line" lang="xml"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC206" class="line" lang="xml">    <span class="nt" style="color: #000080;"><distributionManagement></span></span>

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<br>

</li>

<li id="ba44c1f7e56c2598decf65ca012c856547ff2f0f">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#ba44c1f7e56c2598decf65ca012c856547ff2f0f"><strong>src/main/java/com/actelion/research/chem/SmilesParser.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">@@ -151,57 +151,51 @@ public class SmilesParser {</td>

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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 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="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC152" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</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 old" data-linenumber="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="java">           <span class="k" style="font-weight: 600;"><span class="idiff left deletion">while</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;">start</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">index1</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="155" style="width: 35px; color: rgba(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="154" style="width: 35px; color: rgba(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="LC155" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">i<span class="idiff left deletion">nt</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">ArrayUtils</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">indexOf</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff deletion">byte</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)</span></span><span class="sc" style="color: #d14;"><span class="idiff deletion">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">);</span></span></span>

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<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(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="154" style="width: 35px; color: rgba(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="LC156" 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;">i<span class="idiff left deletion">ndex</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">==</span></span><span class="idiff deletion"> </span><span class="sc" style="color: #d14;"><span class="idiff right deletion">'.'</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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC157" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactant</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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC158" 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;">reactant</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i<span class="idiff left right deletion">ndex</span></span><span class="o" style="font-weight: 600;">);</span></span>

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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="LC159" class="line" lang="java">                           <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</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>

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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="LC160" class="line" lang="java">                           <span class="n" style="color: #333;"><span class="idiff left deletion">start</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">;</span></span></span>

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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(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="154" style="width: 35px; color: rgba(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="LC161" class="line" lang="java">                           <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">continue</span></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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="java">           <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition"><</span></span><span class="n" style="color: #333;">index1</span><span class="o" style="font-weight: 600;"><span class="idiff addition">-</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">++</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC155" class="line" lang="java">                   <span class="k" style="font-weight: 600;">i<span class="idiff left addition">f</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">)</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">{</span></span></span>

</pre></td>

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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="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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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="LC156" class="line" lang="java">                   <span class="idiff left addition">      </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">start</span></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="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="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

157

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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="LC157" class="line" lang="java">                           <span class="idiff left right addition">        </span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactant</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></td>

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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="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

158

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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="LC158" class="line" lang="java">                           <span class="idiff left right addition">        </span><span class="n" style="color: #333;">parse</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;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</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>

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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="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">

159

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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="LC159" class="line" lang="java">                           <span class="idiff left right addition">        </span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</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>

</pre></td>

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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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

160

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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="LC160" class="line" lang="java">                           <span class="idiff left addition">      </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">}</span></span></span>

</pre></td>

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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="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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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="LC161" class="line" lang="java">                           <span class="n" style="color: #333;"><span class="idiff left addition">start</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">2</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" 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 old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

163

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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(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="LC163" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

164

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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(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="LC164" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactants</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></td>

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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

</td>

<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(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="LC165" 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;">reactants</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index1</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="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

166

</td>

<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(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="LC166" class="line" lang="java">                   <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactants</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="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

</td>

<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(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="LC167" class="line" lang="java">                   <span class="k" style="font-weight: 600;">break</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="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

</td>

<td class="new_line diff-line-num" 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">

163

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" 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="169" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactants</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></td>

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<td class="old_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" 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;">reactants</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index1</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="169" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

166

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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="LC166" class="line" lang="java">           <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactants</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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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<td class="new_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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC167" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num" 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">

170

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" 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;">index2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">index1</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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

171

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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="java">                   <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index1</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="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

172

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(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="LC172" class="line" lang="java">                   <span class="k" style="font-weight: 600;"><span class="idiff left deletion">while</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;">start</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">index2</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="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

173

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(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="LC173" class="line" lang="java">                           <span class="kt" style="color: #458; font-weight: 600;">i<span class="idiff left deletion">nt</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">ArrayUtils</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">indexOf</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff deletion">byte</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)</span></span><span class="sc" style="color: #d14;"><span class="idiff deletion">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">);</span></span></span>

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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(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="LC174" 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;">i<span class="idiff left deletion">ndex</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">==</span></span><span class="idiff deletion"> </span><span class="sc" style="color: #d14;"><span class="idiff right deletion">'.'</span></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 old" data-linenumber="175" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(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="LC175" class="line" lang="java">                                   <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalyst</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></td>

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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

176

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(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="LC176" 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;">catalyst</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i<span class="idiff left right deletion">ndex</span></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="177" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(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="LC177" class="line" lang="java">                                   <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</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="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

178

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(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="LC178" class="line" lang="java">                                   <span class="n" style="color: #333;"><span class="idiff left deletion">start</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">;</span></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

179

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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(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="LC179" class="line" lang="java">                                   <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">continue</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="180" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

170

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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="LC170" class="line" lang="java">                   <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition"><</span></span><span class="n" style="color: #333;">index2</span><span class="o" style="font-weight: 600;"><span class="idiff addition">-</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">++</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="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

171

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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="LC171" class="line" lang="java">                           <span class="k" style="font-weight: 600;">i<span class="idiff left addition">f</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">)</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">{</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

172

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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="LC172" class="line" lang="java">                           <span class="idiff left addition">      </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">start</span></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="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

173

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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="LC173" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalyst</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></td>

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<td class="old_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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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="LC174" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</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;">start</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 new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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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="LC175" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

176

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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="LC176" class="line" lang="java">                                   <span class="idiff left addition">      </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">}</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="177" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC177" class="line" lang="java">                                   <span class="n" style="color: #333;"><span class="idiff left addition">start</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">2</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="java">                                   <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(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="LC181" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="182" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(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="LC182" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalysts</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></td>

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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(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="LC183" 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;">catalysts</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index2</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="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

184

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<td class="new_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(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="LC184" class="line" lang="java">                           <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalysts</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="185" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(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="LC185" class="line" lang="java">                           <span class="k" style="font-weight: 600;">break</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="186" style="width: 35px; color: rgba(0,0,0,0.3); 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="179" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC179" 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="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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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC180" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalysts</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></td>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" 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;">catalysts</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index2</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="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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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

182

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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="LC182" class="line" lang="java">                   <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalysts</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="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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<td class="new_line diff-line-num" 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">

183

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" 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="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC184" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<td class="new_line diff-line-num" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC185" class="line" lang="java">           <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index2</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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

190

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(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="LC190" class="line" lang="java">           <span class="k" style="font-weight: 600;"><span class="idiff left deletion">while</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;">start</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">smiles</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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<td class="old_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

191

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(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="LC191" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">i<span class="idiff left deletion">nt</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">ArrayUtils</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">indexOf</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff deletion">byte</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)</span></span><span class="sc" style="color: #d14;"><span class="idiff deletion">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">);</span></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

192

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(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="LC192" 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;">i<span class="idiff left deletion">ndex</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">length</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">==</span></span><span class="idiff deletion"> </span><span class="sc" style="color: #d14;"><span class="idiff right deletion">'.'</span></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 old" data-linenumber="193" style="width: 35px; color: rgba(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="186" style="width: 35px; color: rgba(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="LC193" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">product</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></td>

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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(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="LC194" 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;">product</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;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i<span class="idiff left right deletion">ndex</span></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="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

195

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(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="LC195" class="line" lang="java">                           <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(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="186" style="width: 35px; color: rgba(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="LC196" class="line" lang="java">                           <span class="n" style="color: #333;"><span class="idiff left deletion">start</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">;</span></span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(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="LC197" class="line" lang="java">                           <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">continue</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="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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<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">

186

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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="LC186" class="line" lang="java">           <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition"><</span></span><span class="n" style="color: #333;">smiles</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 class="idiff addition">-</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">++</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="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">

</td>

<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">

187

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC187" class="line" lang="java">                   <span class="k" style="font-weight: 600;">i<span class="idiff left addition">f</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">)</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">{</span></span></span>

</pre></td>

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<td class="old_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">

</td>

<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">

188

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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="LC188" class="line" lang="java">                   <span class="idiff left addition">      </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">start</span></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" style="line-height: 1.6;">

<td class="old_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">

</td>

<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">

189

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC189" class="line" lang="java">                           <span class="idiff left right addition">        </span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">product</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></td>

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<td class="old_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">

</td>

<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">

190

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC190" class="line" lang="java">                           <span class="idiff left right addition">        </span><span class="n" style="color: #333;">parse</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;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</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>

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<td class="old_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">

</td>

<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">

191

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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="LC191" class="line" lang="java">                           <span class="idiff left right addition">        </span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</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>

</pre></td>

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<td class="old_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">

</td>

<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">

192

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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="LC192" class="line" lang="java">                           <span class="idiff left addition">      </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">}</span></span></span>

</pre></td>

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<td class="old_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">

</td>

<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">

193

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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="LC193" class="line" lang="java">                           <span class="n" style="color: #333;"><span class="idiff left addition">start</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">2</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="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<td class="new_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">

194

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC194" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

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<td class="new_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(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="LC199" class="line" lang="java"></span>

</pre></td>

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<td class="old_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">

200

</td>

<td class="new_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(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="LC200" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">products</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></td>

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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

</td>

<td class="new_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(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="LC201" 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;">products</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;">start</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;">length</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="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

202

</td>

<td class="new_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(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="LC202" class="line" lang="java">                   <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">products</span><span class="o" style="font-weight: 600;">);</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

203

</td>

<td class="new_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(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="LC203" class="line" lang="java">                   <span class="k" style="font-weight: 600;">break</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="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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<td class="new_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">

195

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(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="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

196

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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="LC196" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">products</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 new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); 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="197" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC197" 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;">products</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;">start</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;">length</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="java">           <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">products</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC200" class="line" lang="java">           <span class="k" style="font-weight: 600;">return</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" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3"><strong>src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,8 +31,8 @@ import com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian;</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="java"></span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" 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;">PheSAAlignmentOptimizer</span> <span class="o" style="font-weight: 600;">{</span></span>

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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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="java">    </span>

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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(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="LC34" 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="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion">10</span>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="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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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(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="LC35" 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="no" style="color: #008080;">PMI_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion">2</span>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="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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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC34" 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="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right addition">5</span>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="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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" 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="no" style="color: #008080;">PMI_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right addition">1</span>0</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" 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;">double</span> <span class="no" style="color: #008080;">EXIT_VECTOR_WEIGHT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10.0</span><span class="o" style="font-weight: 600;">;</span></span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" 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;">BEST_RESULT_SIZE</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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<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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="java">    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(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="75" style="width: 35px; color: rgba(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">@@ -75,7 +75,7 @@ public class PheSAAlignmentOptimizer {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" 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;">ShapeVolume</span> <span class="n" style="color: #333;">shapeVol</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fitVols</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="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC76" class="line" lang="java">                    <span class="n" style="color: #333;">shapeVol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">removeRings</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC77" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(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="78" style="width: 35px; color: rgba(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="LC78" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">singletonList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</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="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span> </span>

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<td class="old_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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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC78" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">singletonList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</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="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;"><span class="idiff left addition">,</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right addition">true</span></span><span class="o" style="font-weight: 600;">);</span> </span>

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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" 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;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" 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;">AlignmentResult</span> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">alignmentSolutions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">descendingSet</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>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,11 +87,17 @@ public class PheSAAlignmentOptimizer {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" 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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" 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="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">

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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="LC90" class="line" lang="java">    </span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">createAlignmentSolutions</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="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refVols</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="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitVols</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;">ppWeight</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;">optimize</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC91" class="line" lang="java">                    <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">tversky</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;">useDirectionality</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="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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" class="line" lang="java">                            <span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">useDirectionality</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="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" 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="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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<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">

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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="LC95" class="line" lang="java">    </span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">createAlignmentSolutions</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="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refVols</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="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitVols</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;">ppWeight</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;">optimize</span><span class="o" style="font-weight: 600;">,</span></span>

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="java">                    <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">tversky</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;">useDirectionality</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;">exhaustive</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="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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">triangleOpti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exhaustive</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="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">:</span> <span class="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pmiOpti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exhaustive</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="no" style="color: #008080;">PMI_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">:</span> <span class="no" style="color: #008080;">PMI_OPTIMIZATIONS</span><span class="o" style="font-weight: 600;">;</span></span>

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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="100" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC100" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentSolutions</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;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">>();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(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="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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC94" class="line" lang="java"></span>

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<td class="old_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">

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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">

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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 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;">ShapeVolume</span> <span class="n" style="color: #333;">molVol</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">refVols</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="96" style="width: 35px; color: rgba(0,0,0,0.3); 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" 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;">PPGaussian</span> <span class="n" style="color: #333;">ppg</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">molVol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPPGaussians</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="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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">ppg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPharmacophorePoint</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getFunctionalityIndex</span><span class="o" style="font-weight: 600;">()==</span><span class="nc" style="color: #458; font-weight: 600;">PharmacophoreCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">EXIT_VECTOR_ID</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="100" style="width: 35px; color: rgba(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">@@ -100,7 +106,7 @@ public class PheSAAlignmentOptimizer {</td>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC106" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" 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="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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="java"></span>

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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">

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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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC103" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">triangleSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getBestTriangleAlignments</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">triangleSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getBestTriangleAlignments</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;"><span class="idiff left addition">,</span></span><span class="n" style="color: #333;"><span class="idiff right addition">triangleOpti</span></span><span class="o" style="font-weight: 600;">);</span></span>

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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">

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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC110" class="line" lang="java">           <span class="n" style="color: #333;">alignmentSolutions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">triangleSolutions</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); 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="111" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="java">           <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pmiSolutions</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;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">>();</span></span>

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<td class="old_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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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" 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;">refVols</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="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="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="127" style="width: 35px; color: rgba(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 +127,7 @@ public class PheSAAlignmentOptimizer {</td>

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<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC127" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">//optimize best PMI alignments</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC128" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</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="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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC129" 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;">AlignmentResult</span> <span class="n" style="color: #333;">pmiAlignment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pmiSolutions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">descendingSet</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="124" style="width: 35px; color: rgba(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="130" style="width: 35px; color: rgba(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="LC124" 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;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="no" style="color: #008080;"><span class="idiff left right deletion">PMI_OPTIMIZATIONS</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="130" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC130" 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;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="n" style="color: #333;"><span class="idiff left right addition">pmiOpti</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" 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="old_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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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC132" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">refVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refVols</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;">pmiAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefConformerIndex</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC133" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">fitVol</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;">ShapeVolume</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitVols</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;">pmiAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConformerIndex</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="172" style="width: 35px; color: rgba(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">@@ -172,7 +178,7 @@ public class PheSAAlignmentOptimizer {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="java">   </span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC180" class="line" lang="java">   <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getBestTriangleAlignments</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="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refVols</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="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitVols</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;">ppWeight</span><span class="o" style="font-weight: 600;">,</span> </span>

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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(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="181" style="width: 35px; color: rgba(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="LC175" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">optimize</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;">tversky</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;">useDirectionality</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="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">optimize</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;">tversky</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;">useDirectionality</span><span class="o" style="font-weight: 600;"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">nrOptimizations</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="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC182" class="line" lang="java">           <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;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">triangleResults</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;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">>();</span></span>

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">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;">refVols</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="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" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC184" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">refVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refVols</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;">i</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="189" style="width: 35px; color: rgba(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">@@ -189,7 +195,7 @@ public class PheSAAlignmentOptimizer {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" 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;">alignments</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>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" 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;">AlignmentResult</span> <span class="nl">result:</span> <span class="n" style="color: #333;">triangleResults</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">descendingSet</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="192" style="width: 35px; color: rgba(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="198" style="width: 35px; color: rgba(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="LC192" 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;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="no" style="color: #008080;"><span class="idiff left right deletion">TRIANGLE_OPTIMIZATIONS</span></span><span class="o" style="font-weight: 600;">)</span></span>

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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="LC198" 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;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="n" style="color: #333;"><span class="idiff left right addition">nrOptimizations</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC199" 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="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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">refVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refVols</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;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefConformerIndex</span><span class="o" style="font-weight: 600;">());</span></span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">fitVol</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;">ShapeVolume</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitVols</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;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConformerIndex</span><span class="o" style="font-weight: 600;">()));</span></span>

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<br>

</li>

<li id="f678d35a688802dfd7e0cbfc6c14290a34944abc">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#f678d35a688802dfd7e0cbfc6c14290a34944abc"><strong>src/main/java/com/actelion/research/chem/docking/DockingUtils.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(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="111" style="width: 35px; color: rgba(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">@@ -111,7 +111,7 @@ public class DockingUtils {</td>

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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="java">           <span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">normalizeAmbiguousBonds</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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="java">           <span class="n" style="color: #333;">repairQuaternaryNitrogen</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="java">           <span class="n" style="color: #333;">repairCarboxylate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(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="114" style="width: 35px; color: rgba(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="LC114" class="line" lang="java">           <span class="n" style="color: #333;">a<span class="idiff left right deletion">ssignLikelyProtonationState</span>s</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_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">

</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">

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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="n" style="color: #333;">a<span class="idiff left right addition">ddImplicitHydrogen</span>s</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>

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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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<td class="new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC115" 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="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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<td class="new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="java">   </span>

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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">

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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">

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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 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;">repairQuaternaryNitrogen</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>

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<br>

</li>

<li id="f9cb63e80b748296a596a354aa485682819c7904">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#f9cb63e80b748296a596a354aa485682819c7904"><strong>src/main/java/com/actelion/research/chem/hyperspace/SimpleCombinatorialHit.java</strong></a>

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

1

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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="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.hyperspace</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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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="LC2" class="line" lang="java"></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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.io.Serializable</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="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;">SimpleCombinatorialHit</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Serializable</span> <span class="o" style="font-weight: 600;">{</span></span>

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<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

</td>

<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="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="mi" style="color: #099;">1970031554026082875L</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(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="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

</td>

<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="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SimpleSynthon</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">synthons</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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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="LC9" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SimpleCombinatorialHit</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;">rxnId</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">SimpleSynthon</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">synthons</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="0" style="width: 35px; color: rgba(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="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">

10

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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="LC10" 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;">rxnId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">;</span></span>

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<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="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">synthons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">synthons</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

12

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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="LC12" 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="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">

13

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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="LC13" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre></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">\ No newline at end of file</td>

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<br>

</li>

<li id="2d0bffca02cf955165915399414eb28114819627">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#2d0bffca02cf955165915399414eb28114819627"><strong>src/main/java/com/actelion/research/chem/hyperspace/SimpleSynthon.java</strong></a>

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

1

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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="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.hyperspace</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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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="LC2" class="line" lang="java"></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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.io.Serializable</span><span class="o" style="font-weight: 600;">;</span></span>

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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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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

</td>

<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="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;">SimpleSynthon</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Serializable</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(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

</td>

<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="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="mi" style="color: #099;">4625857679359578042L</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">idcode</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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

</td>

<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="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">synthonId</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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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="LC9" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

10

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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="LC10" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">synthonSet</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SimpleSynthon</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;">idcode</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;">id</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;">rxn_id</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;">synthonSet</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

12

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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="LC12" 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;">idcode</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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

13

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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="LC13" 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;">synthonId</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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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="LC14" 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;">rxnId</span>      <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rxn_id</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

15

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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="LC15" 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;">synthonSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">synthonSet</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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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="LC16" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC17" 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="18" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC18" class="line" lang="java"></span></pre></td>

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<br>

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<li id="57834476cf2f3a0474fee1ce1fbff3ada6845cfb">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#57834476cf2f3a0474fee1ce1fbff3ada6845cfb"><strong>src/main/java/com/actelion/research/chem/io/DWARFileParser.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" style="width: 35px; color: rgba(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="238" style="width: 35px; color: rgba(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">@@ -238,8 +238,13 @@ public class DWARFileParser extends CompoundFileParser implements DescriptorCons</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="java"></span>

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<td class="new_line diff-line-num" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC239" 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;">line</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;">"<"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">cColumnProperty</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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC240" 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;">property</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extractValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</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="s" style="color: #d14;">"\\t"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="241" style="width: 35px; color: rgba(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="241" style="width: 35px; color: rgba(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="LC241" class="line" lang="java">                    <span class="n" style="color: #333;">mColumnPropertyMap</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;">columnName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</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;">property</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="242" style="width: 35px; color: rgba(0,0,0,0.3); 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="241" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC241" 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;">property</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="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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<td class="old_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); 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="242" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC242" class="line" lang="java">                           <span class="n" style="color: #333;">mColumnPropertyMap</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;">columnName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</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="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">);</span></span>

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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 class="o" style="font-weight: 600;">}</span></span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC244" 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 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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC245" class="line" lang="java">                           <span class="n" style="color: #333;">mColumnPropertyMap</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;">columnName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</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;">property</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC246" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC248" class="line" lang="java"></span>

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<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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC249" class="line" lang="java">                <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readHeadOrTailLine</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC250" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="d0922db37ba2d4e1c4162276b7b27af29aeca835">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#d0922db37ba2d4e1c4162276b7b27af29aeca835"><strong>src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,8 +22,7 @@ import com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian;</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" 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;">EvaluableOverlap</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Evaluable</span>  <span class="o" style="font-weight: 600;">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="java"></span>

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<td class="old_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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<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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" 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;">PENALTY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">80</span><span class="o" style="font-weight: 600;">;</span> </span>

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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC26" class="line" lang="java">    </span>

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<td class="old_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="java"></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" 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;">ppWeight</span><span class="o" style="font-weight: 600;">;</span></span>

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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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="java"></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">PheSAAlignment</span> <span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +39,6 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" 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="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitAtGaussModCoords</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitPPDirectionalityMod</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="java">    </span>

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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="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">EvaluableOverlap</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PheSAAlignment</span> <span class="n" style="color: #333;">shapeAlign</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="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(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">@@ -59,7 +57,6 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="old_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" 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;">dv0PP</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;">fitPPGaussModCoords</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="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">];</span></span>

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" 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;">dv1PP</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;">fitPPGaussModCoords</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="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">];</span></span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" 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;">dv2PP</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;">fitPPGaussModCoords</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="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">];</span></span>

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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(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="LC62" 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;">fitPPDirectionalityMod</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;">Coordinates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getPPGaussians</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>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" 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;">results</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;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAtomicGaussians</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="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAtomicGaussians</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>

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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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="java">            <span class="n" style="color: #333;">cachedCoords</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;">Coordinates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAtomicGaussians</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>

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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="n" style="color: #333;">cachedCoordsPP</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;">Coordinates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getPPGaussians</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>

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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_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="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,7 +157,7 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="java">           </span>

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<td class="old_line diff-line-num" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="158" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC158" 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;">ppGrad</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;">grad</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>

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<td class="new_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC159" class="line" lang="java">           <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ppWeight</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="na" style="color: #008080;">getFGValueOverlapPP</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppGrad</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">refMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">(),</span></span>

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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(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="160" style="width: 35px; color: rgba(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="LC163" class="line" lang="java">                                           <span class="n" style="color: #333;">dv0PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv1PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv2PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;"><span class="idiff left deletion">,</span></span><span class="n" style="color: #333;"><span class="idiff right deletion">fitPPDirectionalityMod</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC160" class="line" lang="java">                                           <span class="n" style="color: #333;">dv0PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv1PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv2PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); 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="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC161" class="line" lang="java"></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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<td class="new_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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" 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;">grad</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="java">                   <span class="n" style="color: #333;">grad</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="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">atomGrad</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;">ppWeight</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ppGrad</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="diff-line-num unfold js-unfold old_line" data-linenumber="351" style="width: 35px; color: rgba(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="348" style="width: 35px; color: rgba(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">@@ -351,16 +348,12 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="java">   </span>

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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC349" class="line" lang="java">   <span class="o" style="font-weight: 600;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC350" class="line" lang="java">       </span>

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<td class="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(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="LC354" class="line" lang="java">      <span class="idiff left right deletion"> </span></span>

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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="LC355" 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;">getFGValueOverlapPP</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 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;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refMolGauss</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;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitMolGauss</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;">dRdv0</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;">dRdv1</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;">dRdv2</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitGaussModCoords</span><span class="o" style="font-weight: 600;"><span class="idiff left deletion">,</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[]</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff right deletion">fitPPDirectionalityMod</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 new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); 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="351" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC351" class="line" lang="java">      </span>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); 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="352" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC352" 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;">getFGValueOverlapPP</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 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;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refMolGauss</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;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitMolGauss</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;">dRdv0</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;">dRdv1</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;">dRdv2</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitGaussModCoords</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="356" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC353" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;">ExponentialMap</span> <span class="n" style="color: #333;">eMap</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;">ExponentialMap</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="mi" style="color: #099;">0</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="mi" style="color: #099;">1</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC354" class="line" lang="java">               </span>

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<td class="old_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); 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="355" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC355" 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;">rotMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">eMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toQuaternion</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getRotMatrix</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getArray</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC356" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="360" style="width: 35px; color: rgba(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="LC360" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(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="357" style="width: 35px; color: rgba(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="LC361" 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;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fitMolGauss</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="n" style="color: #333;">k</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="362" style="width: 35px; color: rgba(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="357" style="width: 35px; color: rgba(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="LC362" class="line" lang="java">                   <span class="n" style="color: #333;">fitPPDirectionalityMod</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitMolGauss</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;">k</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getRotatedDirectionality</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rotMatrix</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="363" style="width: 35px; color: rgba(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="357" style="width: 35px; color: rgba(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="LC363" 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="364" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC357" class="line" lang="java">               <span class="n" style="color: #333;">getTransformedCoordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitGaussModCoords</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC358" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC359" 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;">getEMapGradient</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dRdv0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">cachedCoordsPP</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="377" style="width: 35px; color: rgba(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="370" style="width: 35px; color: rgba(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">@@ -377,13 +370,9 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="new_line diff-line-num" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC370" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">refAt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refMolGauss</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;">i</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); 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="371" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC371" 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;">fitMolGauss</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="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++){</span></span>

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<td class="old_line diff-line-num" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC372" class="line" lang="java">                                   <span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">fitAt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitMolGauss</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;">j</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="380" style="width: 35px; color: rgba(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="373" style="width: 35px; color: rgba(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="LC380" class="line" lang="java">                                   <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">fitPPDirectionalityVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitPPDirectionalityMod</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>

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<td class="old_line diff-line-num" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC373" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">atomOverlap</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>

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<td class="old_line diff-line-num" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); 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="374" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC374" class="line" lang="java">                                   <span class="n" style="color: #333;">fitCenterModCoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitGaussModCoords</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>

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<td class="old_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); 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="375" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC375" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alphaSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="new_line diff-line-num old" data-linenumber="376" style="width: 35px; color: rgba(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="LC384" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</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>

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<td class="new_line diff-line-num old" data-linenumber="376" style="width: 35px; color: rgba(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="LC385" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</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>

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<td class="old_line diff-line-num old" data-linenumber="386" style="width: 35px; color: rgba(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="376" style="width: 35px; color: rgba(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="LC386" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">zi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</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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<td class="old_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); 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="376" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC376" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</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;">fitCenterModCoord</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>

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<td class="old_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); 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="377" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC377" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</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;">fitCenterModCoord</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>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); 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="378" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC378" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</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 class="n" style="color: #333;">fitCenterModCoord</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" style="width: 35px; color: rgba(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="385" style="width: 35px; color: rgba(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">@@ -396,7 +385,9 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="old_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); 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="385" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC385" class="line" lang="java">                                   <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWeight</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getHeight</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getHeight</span><span class="o" style="font-weight: 600;">()*</span><span class="nc" style="color: #458; font-weight: 600;">QuickMathCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">quickExp</span><span class="o" style="font-weight: 600;">(-(</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span> <span class="nc" style="color: #458; font-weight: 600;">Rij2</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">alphaSum</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="397" style="width: 35px; color: rgba(0,0,0,0.3); 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="386" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC386" class="line" lang="java">                                                   <span class="nc" style="color: #458; font-weight: 600;">QuickMathCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getPrefactor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refAt</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;">fitAt</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>

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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="387" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC387" 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;">atomOverlap</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 class="o" style="font-weight: 600;">{</span></span>

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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">

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<td class="new_line diff-line-num old" data-linenumber="388" style="width: 35px; color: rgba(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="LC399" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fitPPDirectionalityVector</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); 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="388" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC388" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInteractionSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); 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="389" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC389" 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;">sim</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>

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<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); 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="390" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC390" 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="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC391" class="line" lang="java">                                           <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); 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="392" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC392" class="line" lang="java">                                           <span class="n" style="color: #333;">totalOverlap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); 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="393" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC393" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</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="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="395" style="width: 35px; color: rgba(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">@@ -404,12 +395,12 @@ public class EvaluableOverlap implements Evaluable  {</td>

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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="395" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC395" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dv1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dRdv1</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv1</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv1</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dz</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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396

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC396" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dv2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dRdv2</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv2</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv2</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dz</span><span class="o" style="font-weight: 600;">;</span>   </span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" 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">

406

</td>

<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC397" class="line" lang="java"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

407

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC407" class="line" lang="java">                                   <span class="idiff left deletion">    </span><span class="n" style="color: #333;">grad</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="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv0</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_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">

408

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC408" class="line" lang="java">                                   <span class="idiff left deletion">    </span><span class="n" style="color: #333;">grad</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;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv1</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

409

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC409" class="line" lang="java">                                   <span class="idiff left deletion">    </span><span class="n" style="color: #333;">grad</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="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv2</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

410

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC410" class="line" lang="java">                                   <span class="idiff left deletion">    </span><span class="n" style="color: #333;">grad</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;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

411

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC411" class="line" lang="java">                                   <span class="idiff left deletion">    </span><span class="n" style="color: #333;">grad</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;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<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">

412

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC412" class="line" lang="java">                                   <span class="idiff left deletion">    </span><span class="n" style="color: #333;">grad</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="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dz</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(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="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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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="LC398" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">grad</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="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv0</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="413" style="width: 35px; color: rgba(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="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">

399

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC399" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">grad</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;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv1</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="413" style="width: 35px; color: rgba(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="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

400

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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="LC400" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">grad</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="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv2</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="413" style="width: 35px; color: rgba(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="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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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="LC401" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">grad</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;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dx</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="413" style="width: 35px; color: rgba(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="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

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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="LC402" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">grad</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;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dy</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="413" style="width: 35px; color: rgba(0,0,0,0.3); 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="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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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="LC403" class="line" lang="java">                                   <span class="idiff left right addition">        </span><span class="n" style="color: #333;">grad</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="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dz</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="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

413

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<td class="new_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">

404

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="java">                                                                   </span>

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<td class="old_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">

414

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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC405" 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="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">

415

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC406" 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="421" style="width: 35px; color: rgba(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">@@ -421,6 +412,7 @@ public class EvaluableOverlap implements Evaluable  {</td>

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<td class="old_line diff-line-num" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

421

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC412" 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="422" style="width: 35px; color: rgba(0,0,0,0.3); 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="413" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC413" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

423

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC414" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); 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="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

415

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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="LC415" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="java">   <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">EvaluableOverlap</span> <span class="nf" style="color: #900; font-weight: 600;">clone</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="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

425

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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">

417

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC417" 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;">EvaluableOverlap</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></td>

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<td class="old_line diff-line-num" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC418" class="line" lang="java">   <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="7e9910936f51c5883dc0e383abac0f0720181e30">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#7e9910936f51c5883dc0e383abac0f0720181e30"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/PPTriangle.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

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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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<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.chem.phesa.pharmacophore</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

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<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>

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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">

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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="LC3" 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></td>

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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">

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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="LC4" class="line" lang="java"></span>

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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">

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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">

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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;">com.actelion.research.calc.Matrix</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">com.actelion.research.chem.Coordinates</span><span class="o" style="font-weight: 600;">;</span></span>

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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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">com.actelion.research.chem.alignment3d.transformation.Rotation</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="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="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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,6 +36,7 @@ public class PPTriangle {</td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="java">            <span class="n" style="color: #333;">dirs</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="n" style="color: #333;">pp3</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getDirectionality</span><span class="o" style="font-weight: 600;">();</span></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="java">            <span class="n" style="color: #333;">canonizeOrder</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="java"></span>

</pre></td>

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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="39" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC39" class="line" lang="java"></span>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" 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="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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="java">    </span>

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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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" 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;">canonizeOrder</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(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">@@ -72,12 +71,12 @@ public class PPTriangle {</td>

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<td class="old_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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<td class="new_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC71" 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="73" style="width: 35px; color: rgba(0,0,0,0.3); 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" 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="74" style="width: 35px; color: rgba(0,0,0,0.3); 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="73" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC73" 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;">f</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;">f</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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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(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="74" style="width: 35px; color: rgba(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="LC75" 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;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left deletion">0</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></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;">//d1<span class="idiff right deletion">2<=d1</span>3</span></span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left addition">1</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></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;">//d1<span class="idiff right addition">3>d2</span>3</span></span>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="75" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC75" class="line" lang="java">                            <span class="n" style="color: #333;">swap</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>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC76" 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="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">

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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC77" 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="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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" 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;">f</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;">f</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>

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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(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="LC80" 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;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left deletion">1</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></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;">//d12<span class="idiff right deletion"><=</span>d13</span></span>

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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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" 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;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left addition">0</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></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;">//d12<span class="idiff right addition">></span>d13</span></span>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="java">                            <span class="n" style="color: #333;">swap</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;">2</span><span class="o" style="font-weight: 600;">);</span></span>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" 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="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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,31 +84,29 @@ public class PPTriangle {</td>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="java">    </span>

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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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" 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;">swap</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="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="o" style="font-weight: 600;">{</span></span>

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<td class="old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</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 old" data-linenumber="88" style="width: 35px; color: rgba(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="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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">diold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</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>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">dirold</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;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dirs</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>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="java">            <span class="n" style="color: #333;">dirs</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="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dirs</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>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="java">            <span class="n" style="color: #333;">f</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;">f</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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

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<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC92" class="line" lang="java">            <span class="n" style="color: #333;">d</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;">d</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>

</pre></td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java">            <span class="n" style="color: #333;">f</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 class="n" style="color: #333;">fiold</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="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

94

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<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC94" class="line" lang="java">            <span class="n" style="color: #333;">d</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 class="n" style="color: #333;">diold</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="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">

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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC91" class="line" lang="java">            <span class="n" style="color: #333;">dirs</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 class="n" style="color: #333;">dirold</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="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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="java">            <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">ciold</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;">Coordinates</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;">i</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="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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" 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;">i</span><span class="o" style="font-weight: 600;">]</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;">Coordinates</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;">j</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="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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" 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;">j</span><span class="o" style="font-weight: 600;">]</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;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ciold</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="96" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">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;">j</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 old" data-linenumber="97" style="width: 35px; color: rgba(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="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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC97" class="line" lang="java">                    <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion">Coordinates</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">])</span>;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(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="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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC98" class="line" lang="java">                    <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]);</span></span><span class="idiff right deletion"> </span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

99

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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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC99" class="line" lang="java">                    <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">);</span></span><span class="idiff right deletion"> </span></span>

</pre></td>

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<td class="old_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">

</td>

<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">

96

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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="LC96" class="line" lang="java">                    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left addition">double</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">]</span>;</span></span>

</pre></td>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="java">                    <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">];</span></span></span>

</pre></td>

</tr>

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

<td class="old_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">

</td>

<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">

98

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="java">                    <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">;</span></span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

</td>

<td class="new_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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<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

</td>

<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(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="LC101" class="line" lang="java">           </span>

</pre></td>

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

<td class="old_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

</td>

<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" 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;">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;">j</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>

</pre></td>

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

<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

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC103" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion">Coordinates</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">])</span>;</span></span>

</pre></td>

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

<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

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC104" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]);</span></span><span class="idiff right deletion"> </span></span>

</pre></td>

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

<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

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC105" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">);</span></span><span class="idiff right deletion"> </span></span>

</pre></td>

</tr>

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

<td class="old_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">

</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">

101

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left addition">double</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">]</span>;</span></span>

</pre></td>

</tr>

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

<td class="old_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">

</td>

<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">

102

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC102" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">];</span></span></span>

</pre></td>

</tr>

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

<td class="old_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">

</td>

<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">

103

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC103" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">;</span></span></span>

</pre></td>

</tr>

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

<td class="old_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">

106

</td>

<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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

107

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC107" class="line" lang="java">           </span>

</pre></td>

</tr>

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

<td class="old_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

</td>

<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC105" 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;">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;">j</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>

</pre></td>

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

<td class="old_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">

109

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC109" class="line" lang="java">                   <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion">Coordinates</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">])</span>;</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC110" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]);</span></span><span class="idiff right deletion"> </span></span>

</pre></td>

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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">

111

</td>

<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC111" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">);</span></span><span class="idiff right deletion"> </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

112

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<td class="new_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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC112" 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="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">

</td>

<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">

106

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC106" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left addition">double</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">]</span>;</span></span>

</pre></td>

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<td class="old_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">

</td>

<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">

107

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">];</span></span></span>

</pre></td>

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<td class="old_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">

</td>

<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">

108

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="java">                   <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">;</span></span></span>

</pre></td>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span><span class="idiff left right addition">      </span></span>

</pre></td>

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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">

113

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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="java">                   </span>

</pre></td>

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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">

114

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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="java"></span>

</pre></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">

115

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<td class="new_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">

112

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="java">   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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<br>

</li>

<li id="1a2948d1808e5bf4b5ae448818a4c444d9b4870a">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#1a2948d1808e5bf4b5ae448818a4c444d9b4870a"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.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="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +162,7 @@ public class PharmacophoreCalculator {</td>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" 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;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isDonorHydrogen</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</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="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">

163

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<td class="new_line diff-line-num" 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">

163

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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;">mol</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;">h</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="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<td class="new_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC164" class="line" lang="java">                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dh</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;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</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="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(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="LC165" 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="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</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="n" style="color: #333;">mol</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;">dh</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;">mol</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;">dh</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="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion">//charge is not positive -> no acceptor</span></span></span>

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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">

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<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">

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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="LC165" 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="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</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="n" style="color: #333;">mol</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;">dh</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;">mol</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;">dh</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="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="166" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC166" 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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<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">

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<td class="new_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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC167" 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="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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" class="line" lang="java">                   <span class="k" style="font-weight: 600;">else</span> <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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</li>

<li id="86999a714d04156d77451e9ca14c33aff8a98a76">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#86999a714d04156d77451e9ca14c33aff8a98a76"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/PPGaussian.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +86,7 @@ public class PPGaussian extends Gaussian3D {</td>

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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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" 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="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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java"></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" 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;">getSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">ppGauss2</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">directionality</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="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">

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<td class="new_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">

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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="LC89" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left deletion">getInteractionSimilarity</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ppGauss2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">)</span>;</span></span>

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<td class="old_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">

</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">

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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="LC89" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;"><span class="idiff left right addition">1.0</span></span><span class="o" style="font-weight: 600;">;</span></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">vectorSim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getVectorSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppGauss2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">directionality</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); 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="91" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC91" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">similarity</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;">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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">vectorSim</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="n" style="color: #333;">ppSimilarity</span><span class="o" style="font-weight: 600;">)/</span><span class="mf" style="color: #099;">3.0</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

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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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">similarity</span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

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<li id="3dbbe7b950b7f9e3cf1fa45df59255c90fc56046">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#3dbbe7b950b7f9e3cf1fa45df59255c90fc56046"><strong>src/main/java/com/actelion/research/chem/phesaflex/EvaluableFlexibleOverlap.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">@@ -382,13 +382,13 @@ public class EvaluableFlexibleOverlap implements Evaluable  {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC382" class="line" lang="java">                                   </span>

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<td class="old_line diff-line-num" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); 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="383" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC383" 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;">atomOverlap</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 class="o" style="font-weight: 600;">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC384" class="line" lang="java">                                           <span class="n" style="color: #333;">totalOverlap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="385" style="width: 35px; color: rgba(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="385" style="width: 35px; color: rgba(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="LC385" class="line" lang="java">                                           <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">*-</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="old_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); 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="385" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC385" class="line" lang="java">                                           <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">*-</span><span class="mi" style="color: #099;"><span class="idiff left addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">*</span></span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="old_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); 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="386" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC386" 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="387" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC387" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); 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="388" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC388" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(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="389" style="width: 35px; color: rgba(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="LC389" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(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="389" style="width: 35px; color: rgba(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="LC390" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(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="389" style="width: 35px; color: rgba(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="LC391" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); 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="389" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC389" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); 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="390" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC390" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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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="LC391" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC392" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC393" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC394" class="line" lang="java">           </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="420" style="width: 35px; color: rgba(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="420" style="width: 35px; color: rgba(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">@@ -420,9 +420,9 @@ public class EvaluableFlexibleOverlap implements Evaluable  {</td>

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<td class="new_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC420" class="line" lang="java">                                   <span class="o" style="font-weight: 600;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC421" class="line" lang="java"></span>

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<td class="new_line diff-line-num" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC422" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(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="423" style="width: 35px; color: rgba(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="LC423" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(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="LC424" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

425

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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(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="LC425" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC423" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC424" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

425

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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="LC425" class="line" lang="java">                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC426" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC427" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC428" class="line" lang="java">           </span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -473,9 +473,9 @@ public class EvaluableFlexibleOverlap implements Evaluable  {</td>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC473" class="line" lang="java">                                           <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC474" class="line" lang="java">                                           <span class="n" style="color: #333;">totalOverlap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC475" class="line" lang="java">                                           <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</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="n" style="color: #333;">refPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>

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476

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<td class="new_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(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="LC476" class="line" lang="java">                                           <span class="n" style="color: #333;">grad</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;">a</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;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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477

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<td class="new_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(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="LC477" class="line" lang="java">                                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

478

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<td class="new_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(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="LC478" class="line" lang="java">                                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<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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<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="n" style="color: #333;">grad</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;">a</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;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<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">

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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="LC477" class="line" lang="java">                                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC478" class="line" lang="java">                                           <span class="n" style="color: #333;">grad</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;">a</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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC479" class="line" lang="java">                                           <span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPharmacophorePoint</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getDirectionalityDerivativeCartesian</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="n" style="color: #333;">coords</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPharmacophorePoint</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getDirectionality</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sim</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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC480" class="line" lang="java"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC481" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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</li>

<li id="88f7248516cf1351766ec9d506223745b62982c0">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#88f7248516cf1351766ec9d506223745b62982c0"><strong>src/main/java/com/actelion/research/chem/reaction/Reactor.java</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="633" style="width: 35px; color: rgba(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">@@ -633,36 +633,6 @@ public class Reactor {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC633" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC634" 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="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

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<td class="new_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC635" class="line" lang="java"></span>

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<td class="old_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

636

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC636" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>

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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

637

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC637" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">esrGroupsChanged</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="old_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

638

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC638" 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;">genericProduct</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;">j</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="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

639

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC639" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">// copy atom parities of unmapped generic product atoms and potentially convert them according to new neighbour order</span></span>

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640

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="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;">genericProduct</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;">j</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="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

641

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC641" 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="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</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;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

642

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC642" class="line" lang="java">                           <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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;">parity</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="old_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">

643

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC643" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

644

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC644" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>

</pre></td>

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<td class="old_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">

645

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC645" 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;">mIsReactionCenter</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProductNo</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>

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<td class="old_line diff-line-num old" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

646

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC646" 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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</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 class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRxnParityHint</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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(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="636" style="width: 35px; color: rgba(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="LC647" class="line" lang="java">                            <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">useConfigurationFromGenericReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</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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<td class="old_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

648

</td>

<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC648" 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="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</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;">newAtomNo</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="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

649

</td>

<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC649" class="line" lang="java">                                   <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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;">parity</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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<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="636" style="width: 35px; color: rgba(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="LC650" 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;">parity</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>

</pre></td>

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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="636" style="width: 35px; color: rgba(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="LC651" class="line" lang="java">                                    <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">parity</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;">cAtomParity2</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 old" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

652

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC652" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

653

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC653" class="line" lang="java">                                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRGroup</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>

</pre></td>

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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">

654

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC654" 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;">esrType</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;">cESRTypeAnd</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="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">

655

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC655" class="line" lang="java">                                                   <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountAND</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="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

656

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC656" 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;">esrType</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;">cESRTypeOr</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="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

657

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC657" class="line" lang="java">                                                   <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountOR</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="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

658

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC658" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

659

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC659" class="line" lang="java">                                           <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomESR</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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;">esrType</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">esrGroup</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="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

660

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC660" class="line" lang="java">                                           <span class="n" style="color: #333;">esrGroupsChanged</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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<td class="old_line diff-line-num old" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

661

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC661" 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 old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

662

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC662" 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 old" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

663

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC663" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

664

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC664" 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 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">

665

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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(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="LC665" class="line" lang="java"></span>

</pre></td>

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<td class="old_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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<td class="new_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC636" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// copy all bonds of generic product, except for bridge bonds</span></span>

</pre></td>

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<td class="old_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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<td class="new_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

637

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC637" 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;">gpBond</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;">gpBond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericProduct</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;">gpBond</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="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">

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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC638" 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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isBondBridge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gpBond</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="722" style="width: 35px; color: rgba(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="692" style="width: 35px; color: rgba(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">@@ -722,11 +692,51 @@ public class Reactor {</td>

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722

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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC692" 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="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

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<td class="new_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC693" 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="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

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<td class="new_line diff-line-num" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC694" class="line" lang="java"></span>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

695

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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="LC695" class="line" lang="java">           <span class="n" style="color: #333;">product</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;">cHelperNeighbours</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="725" style="width: 35px; color: rgba(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="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

696

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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="LC696" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="697" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC697" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

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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="LC698" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">esrGroupsChanged</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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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

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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="LC699" 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;">genericProduct</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;">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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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

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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="LC700" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">// copy atom parities of unmapped generic product atoms and potentially convert them according to new neighbour order</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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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="LC701" 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;">genericProduct</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;">j</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 new" data-linenumber="725" style="width: 35px; color: rgba(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="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">

702

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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="LC702" 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="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</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;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

703

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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="LC703" class="line" lang="java">                           <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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;">parity</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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</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">

704

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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="LC704" 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="725" style="width: 35px; color: rgba(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="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

705

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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="LC705" class="line" lang="java">                   <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

706

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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="LC706" 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;">mIsReactionCenter</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProductNo</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>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

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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="LC707" class="line" lang="java">                             <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">copyConfigurationFromGenericProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</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;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</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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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

708

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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="LC708" 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="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</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;">newAtomNo</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="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

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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="LC709" class="line" lang="java">                           <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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;">parity</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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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

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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="LC710" 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;">parity</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

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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="LC711" class="line" lang="java">                                           <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">parity</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;">cAtomParity2</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="new_line diff-line-num new" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

712

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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="LC712" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</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>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

713

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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="LC713" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRGroup</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="714" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC714" 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;">esrType</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;">cESRTypeAnd</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="725" style="width: 35px; color: rgba(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="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

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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="LC715" class="line" lang="java">                                           <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountAND</span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

716

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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="LC716" 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;">esrType</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;">cESRTypeOr</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="725" style="width: 35px; color: rgba(0,0,0,0.3); 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="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

717

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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="LC717" class="line" lang="java">                                           <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountOR</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="725" style="width: 35px; color: rgba(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="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC718" class="line" lang="java"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

719

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC719" class="line" lang="java">                                   <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomESR</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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;">esrType</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">esrGroup</span><span class="o" style="font-weight: 600;">);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

720

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC720" class="line" lang="java">                                   <span class="n" style="color: #333;">esrGroupsChanged</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 new" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC721" class="line" lang="java">                                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

722

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC722" 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="725" style="width: 35px; color: rgba(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="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC723" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(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="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC724" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

<td class="new_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC725" 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;">esrGroupsChanged</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="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC726" class="line" lang="java">                   <span class="n" style="color: #333;">esrGroupCountAND</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="na" style="color: #008080;">renumberESRGroups</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;">cESRTypeAnd</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="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

</td>

<td class="new_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC727" class="line" lang="java">                   <span class="n" style="color: #333;">esrGroupCountOR</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="na" style="color: #008080;">renumberESRGroups</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;">cESRTypeOr</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="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

<td class="new_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC728" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

</td>

<td class="new_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC729" class="line" lang="java"></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

730

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC730" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// copy pseudo parities of generic product if there are no parity hints</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

731

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC731" 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;">pseudoParityHandled</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;">genericProduct</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></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

732

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC732" 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;">genericProduct</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;">j</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

733

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC733" 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;">mIsReactionCenter</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProductNo</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>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

734

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC734" 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;">pseudoParityHandled</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>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC735" class="line" lang="java">                    <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAtomParityPseudo</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

736

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC736" 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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</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 class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRxnParityHint</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

737

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC737" class="line" lang="java">                    <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">genericProduct</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;">j</span><span class="o" style="font-weight: 600;">)</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="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(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="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

738

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC738" class="line" lang="java">                           <span class="n" style="color: #333;">copyPseudoParitiesFromGenericProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</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;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pseudoParityHandled</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="730" style="width: 35px; color: rgba(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="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

739

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC739" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

730

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<td class="new_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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC740" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// delete all fragments from product which are not connected to generic product</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

731

</td>

<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC741" 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;">includeAtom</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;">product</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></td>

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<td class="old_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

</td>

<td class="new_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC742" 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;">newAtomNo</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>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="798" style="width: 35px; color: rgba(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">@@ -788,22 +798,101 @@ public class Reactor {</td>

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<td class="old_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

</td>

<td class="new_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC798" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//             return false;</span></span>

</pre></td>

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<td class="old_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

</td>

<td class="new_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC799" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">//             }</span></span>

</pre></td>

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<td class="old_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="new_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC800" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

791

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC791" 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;">useConfigurationFromGenericReaction</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;">genericProduct</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;">productAtom</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 old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

792

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC792" 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="n" style="color: #333;">genericProduct</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;">productAtom</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="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC793" 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></td>

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<td class="old_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">

794

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC794" 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;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactants</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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<td class="old_line diff-line-num old" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

795

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC795" class="line" lang="java">                           <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactant</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>

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<td class="old_line diff-line-num old" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

796

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC796" 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;">reactantAtom</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;">reactantAtom</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="na" style="color: #008080;">getAtoms</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="o" style="font-weight: 600;">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

797

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC797" 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;">reactant</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;">reactantAtom</span><span class="o" style="font-weight: 600;">)</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="o" style="font-weight: 600;">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

798

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC798" class="line" lang="java">                                           <span class="c1" style="color: #998; font-style: italic;">// If the reactant atom is explicitly set to match the stereo center,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

799

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC799" class="line" lang="java">                                           <span class="c1" style="color: #998; font-style: italic;">// we assume that the product also contains a well specified stereo center to be copied.</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

800

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC800" 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;">reactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</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="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;">cAtomQFMatchStereo</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></td>

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<td class="old_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

801

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC801" 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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

802

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC802" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

803

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC803" class="line" lang="java">                                           <span class="c1" style="color: #998; font-style: italic;">// If we have an explicit change of the ESR type, we also assume that this is intentional</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

804

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC804" class="line" lang="java">                                           <span class="c1" style="color: #998; font-style: italic;">// and copy the stereo configuration from the product.</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

805

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC805" 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;">reactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</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="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

806

</td>

<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(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="LC806" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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;">copyPseudoParitiesFromGenericProduct</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;">genericProduct</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;">firstPseudoParityAtom</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;">product</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;">newAtomNo</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;">pseudoParityHandled</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="807" style="width: 35px; color: rgba(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 class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">relatedAtom</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;">genericProduct</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

803

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC803" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">relatedAtomCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRelatedPseudoParityAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">firstPseudoParityAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre></td>

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</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC804" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC805" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">matchingAbsParityFound</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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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC806" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">invertedAbsParityFound</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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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC807" 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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]></span> <span class="n" style="color: #333;">pseudoParityList</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC808" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC809" 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;">relatedAtomCount</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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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

810

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</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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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

811

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC811" class="line" lang="java">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</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;">newAtomNo</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="807" style="width: 35px; color: rgba(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="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

812

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC812" 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;">pseudoParity</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

813

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC813" class="line" lang="java">                            <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pseudoParity</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;">cAtomParity2</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="807" style="width: 35px; color: rgba(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="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

814

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC814" class="line" lang="java">                                   <span class="c1" style="color: #998; font-style: italic;">// Real product parities may not be pseudo if the real reactant has additional features.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

815

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC815" class="line" lang="java">                                   <span class="c1" style="color: #998; font-style: italic;">// These are given and cannot be inverted because of pseudo parity requirements in the generic product.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

816

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC816" class="line" lang="java">                                   <span class="c1" style="color: #998; font-style: italic;">// We check for compatibility and only apply relative pseudo parities, if possible.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

817

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC817" 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="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">relatedAtom</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>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

818

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC818" 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;">parity</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 class="n" style="color: #333;">parity</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;">cAtomParity2</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="807" style="width: 35px; color: rgba(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="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

819

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC819" 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;">pseudoParity</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">)</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

820

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC820" class="line" lang="java">                                                   <span class="n" style="color: #333;">matchingAbsParityFound</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>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

821

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC821" class="line" lang="java">                                           <span class="k" style="font-weight: 600;">else</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

822

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC822" class="line" lang="java">                                                   <span class="n" style="color: #333;">invertedAbsParityFound</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>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

823

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC823" class="line" lang="java">                                           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

824

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC824" class="line" lang="java">                                   <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="807" style="width: 35px; color: rgba(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="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

825

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC825" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

826

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC826" class="line" lang="java">                           <span class="c1" style="color: #998; font-style: italic;">// We collect a list of all pseudo parity atoms with their translated pseudo parities.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

827

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC827" class="line" lang="java">                           <span class="c1" style="color: #998; font-style: italic;">// If where we have existing real parities on the same atoms and if these</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

828

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC828" class="line" lang="java">                           <span class="c1" style="color: #998; font-style: italic;">// - either match the required pseudo parities, then we can add pseudo parities to atoms without a real parity</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

829

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC829" class="line" lang="java">                           <span class="c1" style="color: #998; font-style: italic;">// - or match the all inverted pseudo parities, then we can add inverted pseudo parities to atoms without a real parity</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC830" 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;">ps</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;">2</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="807" style="width: 35px; color: rgba(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="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

831

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC831" class="line" lang="java">                           <span class="n" style="color: #333;">ps</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="n" style="color: #333;">relatedAtom</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>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

832

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC832" class="line" lang="java">                           <span class="n" style="color: #333;">ps</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;">pseudoParity</span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

833

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC833" class="line" lang="java">                           <span class="n" style="color: #333;">pseudoParityList</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;">ps</span><span class="o" style="font-weight: 600;">);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

834

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC834" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

835

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC835" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

836

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC836" class="line" lang="java"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

837

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC837" 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;">pseudoParityList</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="n" style="color: #333;">matchingAbsParityFound</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">invertedAbsParityFound</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="807" style="width: 35px; color: rgba(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="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

838

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pseudoParityList</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="807" style="width: 35px; color: rgba(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="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

839

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC839" class="line" lang="java">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pseudoParity</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 new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

840

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC840" 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;">ps</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 class="n" style="color: #333;">ps</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;">cAtomParity2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">invertedAbsParityFound</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="807" style="width: 35px; color: rgba(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="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

841

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC841" class="line" lang="java">                                   <span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ps</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 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;">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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

842

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC842" class="line" lang="java">                           <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pseudoParity</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;">ps</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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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

843

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC843" 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="807" style="width: 35px; color: rgba(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="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

844

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC844" 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="807" style="width: 35px; color: rgba(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="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

845

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC845" 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="807" style="width: 35px; color: rgba(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="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

846

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC846" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="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">

847

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC847" 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;">findRelatedPseudoParityAtoms</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;">genericProduct</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;">firstAtom</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;">relatedAtom</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="807" style="width: 35px; color: rgba(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="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">

848

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC848" 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;">isRelated</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;">genericProduct</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

849

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC849" class="line" lang="java">           <span class="n" style="color: #333;">relatedAtom</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="n" style="color: #333;">firstAtom</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="807" style="width: 35px; color: rgba(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="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

850

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC850" class="line" lang="java">           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">relatedAtoms</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 new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC851" class="line" lang="java">           <span class="n" style="color: #333;">isRelated</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">firstAtom</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC852" 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;">current</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;">current</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">relatedAtoms</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="o" style="font-weight: 600;">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<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="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;">genericProduct</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;">relatedAtom</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

854

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC854" class="line" lang="java">                           <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connBond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</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;">relatedAtom</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC855" 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;">genericProduct</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;">connBond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">genericProduct</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;">connBond</span><span class="o" style="font-weight: 600;">)</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="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isBINAPChiralityBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connBond</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="807" style="width: 35px; color: rgba(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="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

856

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC856" class="line" lang="java">                                   <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</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;">relatedAtom</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

857

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC857" 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;">isRelated</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</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="807" style="width: 35px; color: rgba(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="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">relatedAtoms</span><span class="o" style="font-weight: 600;">++]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<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="n" style="color: #333;">isRelated</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC860" class="line" lang="java">                                           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

861

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC861" class="line" lang="java">                                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

862

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC862" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

863

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC863" class="line" lang="java">                   <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC864" class="line" lang="java">           <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">relatedAtoms</span><span class="o" style="font-weight: 600;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC865" class="line" lang="java">           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

866

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC866" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

867

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC867" 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;">copyConfigurationFromGenericProduct</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;">genericProduct</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;">genericProductAtom</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;">product</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;">productAtom</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="807" style="width: 35px; color: rgba(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="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

868

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC868" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// If we have a hint on the generic product atom, then we have already taken the generic reactant atom parity.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

869

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC869" class="line" lang="java">           <span class="c1" style="color: #998; font-style: italic;">// Otherwise, if we have a stereo center on the generic product atom, we may consider copying that...</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

870

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC870" 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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</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;">cAtomParityNone</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

871

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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="LC871" 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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</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="807" style="width: 35px; color: rgba(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="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

872

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC872" 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;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</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;">cAtomQFRxnParityHint</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

873

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC873" 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="n" style="color: #333;">genericProduct</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;">genericProductAtom</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="807" style="width: 35px; color: rgba(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="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

874

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC874" 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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

875

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC875" 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;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactants</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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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

876

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC876" class="line" lang="java">                                   <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">genericReactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactant</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>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

877

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC877" 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;">reactantAtom</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;">reactantAtom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericReactant</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;">reactantAtom</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="807" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC878" 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;">genericReactant</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;">reactantAtom</span><span class="o" style="font-weight: 600;">)</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="o" style="font-weight: 600;">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC879" class="line" lang="java">                                                   <span class="c1" style="color: #998; font-style: italic;">// If the generic reactant atom is not even a pseudo stereo center,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

880

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC880" class="line" lang="java">                                                   <span class="c1" style="color: #998; font-style: italic;">// then we assume that any product configuration is intentional and correct</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

881

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC881" 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;">genericProduct</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;">genericProductAtom</span><span class="o" style="font-weight: 600;">)</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="na" style="color: #008080;">getConnAtoms</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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

882

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC882" 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>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

883

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC883" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

884

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC884" class="line" lang="java">                                                   <span class="c1" style="color: #998; font-style: italic;">// If the reactant atom is explicitly set to match the stereo center,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

885

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC885" class="line" lang="java">                                                   <span class="c1" style="color: #998; font-style: italic;">// we assume that the product also contains a well specified stereo center to be copied.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

886

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC886" 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;">genericReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</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="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;">cAtomQFMatchStereo</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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

887

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC887" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

888

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC888" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

889

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC889" class="line" lang="java">                                                   <span class="c1" style="color: #998; font-style: italic;">// If we have an explicit change of the ESR type, we also assume that this is intentional</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

890

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC890" class="line" lang="java">                                                   <span class="c1" style="color: #998; font-style: italic;">// and copy the stereo configuration from the product.</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

891

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC891" 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;">genericReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</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="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</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="807" style="width: 35px; color: rgba(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="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

892

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC892" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

893

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC893" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

894

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC894" 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></td>

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<td class="old_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(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="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

895

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC895" 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="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

</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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC896" 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="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

</td>

<td class="new_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC897" 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="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

</td>

<td class="new_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC898" class="line" lang="java">                           <span class="o" style="font-weight: 600;">}</span></span>

</pre></td>

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<br>

</li>

<li id="b23ac1794ae5ae3ca39c5fd7604dd429cdcd2393">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#b23ac1794ae5ae3ca39c5fd7604dd429cdcd2393"><strong>src/main/java/com/actelion/research/gui/editor/AtomQueryFeatureDialogBuilder.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(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">@@ -169,7 +169,7 @@ public class AtomQueryFeatureDialogBuilder implements DialogEventConsumer {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" 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;">includeReactionHints</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="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">

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="java">                   <span class="n" style="color: #333;">mDialog</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;">mDialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">createLabel</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Stereo center hint for product:"</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;">27</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;">27</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); 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="171" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC171" class="line" lang="java">                   <span class="n" style="color: #333;">mChoiceReactionParityHint</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mDialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">createComboBox</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(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="172" style="width: 35px; color: rgba(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="LC172" class="line" lang="java">                   <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion">Make unknown in</span> product"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); 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="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC172" class="line" lang="java">                   <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right addition">Copy from generic</span> product"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); 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="173" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC173" class="line" lang="java">                   <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Keep reactant configuration"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); 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="174" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC174" class="line" lang="java">                   <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Invert reactant configuration"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="java">                   <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Racemise configuration"</span><span class="o" style="font-weight: 600;">);</span></span>

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</li>

<li id="98ac8c26d9087ed4dfec10db567462ed5ca7be22">

<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3fd5daea1a2beecffbbf04c7bab1d290d5ff9dbb...c520e82c5c7fd14332840598114d7bea96ea5ebb#98ac8c26d9087ed4dfec10db567462ed5ca7be22"><strong>src/main/java/com/actelion/research/util/BrowserControl.java</strong></a>

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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">

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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.util</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

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<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>

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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">

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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="LC3" 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>

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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">

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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>

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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="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="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.net.URI</span><span class="o" style="font-weight: 600;">;</span></span>

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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="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.net.URISyntaxException</span><span class="o" style="font-weight: 600;">;</span></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="java"></span>

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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">

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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">

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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="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;">BrowserControl</span> <span class="o" style="font-weight: 600;">{</span></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" 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">@@ -21,7 +24,19 @@ public class BrowserControl {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="java">                            <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <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;">Platform</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isMacintosh</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="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="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 class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">OSX_PATH</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 class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">;</span></span>

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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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="java">                                    <span class="nc" style="color: #458; font-weight: 600;">Runtime</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRuntime</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">exec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">);</span></span>

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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="27" style="width: 35px; color: rgba(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="LC24" class="line" lang="java">                            <span class="o" style="font-weight: 600;">}</span> <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 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="27" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC27" 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="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="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="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="nc" style="color: #458; font-weight: 600;">Desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDesktopSupported</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="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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="java">                                    <span class="nc" style="color: #458; font-weight: 600;">Desktop</span> <span class="n" style="color: #333;">desktop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getDesktop</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="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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<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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isSupported</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Action</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">BROWSE</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="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="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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" 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="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="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">

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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="LC32" class="line" lang="java">                                                    <span class="n" style="color: #333;">desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">browse</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="no" style="color: #008080;">URI</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">));</span></span>

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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="33" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC33" 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="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="34" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC34" 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;">URISyntaxException</span> <span class="n" style="color: #333;">use</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="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">

</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">

35

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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="LC35" class="line" lang="java">                                                    <span class="n" style="color: #333;">use</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</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="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="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">

36

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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="LC36" 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="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="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">

37

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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="LC37" 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="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="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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" 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="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="39" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC39" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*                              else {</span></span>

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                        // Under Unix, Netscape has to be running for the "-remote"</span></span>

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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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                        // command to work.  So, we try sending the command and</span></span>

</pre></td>

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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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                        // check for an exit value.  If the exit command is 0,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +59,7 @@ public class BrowserControl {</td>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                                                + "'");</span></span>

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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                                System.err.println("Caught: " + x);</span></span>

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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">

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                        }</span></span>

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<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">

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<td class="new_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(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="o" style="font-weight: 600;">}</span></span>

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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="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC62" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                }<span class="idiff left right addition">*/</span></span></span>

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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="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 class="o" style="font-weight: 600;">}</span> <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;">IOException</span> <span class="n" style="color: #333;">x</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="java">                            <span class="c1" style="color: #998; font-style: italic;">// couldn't exec browser</span></span>

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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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" 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;">err</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;">"Could not invoke browser, command="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cmd</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="70" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,8 +85,8 @@ public class BrowserControl {</td>

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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" 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;">UNIX_PATH</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"firefox"</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="java"></span>

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<td class="old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java">    <span class="c1" style="color: #998; font-style: italic;">// The flag to display a url.</span></span>

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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(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="88" style="width: 35px; color: rgba(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="LC73" 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;">UNIX_PARAM_START</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-remote \"openURL("</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(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="88" style="width: 35px; color: rgba(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="LC74" class="line" lang="java"><span class="idiff left right deletion">  </span>  <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;">UNIX_PARAM_END</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="old_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">

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC88" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span> private static final String UNIX_PARAM_START = "-remote \"openURL(";</span></span>

</pre></td>

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<td class="old_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">

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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">

89

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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="LC89" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>  private static final String UNIX_PARAM_END = ")\"";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="java">    <span class="c1" style="color: #998; font-style: italic;">// The open command MacOSX.</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" 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;">OSX_PATH</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"open"</span><span class="o" style="font-weight: 600;">;</span></span>

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