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GitLab

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<h3>

Andrius Merkys pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a">22a8091d</a></strong>

<div>

<span>by Andrius Merkys</span>

<i>at 2021-11-05T04:57:55-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.11.0+dfsg</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">

pom.xml

</a>

</li>

<li class="file-stats">

<a href="#a366ae93c6b2697647f789b85e058d12270016b2">

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

</a>

</li>

<li class="file-stats">

<a href="#3357d4852d9e2d697d79a0b5c96ed0a78ce44afb">

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

</a>

</li>

<li class="file-stats">

<a href="#a00ceed8d5b0f2ffdd41a2cd6238a7f8582d4c76">

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

</a>

</li>

<li class="file-stats">

<a href="#30d84cf3c3cb1f3e258280f49da9e384acc79bf6">

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

</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="#ec05b3badbc5071521d94ee516cf51235293f843">

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

</a>

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<li class="file-stats">

<a href="#cf40108c840165d004c28f26bbfd06fa9b0a6a27">

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

</a>

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<li class="file-stats">

<a href="#88f7248516cf1351766ec9d506223745b62982c0">

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

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</li>

</ul>

<h4>Changes:</h4>

<li id="442292b8a7efeabbe4cc176709b833b1792140ec">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</strong></a>

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

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

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

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<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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<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>

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="xml">    <span class="nt" style="color: #000080;"><version></span>2021.1<span class="idiff left right">0.1</span><span class="nt" style="color: #000080;"></version></span></span>

</pre>

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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">

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="xml">    <span class="nt" style="color: #000080;"><version></span>2021.1<span class="idiff left right">1.0</span><span class="nt" style="color: #000080;"></version></span></span>

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

</pre>

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

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

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

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

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

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="xml">      <span class="nt" style="color: #000080;"><tag></span>openchemlib-2021.1<span class="idiff left right">0.1</span><span class="nt" style="color: #000080;"></tag></span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="xml">      <span class="nt" style="color: #000080;"><tag></span>openchemlib-2021.1<span class="idiff left right">1.0</span><span class="nt" style="color: #000080;"></tag></span></span>

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

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

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

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</li>

<li id="a366ae93c6b2697647f789b85e058d12270016b2">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#a366ae93c6b2697647f789b85e058d12270016b2"><strong>src/main/java/com/actelion/research/chem/ExtendedMolecule.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1664,8 +1664,9 @@ public class ExtendedMolecule extends Molecule implements Serializable {</td>

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<pre style="margin: 0;"> <span id="LC1664" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="java"></span>

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<td class="old_line diff-line-num" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="java">        <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">-<span id="LC1667" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Converts any stereo bond attached with its pointed tip</span></span>

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<pre style="margin: 0;">-<span id="LC1668" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * to this atom into a single bond.</span></span>

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<pre style="margin: 0;">+<span id="LC1667" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Converts any stereo bond being attached with the pointed tip to the given potential stereocenter</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * (TH or allene) into a single bond. For allenic stereo centers, stereo bonds at the allene end atoms</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * are converted. Atoms with PI electrons are not touched, unless they are P,S,...</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param atom</span></span>

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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="java">        <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">convertStereoBondsToSingleBonds</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1673,12 +1674,13 @@ public class ExtendedMolecule extends Molecule implements Serializable {</td>

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<pre style="margin: 0;"> <span id="LC1674" 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="mi" style="color: #099;">2</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="1675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1675" class="line" lang="java">                                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alleneEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findAlleneEndAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mConnAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>

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<td class="new_line diff-line-num" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1676" 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;">alleneEnd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1676" class="line" lang="java">                                        <span class="n" style="color: #333;">convertStereoBondsToSingleBonds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">alleneEnd</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC1677" 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;">mConnAtoms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">alleneEnd</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>

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<td class="new_line diff-line-num new" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1678" 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;">isStereoBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mConnBond</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">alleneEnd</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>

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<td class="new_line diff-line-num new" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="java">                                                        <span class="n" style="color: #333;">mBondType</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mConnBond</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">alleneEnd</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;">cBondTypeSingle</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1680" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="java">                        <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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1679

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<td class="new_line diff-line-num" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1683" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="1684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1681" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">// avoid flattening allene stereo bonds</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1684" 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;">mPi</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mAtomicNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1685" 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;">mAllConnAtoms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">];</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1686" 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;">mConnBond</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<br>

</li>

<li id="3357d4852d9e2d697d79a0b5c96ed0a78ce44afb">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#3357d4852d9e2d697d79a0b5c96ed0a78ce44afb"><strong>src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,6 +42,7 @@ import java.util.List;</td>

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<pre style="margin: 0;"> <span id="LC42" 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;">IsomericSmilesCreator</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_CREATE_SMARTS</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" 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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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_INCLUDE_MAPPING</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="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_KEKULIZED_OUTPUT</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="c1" style="color: #998; font-style: italic;">// no lower case atom labels and single/double bonds to represent aromaticity</span></span>

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45

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

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"></span>

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46

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

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">;</span></span>

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<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="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Canonizer</span> <span class="n" style="color: #333;">mCanonizer</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="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -430,6 +431,7 @@ public class IsomericSmilesCreator {</td>

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<td class="old_line diff-line-num" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

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<td class="new_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC431" 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;">isAnyAtom</span></span>

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<td class="old_line diff-line-num" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

431

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<td class="new_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="java">          <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atomList</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

432

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<td class="new_line diff-line-num" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="java">          <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC434" 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;">mMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_KEKULIZED_OUTPUT</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>

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<td class="new_line diff-line-num" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC435" 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;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomPi</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="old_line diff-line-num" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC436" 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;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomAbnormalValence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

435

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<td class="new_line diff-line-num" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="java">            <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomRadical</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomRadicalStateNone</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -461,7 +463,7 @@ public class IsomericSmilesCreator {</td>

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

461

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<td class="new_line diff-line-num" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

463

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="java">                         <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">isAnyAtom</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isOrganic</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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

462

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<td class="new_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">atomList</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span></span>

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<td class="old_line diff-line-num" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">qualifiesForAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

464

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<td class="new_line diff-line-num old" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC464" 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;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomPi</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC466" 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;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomPi</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff">MODE_KEKULIZED_OUTPUT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isotop</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="java">                         <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -513,13 +515,13 @@ public class IsomericSmilesCreator {</td>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">createMultiAtomLabel</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">atomicNo</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="java">         <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setLength</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="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC516" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">is<span class="idiff left right">Aromatic</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">is<span class="idiff left">LowerCase</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff">MODE_KEKULIZED_OUTPUT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="java"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nl">a:</span><span class="n" style="color: #333;">atomicNo</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC521" 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;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="java">                         <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">','</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="java">                 <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">label</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;">cAtomLabel</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>

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522

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<pre style="margin: 0;">-<span id="LC522" class="line" lang="java">                         <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">is<span class="idiff left right">Aromatic</span></span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toLowerCase</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="java">                         <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">is<span class="idiff left right">LowerCase</span></span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toLowerCase</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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524

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<td class="new_line diff-line-num" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -740,11 +742,12 @@ public class IsomericSmilesCreator {</td>

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<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">

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC743" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC744" 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="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC743" 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;">startLength</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC745" 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;">startLength</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">(</span>!</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mMode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff">MODE_KEKULIZED_OUTPUT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC746" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondTypeMaskSimple</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC747" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondTypeSingle</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC748" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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747

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<td class="new_line diff-line-num old" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC747" class="line" lang="java">                          <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

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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="LC749" class="line" lang="java">                          <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</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="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

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<pre style="margin: 0;">+<span id="LC750" 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;">mMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="no" style="color: #008080;">MODE_KEKULIZED_OUTPUT</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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<pre style="margin: 0;"> <span id="LC751" class="line" lang="java">                                 <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'-'</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="new_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

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<pre style="margin: 0;"> <span id="LC752" 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="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondTypeDouble</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

</td>

<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

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

<pre style="margin: 0;"> <span id="LC753" class="line" lang="java">                         <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">'='</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="a00ceed8d5b0f2ffdd41a2cd6238a7f8582d4c76">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#a00ceed8d5b0f2ffdd41a2cd6238a7f8582d4c76"><strong>src/main/java/com/actelion/research/chem/Mutator.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1521,20 +1521,19 @@ public class Mutator {</td>

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<td class="old_line diff-line-num" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1521

</td>

<td class="new_line diff-line-num" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1521

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<pre style="margin: 0;"> <span id="LC1521" 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="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1522

</td>

<td class="new_line diff-line-num" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1522

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

<pre style="margin: 0;"> <span id="LC1522" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1523

</td>

<td class="new_line diff-line-num" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1523

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<pre style="margin: 0;"> <span id="LC1523" 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;">repairStereoChemistry</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="o" style="font-weight: 600;">{</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1524

</td>

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

<pre style="margin: 0;">+<span id="LC1524" class="line" lang="java">                <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllBonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1525

</td>

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

<pre style="margin: 0;">+<span id="LC1525" class="line" lang="java">                        <span class="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;">isStereoBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1526

</td>

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

<pre style="margin: 0;">+<span id="LC1526" class="line" lang="java">                                <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cBondTypeSingle</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1527

</td>

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

<pre style="margin: 0;">+<span id="LC1527" class="line" lang="java"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1524

</td>

<td class="new_line diff-line-num" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1528

</td>

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

<pre style="margin: 0;"> <span id="LC1528" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1525

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(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="LC1525" class="line" lang="java">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">switch</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;">mol</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;">atom</span><span class="o" style="font-weight: 600;">)<span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">{</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1526

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1526" class="line" lang="java">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">case</span></span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParityUnknown</span><span class="o" style="font-weight: 600;"><span class="idiff right">:</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1527

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1527" class="line" lang="java"><span class="idiff left">         </span>       <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mRandom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextDouble</span><span class="o" style="font-weight: 600;">()</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff right"> </span><span class="mf" style="color: #099;">0.5</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;">cAtomParity1</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1528

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1528" class="line" lang="java"><span class="idiff left right">        </span>        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isPseudo</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;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1529

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1529" class="line" lang="java"><span class="idiff left right">        </span>        <span class="n" style="color: #333;">mol</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;">atom</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="n" style="color: #333;">isPseudo</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1530

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1530" class="line" lang="java">            <span class="k" style="font-weight: 600;"><span class="idiff left">case</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Molecule</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">cAtomParity1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">:</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1531

</td>

<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1531" class="line" lang="java">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">case</span></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;">cAtomParity<span class="idiff">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">:</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1529

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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="LC1529" class="line" lang="java">        <span class="idiff left">       </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">parity</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;">mol</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;">atom</span><span class="o" style="font-weight: 600;">)<span class="idiff right">;</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1530

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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="java">        <span class="idiff left">       </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parity</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParityUnknown</span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">{</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1531

</td>

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

<pre style="margin: 0;">+<span id="LC1531" class="line" lang="java"><span class="idiff left">               </span>        <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mRandom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextDouble</span><span class="o" style="font-weight: 600;">()<span class="idiff right"><</span></span><span class="mf" style="color: #099;">0.5</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;">cAtomParity1</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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1532

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

<pre style="margin: 0;">+<span id="LC1532" class="line" lang="java"><span class="idiff left right">         </span>        <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isPseudo</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;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1533

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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="LC1533" class="line" lang="java"><span class="idiff left right">         </span>        <span class="n" style="color: #333;">mol</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;">atom</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="n" style="color: #333;">isPseudo</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1534

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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="LC1534" class="line" lang="java"><span class="idiff left">       </span>            <span class="o" style="font-weight: 600;"><span class="idiff right">}</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1535

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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="LC1535" class="line" lang="java">        <span class="idiff left">       </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">parity</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></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;">cAtomParity<span class="idiff">None</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1532

</td>

<td class="new_line diff-line-num" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="java">                <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setStereoBondFromAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1533

</td>

<td class="new_line diff-line-num old" data-linenumber="1537" style="width: 35px; color: rgba(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="LC1533" 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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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1534

</td>

<td class="new_line diff-line-num old" data-linenumber="1537" style="width: 35px; color: rgba(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="LC1534" class="line" lang="java">            <span class="k" style="font-weight: 600;">case</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 class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1535

</td>

<td class="new_line diff-line-num old" data-linenumber="1537" style="width: 35px; color: rgba(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="LC1535" class="line" lang="java">                <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertStereoBondsToSingleBonds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1536

</td>

<td class="new_line diff-line-num old" data-linenumber="1537" style="width: 35px; color: rgba(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="LC1536" 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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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1537

</td>

<td class="new_line diff-line-num old" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1537" 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="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

</td>

<td class="new_line diff-line-num" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1537

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

<pre style="margin: 0;"> <span id="LC1537" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1539

</td>

<td class="new_line diff-line-num" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

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

<pre style="margin: 0;"> <span id="LC1538" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1540

</td>

<td class="new_line diff-line-num" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1539

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

<pre style="margin: 0;"> <span id="LC1539" 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;">isBINAPChiralityBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1547,10 +1546,6 @@ public class Mutator {</td>

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<td class="old_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

</td>

<td class="new_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1546

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

<pre style="margin: 0;"> <span id="LC1546" class="line" lang="java">                    <span class="k" style="font-weight: 600;">case</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;">cBondParityZor2</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="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

</td>

<td class="new_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

</td>

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

<pre style="margin: 0;"> <span id="LC1547" class="line" lang="java">                        <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setStereoBondFromBondParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1549

</td>

<td class="new_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

</td>

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

<pre style="margin: 0;"> <span id="LC1548" class="line" lang="java">                        <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1550

</td>

<td class="new_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1550" class="line" lang="java">                    <span class="k" style="font-weight: 600;">case</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;">cBondParityNone</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1551

</td>

<td class="new_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1551" class="line" lang="java">                        <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertStereoBondsToSingleBonds</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</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="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1552

</td>

<td class="new_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC1552" class="line" lang="java">                        <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertStereoBondsToSingleBonds</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC1553" class="line" lang="java">                        <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC1549" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC1550" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="30d84cf3c3cb1f3e258280f49da9e384acc79bf6">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#30d84cf3c3cb1f3e258280f49da9e384acc79bf6"><strong>src/main/java/com/actelion/research/chem/RingCollection.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,6 +50,7 @@ public class RingCollection {</td>

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

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java">                                                                                                                                     <span class="o" style="font-weight: 600;">|</span> <span class="no" style="color: #008080;">MODE_LARGE_RINGS</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java">                                                                                                                                     <span class="o" style="font-weight: 600;">|</span> <span class="no" style="color: #008080;">MODE_AROMATICITY</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MODE_INCLUDE_TAUTOMERIC_BONDS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"></span>

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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">ExtendedMolecule</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">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;">mRingAtomSet</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,7 +172,7 @@ public class RingCollection {</td>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java">                 <span class="n" style="color: #333;">mIsAromatic</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;">mRingAtomSet</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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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java">                 <span class="n" style="color: #333;">mIsDelocalized</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;">mRingAtomSet</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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<pre style="margin: 0;"> <span id="LC174" class="line" lang="java">                 <span class="n" style="color: #333;">mHeteroPosition</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;">mRingAtomSet</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="new_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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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java">                 <span class="n" style="color: #333;">determineAromaticity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mIsAromatic</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mIsDelocalized</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mHeteroPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;"><span class="idiff left right">false</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="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">

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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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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java">                 <span class="n" style="color: #333;">determineAromaticity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mIsAromatic</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mIsDelocalized</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mHeteroPosition</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff">MODE_INCLUDE_TAUTOMERIC_BONDS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

175

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<td class="new_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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<td class="new_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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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">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// find large rings by examining every potential ring bond</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -729,7 +730,7 @@ public class RingCollection {</td>

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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="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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<pre style="margin: 0;"> <span id="LC730" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">qualifiesAsAmideTypeBond</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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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="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

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<pre style="margin: 0;"> <span id="LC731" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="old_line diff-line-num" 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="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

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<pre style="margin: 0;"> <span id="LC732" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</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;">bond</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="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

732

</td>

<td class="new_line diff-line-num old" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC732" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span></span>

</pre>

</td>

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<td class="old_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">

</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 class="idiff left">(</span>(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom1</span><span class="o" style="font-weight: 600;">)</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 class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

</td>

<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

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

<pre style="margin: 0;"> <span id="LC734" class="line" lang="java">                  <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span 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>

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<td class="old_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

</td>

<td class="new_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

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

<pre style="margin: 0;"> <span id="LC735" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

</td>

<td class="new_line diff-line-num" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

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

<pre style="margin: 0;"> <span id="LC736" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<br>

</li>

<li id="ba44c1f7e56c2598decf65ca012c856547ff2f0f">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#ba44c1f7e56c2598decf65ca012c856547ff2f0f"><strong>src/main/java/com/actelion/research/chem/SmilesParser.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +54,7 @@ public class SmilesParser {</td>

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54

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

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55

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">INITIAL_CONNECTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

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<td class="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_CONNECTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// largest allowed one in SMILES is 99</span></span>

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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

57

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<td class="new_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;"><span class="idiff left">MAX_</span>BRACKET_LEVELS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff right">64</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java">  <span class="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;">BRACKET_LEVELS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">32</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="old_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="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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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_AROMATIC_RING_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>

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<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="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">HYDROGEN_ANY</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,7 +239,7 @@ public class SmilesParser {</td>

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<td class="old_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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<pre style="margin: 0;"> <span id="LC239" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">TreeMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">THParity</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parityMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); 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="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">baseAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;"><span class="idiff left right">MAX_</span>BRACKET_LEVELS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="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="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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<pre style="margin: 0;">+<span id="LC242" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">baseAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;">BRACKET_LEVELS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="java"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ringClosureAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="no" style="color: #008080;">INITIAL_CONNECTIONS</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -857,8 +857,10 @@ public class SmilesParser {</td>

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<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;">theChar</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'('</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC858" 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;">baseAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bracketLevel</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC859" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Smiles with leading parenthesis are not supported"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC861" 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;">baseAtom</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;">bracketLevel</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC862" class="line" lang="java">                                 <span class="n" style="color: #333;">baseAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">baseAtom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">BRACKET_LEVELS</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC863" class="line" lang="java">                         <span class="n" style="color: #333;">baseAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bracketLevel</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baseAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bracketLevel</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC864" class="line" lang="java">                         <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC865" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC866" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1213" style="width: 35px; color: rgba(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="1215" style="width: 35px; color: rgba(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">@@ -1213,6 +1215,22 @@ public class SmilesParser {</td>

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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="java">                                <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">qualifyingBondFound</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="java">                <span class="cm" style="color: #998; font-style: italic;">/* Some SMILES still contain kekulized aromatic rings with lowercase hetero atoms, e.g. C1=CC=C[se]1</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">            // If we recognize those rings to be aromatic, we remove the aromaticity marker from all ring atoms.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">            if (mAromaticAtoms != 0) {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1221

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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                    RingCollection daylightTypeRingSet = new RingCollection(mMol, RingCollection.MODE_SMALL_RINGS_AND_AROMATICITY | RingCollection.MODE_INCLUDE_TAUTOMERIC_BONDS);</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1222

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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                    for (int ring=0; ring<daylightTypeRingSet.getSize(); ring++) {</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1223

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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                            if (daylightTypeRingSet.isAromatic(ring)) {</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1224

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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                    int[] ringAtom = daylightTypeRingSet.getRingAtoms(ring);</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1225

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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                    for (int atom:ringAtom)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1226

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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                            if (mMol.isMarkedAtom(atom)) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1227

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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                                    mMol.setAtomMarker(atom, false);</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1228

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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                                    mAromaticAtoms--;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1229

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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                            }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1230

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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                                    }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1231

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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                            }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1232

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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">                    } taken out, because OpenChemLib should not start interpreting invalid SMILES; TLS 20-Oct-2021 */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-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="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1233

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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="java"></span>

</pre>

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1216

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<td class="new_line diff-line-num" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1234

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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="java">                <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAromaticAtoms</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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1217

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<td class="new_line diff-line-num" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1235

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<pre style="margin: 0;"> <span id="LC1235" 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;">connectConjugatedRadicalPairs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isAromaticBond</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1218

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<td class="new_line diff-line-num" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1236

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<pre style="margin: 0;"> <span id="LC1236" class="line" lang="java">                                <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<br>

</li>

<li id="ec05b3badbc5071521d94ee516cf51235293f843">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#ec05b3badbc5071521d94ee516cf51235293f843"><strong>src/main/java/com/actelion/research/chem/docking/DockingEngine.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,8 +90,11 @@ public class DockingEngine {</td>

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90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"></span>

</pre>

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91

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91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java">  </span>

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DockingEngine</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;">rec</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;">nativeLig</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;">mcSteps</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;">startPositions</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">ScoringFunction</span> <span class="n" style="color: #333;">scoringFunction</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java">                  <span class="nc" style="color: #458; font-weight: 600;">ScoringFunction</span> <span class="n" style="color: #333;">scoringFunction</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">DockingFailedException</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="old_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="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">          <span class="k" style="font-weight: 600;">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;">ra</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;">ra</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rec</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;">ra</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="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;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getImplicitHydrogens</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ra</span><span class="o" style="font-weight: 600;">)></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java">                          <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">DockingFailedException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"please add hydrogen atoms to receptor structure!"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">          <span class="n" style="color: #333;">nativeLigand</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;">Molecule3D</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nativeLig</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java">          <span class="n" style="color: #333;">nativeLigand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java">         <span class="nc" style="color: #458; font-weight: 600;">Molecule3D</span> <span class="n" style="color: #333;">receptor</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;">Molecule3D</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,7 +131,7 @@ public class DockingEngine {</td>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="java"> </span>

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<td class="new_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DockingEngine</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;">receptor</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;">nativeLigand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">DockingEngine</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;">receptor</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;">nativeLigand</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">throws</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">DockingFailedException</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">receptor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nativeLigand</span><span class="o" style="font-weight: 600;">,</span><span class="no" style="color: #008080;">DEFAULT_NR_MC_STEPS</span><span class="o" style="font-weight: 600;">,</span><span class="no" style="color: #008080;">DEFAULT_START_POSITIONS</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">ScoringFunction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">CHEMPLP</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC136" 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="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java"> </span>

</pre>

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<li id="cf40108c840165d004c28f26bbfd06fa9b0a6a27">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#cf40108c840165d004c28f26bbfd06fa9b0a6a27"><strong>src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,6 +173,8 @@ public interface CompoundTableConstants {</td>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyReferenceTypeTopDown</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"topdown"</span><span class="o" style="font-weight: 600;">;</span>   <span class="c1" style="color: #998; font-style: italic;">// a connection is only referenced from top record</span></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyFormula</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"formula"</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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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertySuperposeMolecule</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"superposeMol"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// idcode+coords to be displayed in every cell</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="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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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyProteinCavity</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"proteinCavity"</span><span class="o" style="font-weight: 600;">;</span>    <span class="c1" style="color: #998; font-style: italic;">// idcode+coords of protein cavity to be displayed in every cell</span></span>

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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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<pre style="margin: 0;">+<span id="LC177" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyNaturalLigand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"naturalLigand"</span><span class="o" style="font-weight: 600;">;</span>    <span class="c1" style="color: #998; font-style: italic;">// idcode+coords of natural ligand, if proteinCavity is given (not shown, used for surface creation)</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertySuperpose</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"superpose"</span><span class="o" style="font-weight: 600;">;</span>  <span class="c1" style="color: #998; font-style: italic;">// cSuperposeValueReferenceRow or null</span></span>

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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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<pre style="margin: 0;"> <span id="LC179" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertySuperposeAlign</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"align"</span><span class="o" style="font-weight: 600;">;</span>  <span class="c1" style="color: #998; font-style: italic;">// cSuperposeAlignValueShape or null</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java">    <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyCommentUploadStatus</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"commentUploadStatus"</span><span class="o" style="font-weight: 600;">;</span></span>

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<li id="88f7248516cf1351766ec9d506223745b62982c0">

<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/22a8091d1e0be92c7f1ef4c65c7cf754bac2680a#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 old_line" data-linenumber="270" style="width: 35px; color: rgba(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="270" style="width: 35px; color: rgba(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">@@ -270,7 +270,7 @@ public class Reactor {</td>

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<pre style="margin: 0;"> <span id="LC270" 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;">no</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="java">         <span class="n" style="color: #333;">mSSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setMol</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="n" style="color: #333;">mReactant</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">no</span><span class="o" style="font-weight: 600;">]);</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matchMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">c<span class="idiff left right">MatchDBondToDelocalized</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAllowChargeCorrections</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="nc" style="color: #458; font-weight: 600;">SSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cMatchAtomCharge</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">matchMode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">c<span class="idiff left right">DefaultMatchMode</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAllowChargeCorrections</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="nc" style="color: #458; font-weight: 600;">SSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cMatchAtomCharge</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC274" 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;">mSSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">findFragmentInMolecule</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SSSearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cCountModeRigorous</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">matchMode</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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<pre style="margin: 0;"> <span id="LC275" class="line" lang="java">                 <span class="n" style="color: #333;">mMatchList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">no</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;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="java">                 <span class="n" style="color: #333;">mReactantMatchCombinationCount</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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