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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>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad">b7b04036</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-04-14T02:54:07-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2022.4.2+dfsg</pre>
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<h4>16 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">
pom.xml
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<li class="file-stats">
<a href="#ba44c1f7e56c2598decf65ca012c856547ff2f0f">
src/main/java/com/actelion/research/chem/SmilesParser.java
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<li class="file-stats">
<a href="#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3">
src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java
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<li class="file-stats">
<a href="#f678d35a688802dfd7e0cbfc6c14290a34944abc">
src/main/java/com/actelion/research/chem/docking/DockingUtils.java
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<a href="#f9cb63e80b748296a596a354aa485682819c7904">
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src/main/java/com/actelion/research/chem/hyperspace/SimpleCombinatorialHit.java
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<a href="#2d0bffca02cf955165915399414eb28114819627">
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src/main/java/com/actelion/research/chem/hyperspace/SimpleSynthon.java
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<a href="#57834476cf2f3a0474fee1ce1fbff3ada6845cfb">
src/main/java/com/actelion/research/chem/io/DWARFileParser.java
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<a href="#d0922db37ba2d4e1c4162276b7b27af29aeca835">
src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java
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<li class="file-stats">
<a href="#7e9910936f51c5883dc0e383abac0f0720181e30">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/PPTriangle.java
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<a href="#1a2948d1808e5bf4b5ae448818a4c444d9b4870a">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java
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<a href="#86999a714d04156d77451e9ca14c33aff8a98a76">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/PPGaussian.java
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<a href="#3dbbe7b950b7f9e3cf1fa45df59255c90fc56046">
src/main/java/com/actelion/research/chem/phesaflex/EvaluableFlexibleOverlap.java
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<a href="#88f7248516cf1351766ec9d506223745b62982c0">
src/main/java/com/actelion/research/chem/reaction/Reactor.java
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<a href="#b23ac1794ae5ae3ca39c5fd7604dd429cdcd2393">
src/main/java/com/actelion/research/gui/editor/AtomQueryFeatureDialogBuilder.java
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<a href="#98ac8c26d9087ed4dfec10db567462ed5ca7be22">
src/main/java/com/actelion/research/util/BrowserControl.java
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OpenChemLib</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*OpenChemLib*</span> is Java based framework providing cheminformatics core functionality and user interface components. Its main focus is on organics chemistry and small molecules. It is built around a StereoMolecule class, which represents a molecule using atom and bond tables, provides atom neighbours, ring and aromaticity information, and supports MDL's concept of enhanced stereo representation. Additional classes provide, 2D-depiction, descriptor calculation, molecular similarity and substructure search, reaction search, property prediction, conformer generation, support for molfile and SMILES formats, energy minimization, ligand-protein interactions, and more. <span class="ge" style="font-style: italic;">*OpenChemLib's idcode*</span> represents molecules, fragments or reactions as canonical, very compact string that includes stereo and query features.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">Different to other cheminformatics frameworks, <span class="ge" style="font-style: italic;">*OpenChemLib*</span> also provides user interface components that allow to easily embed chemical functionality into Java applications, e.g. to display or edit chemical structures or reactions.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,8 +6,15 @@ Different to other cheminformatics frameworks, *OpenChemLib* also provides user</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*OpenChemLib*</span> requires JRE 8 or newer including JavaFX. Otherwise, there are no dependencies.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### How to download the project</span></span>
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">git clone https://github.com/Actelion/openchemlib.git</span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Build the project</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">To build the project run the following from within the project directory.</span>
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<td class="old_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">./mvnw package</span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Folder 'examples'</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">Contains examples for working with the <span class="ge" style="font-style: italic;">*OpenChemLib*</span> library.</span>
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<li id="442292b8a7efeabbe4cc176709b833b1792140ec">
<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH</span></span>
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> (eg. 2016.4.1 for second release in Apr 2016)</span></span>
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> --></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC11" class="line" lang="xml"> <span class="nt" style="color: #000080;"><version></span>2022.<span class="idiff left right deletion">3</span>.2<span class="nt" style="color: #000080;"></version></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="xml"> <span class="nt" style="color: #000080;"><version></span>2022.<span class="idiff left right addition">4</span>.2<span class="nt" style="color: #000080;"></version></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="xml"> <span class="nt" style="color: #000080;"><name></span>OpenChemLib<span class="nt" style="color: #000080;"></name></span></span>
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14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="xml"> <span class="nt" style="color: #000080;"><description></span>Open Source Chemistry Library<span class="nt" style="color: #000080;"></description></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="xml"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="xml"> <span class="nt" style="color: #000080;"><packaging></span>jar<span class="nt" style="color: #000080;"></packaging></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="xml"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="xml"> <span class="nt" style="color: #000080;"><project.build.sourceEncoding></span>UTF-8<span class="nt" style="color: #000080;"></project.build.sourceEncoding></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC54" class="line" lang="xml"> <span class="c" style="color: #998; font-style: italic;"><!-- Disable doclint for Java 8 --></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">@@ -195,7 +200,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="xml"> <span class="nt" style="color: #000080;"><developerConnection></span>scm:git:git@github.com:Actelion/openchemlib.git<span class="nt" style="color: #000080;"></developerConnection></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC202" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC198" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-2022.<span class="idiff left right deletion">3</span>.2<span class="nt" style="color: #000080;"></tag></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-2022.<span class="idiff left right addition">4</span>.2<span class="nt" style="color: #000080;"></tag></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC204" class="line" lang="xml"> <span class="nt" style="color: #000080;"></scm></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC206" class="line" lang="xml"> <span class="nt" style="color: #000080;"><distributionManagement></span></span>
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<li id="ba44c1f7e56c2598decf65ca012c856547ff2f0f">
<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#ba44c1f7e56c2598decf65ca012c856547ff2f0f"><strong>src/main/java/com/actelion/research/chem/SmilesParser.java</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -151,57 +151,51 @@ public class SmilesParser {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC151" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">rxn</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">while</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;">start</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">index1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">i<span class="idiff left deletion">nt</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">ArrayUtils</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">indexOf</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff deletion">byte</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)</span></span><span class="sc" style="color: #d14;"><span class="idiff deletion">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">);</span></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i<span class="idiff left deletion">ndex</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">==</span></span><span class="idiff deletion"> </span><span class="sc" style="color: #d14;"><span class="idiff right deletion">'.'</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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157
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<td class="new_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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158
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<td class="new_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i<span class="idiff left right deletion">ndex</span></span><span class="o" style="font-weight: 600;">);</span></span>
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159
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<td class="new_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">);</span></span>
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160
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">start</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">;</span></span></span>
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161
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<td class="new_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">continue</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition"><</span></span><span class="n" style="color: #333;">index1</span><span class="o" style="font-weight: 600;"><span class="idiff addition">-</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">++</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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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="LC155" class="line" lang="java"> <span class="k" style="font-weight: 600;">i<span class="idiff left addition">f</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">)</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">{</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="java"> <span class="idiff left addition"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">start</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">);</span></span>
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160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="idiff left addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">}</span></span></span>
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161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">start</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">2</span></span><span class="o" style="font-weight: 600;">;</span></span>
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162
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162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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163
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC163" class="line" lang="java"></span>
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164
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC164" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactants</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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165
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactants</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC166" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactants</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC167" 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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168
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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164
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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="LC164" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactants</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactants</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index1</span><span class="o" style="font-weight: 600;">);</span></span>
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166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactants</span><span class="o" style="font-weight: 600;">);</span></span>
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169
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167
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC167" class="line" lang="java"></span>
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170
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168
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">index1</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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171
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169
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="java"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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172
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">while</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;">start</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">index2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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173
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">i<span class="idiff left deletion">nt</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">ArrayUtils</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">indexOf</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff deletion">byte</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)</span></span><span class="sc" style="color: #d14;"><span class="idiff deletion">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">);</span></span></span>
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174
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i<span class="idiff left deletion">ndex</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">==</span></span><span class="idiff deletion"> </span><span class="sc" style="color: #d14;"><span class="idiff right deletion">'.'</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
175
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalyst</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC176" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i<span class="idiff left right deletion">ndex</span></span><span class="o" style="font-weight: 600;">);</span></span>
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177
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC178" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">start</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">;</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC179" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">continue</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC170" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition"><</span></span><span class="n" style="color: #333;">index2</span><span class="o" style="font-weight: 600;"><span class="idiff addition">-</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">++</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="java"> <span class="k" style="font-weight: 600;">i<span class="idiff left addition">f</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">)</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">{</span></span></span>
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172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> <span class="idiff left addition"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">start</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalyst</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalyst</span><span class="o" style="font-weight: 600;">);</span></span>
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176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> <span class="idiff left addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">}</span></span></span>
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177
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">start</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">2</span></span><span class="o" style="font-weight: 600;">;</span></span>
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178
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC181" class="line" lang="java"></span>
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182
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<td class="new_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalysts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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183
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<td class="new_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalysts</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index2</span><span class="o" style="font-weight: 600;">);</span></span>
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184
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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="LC184" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalysts</span><span class="o" style="font-weight: 600;">);</span></span>
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185
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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="LC185" 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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179
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">catalysts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalysts</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index2</span><span class="o" style="font-weight: 600;">);</span></span>
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182
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addCatalyst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">catalysts</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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185
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC185" class="line" lang="java"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index2</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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190
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC190" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">while</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;">start</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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191
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC191" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">i<span class="idiff left deletion">nt</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">ArrayUtils</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">indexOf</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff deletion">byte</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)</span></span><span class="sc" style="color: #d14;"><span class="idiff deletion">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">);</span></span></span>
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192
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i<span class="idiff left deletion">ndex</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">.</span></span><span class="na" style="color: #008080;"><span class="idiff deletion">length</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">&&</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">==</span></span><span class="idiff deletion"> </span><span class="sc" style="color: #d14;"><span class="idiff right deletion">'.'</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">product</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
194
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC194" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i<span class="idiff left right deletion">ndex</span></span><span class="o" style="font-weight: 600;">);</span></span>
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195
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC195" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">);</span></span>
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196
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">start</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">index</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">;</span></span></span>
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197
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC197" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left right deletion">continue</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC186" class="line" lang="java"> <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition"><</span></span><span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;"><span class="idiff addition">-</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">;</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">++</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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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="LC187" class="line" lang="java"> <span class="k" style="font-weight: 600;">i<span class="idiff left addition">f</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">smiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="sc" style="color: #d14;"><span class="idiff addition">'.'</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">)</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">{</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="idiff left addition"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">start</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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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="LC189" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">product</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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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="LC190" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> <span class="idiff left addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">}</span></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC193" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">start</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">i</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">+</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">2</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC194" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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="LC199" class="line" lang="java"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC200" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">products</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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201
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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="LC201" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">products</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC202" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">products</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC203" 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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204
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195
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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196
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC196" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">products</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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197
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC197" class="line" lang="java"> <span class="n" style="color: #333;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">products</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">smiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="java"> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">products</span><span class="o" style="font-weight: 600;">);</span></span>
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199
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">;</span></span>
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201
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3"><strong>src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,8 +31,8 @@ import com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian;</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PheSAAlignmentOptimizer</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="java"> </span>
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion">10</span>0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">PMI_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion">2</span>0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right addition">5</span>0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">PMI_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right addition">1</span>0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="no" style="color: #008080;">EXIT_VECTOR_WEIGHT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10.0</span><span class="o" style="font-weight: 600;">;</span></span>
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37
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">BEST_RESULT_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="java"> </span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,7 @@ public class PheSAAlignmentOptimizer {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">shapeVol</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="n" style="color: #333;">shapeVol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">removeRings</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">singletonList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">singletonList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">),</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;"><span class="idiff left addition">,</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right addition">true</span></span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">alignmentSolutions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">descendingSet</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,11 +87,17 @@ public class PheSAAlignmentOptimizer {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span></span>
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92
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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94
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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95
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> </span>
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96
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">createAlignmentSolutions</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">exhaustive</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">triangleOpti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exhaustive</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">:</span> <span class="no" style="color: #008080;">TRIANGLE_OPTIMIZATIONS</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pmiOpti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exhaustive</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="no" style="color: #008080;">PMI_OPTIMIZATIONS</span> <span class="o" style="font-weight: 600;">:</span> <span class="no" style="color: #008080;">PMI_OPTIMIZATIONS</span><span class="o" style="font-weight: 600;">;</span></span>
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93
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100
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">>();</span></span>
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94
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC94" class="line" lang="java"></span>
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95
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101
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC101" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">molVol</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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96
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102
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">ppg</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">molVol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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97
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103
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPharmacophorePoint</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getFunctionalityIndex</span><span class="o" style="font-weight: 600;">()==</span><span class="nc" style="color: #458; font-weight: 600;">PharmacophoreCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">EXIT_VECTOR_ID</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,7 +106,7 @@ public class PheSAAlignmentOptimizer {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC106" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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101
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107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="java"></span>
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103
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<td class="new_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">triangleSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getBestTriangleAlignments</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">triangleSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getBestTriangleAlignments</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;"><span class="idiff left addition">,</span></span><span class="n" style="color: #333;"><span class="idiff right addition">triangleOpti</span></span><span class="o" style="font-weight: 600;">);</span></span>
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104
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110
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">alignmentSolutions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">triangleSolutions</span><span class="o" style="font-weight: 600;">);</span></span>
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105
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111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pmiSolutions</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">>();</span></span>
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106
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +127,7 @@ public class PheSAAlignmentOptimizer {</td>
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121
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127
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC127" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//optimize best PMI alignments</span></span>
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122
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128
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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123
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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC129" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span> <span class="n" style="color: #333;">pmiAlignment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pmiSolutions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">descendingSet</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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124
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="no" style="color: #008080;"><span class="idiff left right deletion">PMI_OPTIMIZATIONS</span></span><span class="o" style="font-weight: 600;">)</span></span>
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130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="n" style="color: #333;"><span class="idiff left right addition">pmiOpti</span></span><span class="o" style="font-weight: 600;">)</span></span>
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125
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131
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>
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126
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132
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC132" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">refVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pmiAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefConformerIndex</span><span class="o" style="font-weight: 600;">());</span></span>
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127
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133
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC133" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">fitVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pmiAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConformerIndex</span><span class="o" style="font-weight: 600;">()));</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -172,7 +178,7 @@ public class PheSAAlignmentOptimizer {</td>
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172
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178
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="java"></span>
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173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC180" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">NavigableSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getBestTriangleAlignments</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">,</span> </span>
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175
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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">optimize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">tversky</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useDirectionality</span><span class="o" style="font-weight: 600;"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">nrOptimizations</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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176
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182
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC182" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">triangleResults</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">TreeSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span><span class="o" style="font-weight: 600;">>();</span></span>
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177
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183
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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178
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184
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC184" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">refVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,7 +195,7 @@ public class PheSAAlignmentOptimizer {</td>
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189
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195
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">PheSAAlignment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">initialTransform</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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190
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196
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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191
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197
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentResult</span> <span class="nl">result:</span> <span class="n" style="color: #333;">triangleResults</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">descendingSet</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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192
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="no" style="color: #008080;"><span class="idiff left right deletion">TRIANGLE_OPTIMIZATIONS</span></span><span class="o" style="font-weight: 600;">)</span></span>
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198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++></span><span class="n" style="color: #333;"><span class="idiff left right addition">nrOptimizations</span></span><span class="o" style="font-weight: 600;">)</span></span>
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193
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199
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>
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194
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200
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">refVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefConformerIndex</span><span class="o" style="font-weight: 600;">());</span></span>
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195
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201
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span> <span class="n" style="color: #333;">fitVol</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ShapeVolume</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitVols</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConformerIndex</span><span class="o" style="font-weight: 600;">()));</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#f678d35a688802dfd7e0cbfc6c14290a34944abc"><strong>src/main/java/com/actelion/research/chem/docking/DockingUtils.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,7 +111,7 @@ public class DockingUtils {</td>
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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="java"> <span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">normalizeAmbiguousBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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112
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">repairQuaternaryNitrogen</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="java"> <span class="n" style="color: #333;">repairCarboxylate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">a<span class="idiff left right deletion">ssignLikelyProtonationState</span>s</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">a<span class="idiff left right addition">ddImplicitHydrogen</span>s</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">lig</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">repairQuaternaryNitrogen</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">){</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#f9cb63e80b748296a596a354aa485682819c7904"><strong>src/main/java/com/actelion/research/chem/hyperspace/SimpleCombinatorialHit.java</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.hyperspace</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.Serializable</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SimpleCombinatorialHit</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Serializable</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">serialVersionUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1970031554026082875L</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">;</span></span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SimpleSynthon</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">synthons</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SimpleCombinatorialHit</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">SimpleSynthon</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">synthons</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">rxnId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">synthons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">synthons</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#2d0bffca02cf955165915399414eb28114819627"><strong>src/main/java/com/actelion/research/chem/hyperspace/SimpleSynthon.java</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.hyperspace</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.Serializable</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SimpleSynthon</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Serializable</span> <span class="o" style="font-weight: 600;">{</span></span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">serialVersionUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4625857679359578042L</span><span class="o" style="font-weight: 600;">;</span></span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">idcode</span><span class="o" style="font-weight: 600;">;</span></span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">synthonId</span><span class="o" style="font-weight: 600;">;</span></span>
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9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rxnId</span><span class="o" style="font-weight: 600;">;</span></span>
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">synthonSet</span><span class="o" style="font-weight: 600;">;</span></span>
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11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SimpleSynthon</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">idcode</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">rxn_id</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">synthonSet</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">idcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idcode</span><span class="o" style="font-weight: 600;">;</span></span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">synthonId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">rxnId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rxn_id</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">synthonSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">synthonSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#57834476cf2f3a0474fee1ce1fbff3ada6845cfb"><strong>src/main/java/com/actelion/research/chem/io/DWARFileParser.java</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -238,8 +238,13 @@ public class DWARFileParser extends CompoundFileParser implements DescriptorCons</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC239" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">cColumnProperty</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC240" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">property</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extractValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC241" class="line" lang="java"> <span class="n" style="color: #333;">mColumnPropertyMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">columnName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">property</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC241" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC242" class="line" lang="java"> <span class="n" style="color: #333;">mColumnPropertyMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">columnName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC244" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC245" class="line" lang="java"> <span class="n" style="color: #333;">mColumnPropertyMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">columnName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">setProperty</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">property</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">property</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC248" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC249" class="line" lang="java"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readHeadOrTailLine</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC250" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#d0922db37ba2d4e1c4162276b7b27af29aeca835"><strong>src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,8 +22,7 @@ import com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian;</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">EvaluableOverlap</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Evaluable</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="java"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">PENALTY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">80</span><span class="o" style="font-weight: 600;">;</span> </span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">PheSAAlignment</span> <span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +39,6 @@ public class EvaluableOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitAtGaussModCoords</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitPPDirectionalityMod</span><span class="o" style="font-weight: 600;">;</span></span>
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42
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="java"> </span>
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44
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">EvaluableOverlap</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PheSAAlignment</span> <span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,7 +57,6 @@ public class EvaluableOverlap implements Evaluable {</td>
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59
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57
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">dv0PP</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">];</span></span>
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60
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">dv1PP</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">];</span></span>
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59
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">dv2PP</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fitPPDirectionalityMod</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()];</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAtomicGaussians</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()][</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRefMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAtomicGaussians</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()];</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="java"> <span class="n" style="color: #333;">cachedCoords</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAtomicGaussians</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()];</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="java"> <span class="n" style="color: #333;">cachedCoordsPP</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">shapeAlign</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMolGauss</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,7 +157,7 @@ public class EvaluableOverlap implements Evaluable {</td>
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160
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157
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> </span>
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161
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ppGrad</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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159
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFGValueOverlapPP</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppGrad</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">refMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPPGaussians</span><span class="o" style="font-weight: 600;">(),</span></span>
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163
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="n" style="color: #333;">dv0PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv1PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv2PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;"><span class="idiff left deletion">,</span></span><span class="n" style="color: #333;"><span class="idiff right deletion">fitPPDirectionalityMod</span></span><span class="o" style="font-weight: 600;">);</span></span>
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160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="n" style="color: #333;">dv0PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv1PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dv2PP</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitPPGaussModCoords</span><span class="o" style="font-weight: 600;">);</span></span>
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164
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161
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC161" class="line" lang="java"></span>
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162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> </span>
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">atomGrad</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]+</span> <span class="n" style="color: #333;">ppWeight</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ppGrad</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -351,16 +348,12 @@ public class EvaluableOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC349" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC350" class="line" lang="java"> </span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC354" class="line" lang="java"> <span class="idiff left right deletion"> </span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC355" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getFGValueOverlapPP</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refMolGauss</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">dRdv0</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitGaussModCoords</span><span class="o" style="font-weight: 600;"><span class="idiff left deletion">,</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[]</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff right deletion">fitPPDirectionalityMod</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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351
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC351" class="line" lang="java"> </span>
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352
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC352" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getFGValueOverlapPP</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">refMolGauss</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">dRdv0</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fitGaussModCoords</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC353" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ExponentialMap</span> <span class="n" style="color: #333;">eMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ExponentialMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span><span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">],</span><span class="n" style="color: #333;">transform</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC355" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">rotMatrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">eMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toQuaternion</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getRotMatrix</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getArray</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC360" class="line" lang="java"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC361" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC362" class="line" lang="java"> <span class="n" style="color: #333;">fitPPDirectionalityMod</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getRotatedDirectionality</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rotMatrix</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC363" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC357" class="line" lang="java"> <span class="n" style="color: #333;">getTransformedCoordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitGaussModCoords</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC358" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC359" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getEMapGradient</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dRdv0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">cachedCoordsPP</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -377,13 +370,9 @@ public class EvaluableOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC370" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">refAt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC371" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++){</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC372" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">fitAt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitMolGauss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC380" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">fitPPDirectionalityVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitPPDirectionalityMod</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">];</span></span>
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381
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC373" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC374" class="line" lang="java"> <span class="n" style="color: #333;">fitCenterModCoord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fitGaussModCoords</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC375" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alphaSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC384" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC385" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">y</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC386" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">zi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
387
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<td class="new_line diff-line-num" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
376
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC376" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">fitCenterModCoord</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
388
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<td class="new_line diff-line-num" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
377
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC377" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">y</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">fitCenterModCoord</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">y</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
389
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<td class="new_line diff-line-num" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
378
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC378" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCenter</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">fitCenterModCoord</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">z</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -396,7 +385,9 @@ public class EvaluableOverlap implements Evaluable {</td>
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<td class="old_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
396
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<td class="new_line diff-line-num" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
385
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC385" class="line" lang="java"> <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWeight</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getHeight</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getHeight</span><span class="o" style="font-weight: 600;">()*</span><span class="nc" style="color: #458; font-weight: 600;">QuickMathCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">quickExp</span><span class="o" style="font-weight: 600;">(-(</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span> <span class="nc" style="color: #458; font-weight: 600;">Rij2</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">alphaSum</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">*</span></span>
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397
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<td class="new_line diff-line-num" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
386
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC386" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QuickMathCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getPrefactor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">());</span></span>
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398
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<td class="new_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
387
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC387" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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399
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<td class="new_line diff-line-num old" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC399" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fitPPDirectionalityVector</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC388" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInteractionSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC389" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">==</span><span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
400
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<td class="new_line diff-line-num" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
391
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC391" class="line" lang="java"> <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
401
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<td class="new_line diff-line-num" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
392
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC392" class="line" lang="java"> <span class="n" style="color: #333;">totalOverlap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
402
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<td class="new_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
393
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC393" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">*-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -404,12 +395,12 @@ public class EvaluableOverlap implements Evaluable {</td>
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<td class="old_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
404
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<td class="new_line diff-line-num" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
395
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC395" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dv1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dz</span><span class="o" style="font-weight: 600;">;</span> </span>
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405
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396
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC396" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dv2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dRdv2</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">dz</span><span class="o" style="font-weight: 600;">;</span> </span>
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406
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397
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC397" class="line" lang="java"></span>
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407
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<td class="new_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC407" class="line" lang="java"> <span class="idiff left deletion"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv0</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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408
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<td class="new_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC408" class="line" lang="java"> <span class="idiff left deletion"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv1</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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409
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<td class="new_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC409" class="line" lang="java"> <span class="idiff left deletion"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv2</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">dRdv2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">][</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">)/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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410
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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="LC410" class="line" lang="java"> <span class="idiff left deletion"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">xi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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411
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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="LC411" class="line" lang="java"> <span class="idiff left deletion"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">yi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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412
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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="LC412" class="line" lang="java"> <span class="idiff left deletion"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;"><span class="idiff deletion">sim</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dz</span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">atomOverlap</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;"><span class="idiff deletion">zi</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">/</span></span><span class="mf" style="color: #099;"><span class="idiff right deletion">3.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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398
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC398" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv0</span><span class="o" style="font-weight: 600;">;</span></span>
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399
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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="LC399" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv1</span><span class="o" style="font-weight: 600;">;</span></span>
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400
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC400" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dv2</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC401" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dx</span><span class="o" style="font-weight: 600;">;</span></span>
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402
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC402" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dy</span><span class="o" style="font-weight: 600;">;</span></span>
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403
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC403" class="line" lang="java"> <span class="idiff left right addition"> </span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dz</span><span class="o" style="font-weight: 600;">;</span></span>
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404
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC405" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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406
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC406" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -421,6 +412,7 @@ public class EvaluableOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC412" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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413
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC413" class="line" lang="java"></span>
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414
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC414" class="line" lang="java"></span>
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424
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416
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">EvaluableOverlap</span> <span class="nf" style="color: #900; font-weight: 600;">clone</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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425
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417
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC417" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">EvaluableOverlap</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">);</span></span>
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418
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC418" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#7e9910936f51c5883dc0e383abac0f0720181e30"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/PPTriangle.java</strong></a>
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1
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.phesa.pharmacophore</span><span class="o" style="font-weight: 600;">;</span></span>
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2
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>
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3
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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="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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4
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC4" class="line" lang="java"></span>
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5
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.calc.Matrix</span><span class="o" style="font-weight: 600;">;</span></span>
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6
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Coordinates</span><span class="o" style="font-weight: 600;">;</span></span>
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7
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.alignment3d.transformation.Rotation</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -38,6 +36,7 @@ public class PPTriangle {</td>
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38
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="java"> <span class="n" style="color: #333;">dirs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pp3</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getDirectionality</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="java"> <span class="n" style="color: #333;">canonizeOrder</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="java"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">canonizeOrder</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,12 +71,12 @@ public class PPTriangle {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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75
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left deletion">0</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//d1<span class="idiff right deletion">2<=d1</span>3</span></span>
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74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left addition">1</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//d1<span class="idiff right addition">3>d2</span>3</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="java"> <span class="n" style="color: #333;">swap</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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76
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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78
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77
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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79
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78
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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80
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<td class="new_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC80" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left deletion">1</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//d12<span class="idiff right deletion"><=</span>d13</span></span>
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<td class="old_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff left addition">0</span></span><span class="o" style="font-weight: 600;">]></span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//d12<span class="idiff right addition">></span>d13</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="n" style="color: #333;">swap</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">);</span></span>
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81
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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82
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,31 +84,29 @@ public class PPTriangle {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">swap</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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87
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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">diold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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89
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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">dirold</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dirs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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90
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88
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <span class="n" style="color: #333;">dirs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dirs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]);</span></span>
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91
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89
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">];</span></span>
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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="LC92" class="line" lang="java"> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">];</span></span>
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90
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiold</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diold</span><span class="o" style="font-weight: 600;">;</span></span>
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">dirs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dirold</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">ciold</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]);</span> </span>
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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">
94
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ciold</span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion">Coordinates</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">])</span>;</span></span>
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]);</span></span><span class="idiff right deletion"> </span></span>
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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="LC99" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">);</span></span><span class="idiff right deletion"> </span></span>
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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">
96
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left addition">double</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">]</span>;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">];</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">;</span></span></span>
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100
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99
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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101
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<td class="new_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC101" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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103
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion">Coordinates</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">])</span>;</span></span>
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104
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]);</span></span><span class="idiff right deletion"> </span></span>
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105
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">);</span></span><span class="idiff right deletion"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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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="LC101" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left addition">double</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">]</span>;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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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="LC102" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">];</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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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="LC103" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">;</span></span></span>
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106
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104
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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107
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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="LC107" class="line" lang="java"> </span>
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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="new_line diff-line-num" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC105" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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109
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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC109" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left deletion">Coordinates</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">])</span>;</span></span>
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110
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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="LC110" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]);</span></span><span class="idiff right deletion"> </span></span>
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111
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<td class="new_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC111" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left deletion">c</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">new</span></span><span class="idiff deletion"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff deletion">Coordinates</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ciold</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">);</span></span><span class="idiff right deletion"> </span></span>
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112
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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="LC112" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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106
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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="LC106" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left addition">double</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">]</span>;</span></span>
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107
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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="LC107" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">];</span></span></span>
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108
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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="LC108" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left addition">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">[</span></span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">]=</span></span><span class="n" style="color: #333;"><span class="idiff addition">dold</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">;</span></span></span>
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109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span><span class="idiff left right addition"> </span></span>
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113
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110
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> </span>
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111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="java"></span>
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#1a2948d1808e5bf4b5ae448818a4c444d9b4870a"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +162,7 @@ public class PharmacophoreCalculator {</td>
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162
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162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isDonorHydrogen</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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163
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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164
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<td class="new_line diff-line-num" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
164
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC164" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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165
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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</span><span class="o" style="font-weight: 600;">)>=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">7</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion">//charge is not positive -> no acceptor</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</span><span class="o" style="font-weight: 600;">)>=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">7</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dh</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> </span>
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166
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<td class="new_line diff-line-num" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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167
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167
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC167" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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168
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168
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#86999a714d04156d77451e9ca14c33aff8a98a76"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/PPGaussian.java</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +86,7 @@ public class PPGaussian extends Gaussian3D {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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87
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java"></span>
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88
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PPGaussian</span> <span class="n" style="color: #333;">ppGauss2</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Coordinates</span> <span class="n" style="color: #333;">directionality</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left deletion">getInteractionSimilarity</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ppGauss2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">)</span>;</span></span>
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89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ppSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;"><span class="idiff left right addition">1.0</span></span><span class="o" style="font-weight: 600;">;</span></span>
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90
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">vectorSim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getVectorSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppGauss2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">directionality</span><span class="o" style="font-weight: 600;">);</span></span>
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91
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">vectorSim</span><span class="o" style="font-weight: 600;">)+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ppSimilarity</span><span class="o" style="font-weight: 600;">)/</span><span class="mf" style="color: #099;">3.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">similarity</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#3dbbe7b950b7f9e3cf1fa45df59255c90fc56046"><strong>src/main/java/com/actelion/research/chem/phesaflex/EvaluableFlexibleOverlap.java</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -382,13 +382,13 @@ public class EvaluableFlexibleOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC382" class="line" lang="java"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC383" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC384" class="line" lang="java"> <span class="n" style="color: #333;">totalOverlap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC385" class="line" lang="java"> <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">*-</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC385" class="line" lang="java"> <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">*-</span><span class="mi" style="color: #099;"><span class="idiff left addition">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right addition">*</span></span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitAt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC386" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC388" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC389" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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390
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC390" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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391
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<td class="new_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC391" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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389
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC389" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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390
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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391
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC391" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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392
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC392" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC394" class="line" lang="java"> </span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -420,9 +420,9 @@ public class EvaluableFlexibleOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC421" class="line" lang="java"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC422" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC423" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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424
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<td class="new_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC424" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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425
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC425" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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423
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC423" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC424" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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425
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC425" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC426" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC428" class="line" lang="java"> </span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -473,9 +473,9 @@ public class EvaluableFlexibleOverlap implements Evaluable {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC473" class="line" lang="java"> <span class="n" style="color: #333;">atomOverlap</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC474" class="line" lang="java"> <span class="n" style="color: #333;">totalOverlap</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC475" class="line" lang="java"> <span class="n" style="color: #333;">gradientPrefactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atomOverlap</span><span class="o" style="font-weight: 600;">*-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">refPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()*</span><span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()/(</span><span class="n" style="color: #333;">refPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">()+</span><span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getWidth</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC476" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC477" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC478" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;"><span class="idiff left deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">*</span></span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;"><span class="idiff deletion">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right deletion">*</span></span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC476" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">xi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC477" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">yj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">yi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC478" class="line" lang="java"> <span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">zj</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">zi</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">gradientPrefactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC479" class="line" lang="java"> <span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPharmacophorePoint</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getDirectionalityDerivativeCartesian</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">grad</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">coords</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">fitPP</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPharmacophorePoint</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getDirectionality</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">);</span> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC481" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#88f7248516cf1351766ec9d506223745b62982c0"><strong>src/main/java/com/actelion/research/chem/reaction/Reactor.java</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -633,36 +633,6 @@ public class Reactor {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC634" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC635" class="line" lang="java"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC636" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC637" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">esrGroupsChanged</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC638" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC639" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy atom parities of unmapped generic product atoms and potentially convert them according to new neighbour order</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC640" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC641" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC642" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC643" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC644" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC645" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mIsReactionCenter</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProductNo</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC646" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRxnParityHint</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC647" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">useConfigurationFromGenericReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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648
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC648" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC649" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC650" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span></span>
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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="LC651" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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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="LC652" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC653" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRGroup</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC654" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cESRTypeAnd</span><span class="o" style="font-weight: 600;">)</span></span>
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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="LC655" class="line" lang="java"> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountAND</span><span class="o" style="font-weight: 600;">;</span></span>
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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="LC656" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cESRTypeOr</span><span class="o" style="font-weight: 600;">)</span></span>
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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="LC657" class="line" lang="java"> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountOR</span><span class="o" style="font-weight: 600;">;</span></span>
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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="LC659" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomESR</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">esrType</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">esrGroup</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC660" class="line" lang="java"> <span class="n" style="color: #333;">esrGroupsChanged</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC636" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy all bonds of generic product, except for bridge bonds</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC637" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gpBond</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">gpBond</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">gpBond</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC638" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isBondBridge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gpBond</span><span class="o" style="font-weight: 600;">))</span></span>
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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">@@ -722,11 +692,51 @@ public class Reactor {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC692" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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693
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC693" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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694
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC694" class="line" lang="java"></span>
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695
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC695" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperNeighbours</span><span class="o" style="font-weight: 600;">);</span></span>
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696
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC696" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
697
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC697" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>
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698
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC698" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">esrGroupsChanged</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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699
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC699" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
700
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC700" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy atom parities of unmapped generic product atoms and potentially convert them according to new neighbour order</span></span>
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701
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC701" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
702
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC702" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>
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703
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC703" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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704
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC704" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
705
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC705" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy corrected atom parities of generic product reaction center atoms</span></span>
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706
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC706" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mIsReactionCenter</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProductNo</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span></span>
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707
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC707" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">copyConfigurationFromGenericProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
708
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC708" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
709
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC709" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
710
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC710" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span></span>
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711
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC711" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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712
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC712" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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713
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC713" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRGroup</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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714
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC714" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cESRTypeAnd</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC715" class="line" lang="java"> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountAND</span><span class="o" style="font-weight: 600;">;</span></span>
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716
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC716" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">esrType</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cESRTypeOr</span><span class="o" style="font-weight: 600;">)</span></span>
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717
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC717" class="line" lang="java"> <span class="n" style="color: #333;">esrGroup</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esrGroupCountOR</span><span class="o" style="font-weight: 600;">;</span></span>
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718
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719
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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="LC719" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomESR</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">esrType</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">esrGroup</span><span class="o" style="font-weight: 600;">);</span></span>
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720
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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="LC720" class="line" lang="java"> <span class="n" style="color: #333;">esrGroupsChanged</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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721
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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="LC721" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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722
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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="LC722" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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723
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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="LC723" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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724
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725
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725
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC725" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">esrGroupsChanged</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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726
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726
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC726" class="line" lang="java"> <span class="n" style="color: #333;">esrGroupCountAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">renumberESRGroups</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cESRTypeAnd</span><span class="o" style="font-weight: 600;">);</span></span>
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727
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727
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC727" class="line" lang="java"> <span class="n" style="color: #333;">esrGroupCountOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">renumberESRGroups</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cESRTypeOr</span><span class="o" style="font-weight: 600;">);</span></span>
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728
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC728" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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729
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729
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC729" class="line" lang="java"></span>
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730
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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="LC730" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// copy pseudo parities of generic product if there are no parity hints</span></span>
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<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
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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="LC731" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pseudoParityHandled</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>
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732
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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="LC732" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span></span>
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<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
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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="LC733" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mIsReactionCenter</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProductNo</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
734
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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="LC734" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pseudoParityHandled</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
735
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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="LC735" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
736
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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="LC736" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRxnParityHint</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
737
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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="LC737" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
738
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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="LC738" class="line" lang="java"> <span class="n" style="color: #333;">copyPseudoParitiesFromGenericProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pseudoParityHandled</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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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="LC739" class="line" lang="java"></span>
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730
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740
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC740" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// delete all fragments from product which are not connected to generic product</span></span>
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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
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<td class="new_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
741
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC741" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">includeAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>
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732
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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">
742
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC742" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -788,22 +798,101 @@ public class Reactor {</td>
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788
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<td class="new_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
798
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC798" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// return false;</span></span>
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789
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<td class="new_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
799
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC799" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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790
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800
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC800" class="line" lang="java"></span>
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<td class="old_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
791
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC791" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">useConfigurationFromGenericReaction</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
792
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC792" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
793
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC793" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
794
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC794" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactants</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
795
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC795" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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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="LC796" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactantAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">reactantAtom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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797
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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="LC797" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mapNo</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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798
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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="LC798" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If the reactant atom is explicitly set to match the stereo center,</span></span>
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC799" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we assume that the product also contains a well specified stereo center to be copied.</span></span>
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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="LC800" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFMatchStereo</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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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="LC801" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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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="LC802" class="line" lang="java"></span>
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC803" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If we have an explicit change of the ESR type, we also assume that this is intentional</span></span>
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804
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<td class="new_line diff-line-num old" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC804" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// and copy the stereo configuration from the product.</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC805" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">))</span></span>
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806
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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="LC806" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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801
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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="LC801" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">copyPseudoParitiesFromGenericProduct</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">firstPseudoParityAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pseudoParityHandled</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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802
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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="LC802" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">relatedAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>
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803
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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="LC803" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">relatedAtomCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRelatedPseudoParityAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">firstPseudoParityAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">);</span></span>
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804
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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="LC804" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
805
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC805" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">matchingAbsParityFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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806
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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="LC806" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">invertedAbsParityFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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807
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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="LC807" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]></span> <span class="n" style="color: #333;">pseudoParityList</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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808
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC808" class="line" lang="java"></span>
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809
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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="LC809" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">relatedAtomCount</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
810
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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="LC810" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
811
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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="LC811" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">translateTHParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
812
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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="LC812" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
813
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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="LC813" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
814
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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="LC814" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Real product parities may not be pseudo if the real reactant has additional features.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
815
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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="LC815" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// These are given and cannot be inverted because of pseudo parity requirements in the generic product.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
816
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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="LC816" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We check for compatibility and only apply relative pseudo parities, if possible.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
817
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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="LC817" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
818
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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="LC818" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">parity</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
819
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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="LC819" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">parity</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
820
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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="LC820" class="line" lang="java"> <span class="n" style="color: #333;">matchingAbsParityFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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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="LC821" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
822
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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="LC822" class="line" lang="java"> <span class="n" style="color: #333;">invertedAbsParityFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
823
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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="LC823" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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824
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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="LC824" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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825
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<td class="new_line diff-line-num new" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
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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="LC826" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We collect a list of all pseudo parity atoms with their translated pseudo parities.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
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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="LC827" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If where we have existing real parities on the same atoms and if these</span></span>
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828
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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="LC828" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// - either match the required pseudo parities, then we can add pseudo parities to atoms without a real parity</span></span>
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<td class="new_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
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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="LC829" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// - or match the all inverted pseudo parities, then we can add inverted pseudo parities to atoms without a real parity</span></span>
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830
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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="LC830" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
831
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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="LC831" class="line" lang="java"> <span class="n" style="color: #333;">ps</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
832
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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="LC832" class="line" lang="java"> <span class="n" style="color: #333;">ps</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pseudoParity</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
833
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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="LC833" class="line" lang="java"> <span class="n" style="color: #333;">pseudoParityList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ps</span><span class="o" style="font-weight: 600;">);</span></span>
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834
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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="LC834" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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835
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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="LC835" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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836
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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="LC836" class="line" lang="java"></span>
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<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
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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="LC837" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pseudoParityList</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">matchingAbsParityFound</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">invertedAbsParityFound</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
838
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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="LC838" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pseudoParity</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pseudoParityList</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
839
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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="LC839" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pseudoParity</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
840
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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="LC840" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">invertedAbsParityFound</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
841
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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="LC841" class="line" lang="java"> <span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ps</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity2</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParity1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
842
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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="LC842" class="line" lang="java"> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newAtomNo</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pseudoParity</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]],</span> <span class="n" style="color: #333;">ps</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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843
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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="LC843" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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844
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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="LC844" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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845
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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="LC845" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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846
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<td class="new_line diff-line-num new" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
847
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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="LC847" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">findRelatedPseudoParityAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">firstAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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848
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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="LC848" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">isRelated</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
849
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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="LC849" class="line" lang="java"> <span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstAtom</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
850
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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="LC850" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">relatedAtoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
851
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC851" class="line" lang="java"> <span class="n" style="color: #333;">isRelated</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">firstAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
852
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC852" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">relatedAtoms</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
853
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC853" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">]);</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
854
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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="LC854" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connBond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">],</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
855
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC855" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isRingBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connBond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connBond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isBINAPChiralityBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connBond</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
856
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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="LC856" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">current</span><span class="o" style="font-weight: 600;">],</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
857
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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="LC857" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">isRelated</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
858
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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="LC858" class="line" lang="java"> <span class="n" style="color: #333;">relatedAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">relatedAtoms</span><span class="o" style="font-weight: 600;">++]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
859
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC859" class="line" lang="java"> <span class="n" style="color: #333;">isRelated</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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860
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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="LC860" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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861
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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="LC861" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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862
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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="LC862" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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863
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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="LC863" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
864
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC864" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">relatedAtoms</span><span class="o" style="font-weight: 600;">;</span></span>
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865
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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="LC865" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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866
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867
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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="LC867" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">copyConfigurationFromGenericProduct</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
868
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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="LC868" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If we have a hint on the generic product atom, then we have already taken the generic reactant atom parity.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
869
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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="LC869" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Otherwise, if we have a stereo center on the generic product atom, we may consider copying that...</span></span>
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870
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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="LC870" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomParity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomParityNone</span></span>
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871
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC871" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAtomParityPseudo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">)</span></span>
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872
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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="LC872" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFRxnParityHint</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
873
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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="LC873" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">);</span></span>
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874
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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="LC874" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapNo</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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875
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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="LC875" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactants</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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876
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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="LC876" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">genericReactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mGenericReaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactant</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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877
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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="LC877" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genericReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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878
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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="LC878" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mapNo</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
879
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC879" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If the generic reactant atom is not even a pseudo stereo center,</span></span>
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880
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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="LC880" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// then we assume that any product configuration is intentional and correct</span></span>
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881
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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="LC881" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">productAtom</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
882
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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="LC882" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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883
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<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
884
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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="LC884" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If the reactant atom is explicitly set to match the stereo center,</span></span>
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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="LC885" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we assume that the product also contains a well specified stereo center to be copied.</span></span>
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886
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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="LC886" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">genericReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFMatchStereo</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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887
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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="LC887" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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888
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889
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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="LC889" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If we have an explicit change of the ESR type, we also assume that this is intentional</span></span>
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890
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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="LC890" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// and copy the stereo configuration from the product.</span></span>
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891
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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="LC891" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantAtom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">genericProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomESRType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genericProductAtom</span><span class="o" style="font-weight: 600;">))</span></span>
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892
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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="LC892" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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893
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894
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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="LC894" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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895
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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="LC895" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC896" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC897" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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898
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC898" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#b23ac1794ae5ae3ca39c5fd7604dd429cdcd2393"><strong>src/main/java/com/actelion/research/gui/editor/AtomQueryFeatureDialogBuilder.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -169,7 +169,7 @@ public class AtomQueryFeatureDialogBuilder implements DialogEventConsumer {</td>
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169
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169
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">includeReactionHints</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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170
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170
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="java"> <span class="n" style="color: #333;">mDialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">createLabel</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Stereo center hint for product:"</span><span class="o" style="font-weight: 600;">),</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">27</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">27</span><span class="o" style="font-weight: 600;">);</span></span>
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171
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171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">mChoiceReactionParityHint</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mDialog</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">createComboBox</span><span class="o" style="font-weight: 600;">();</span></span>
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172
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<td class="new_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion">Make unknown in</span> product"</span><span class="o" style="font-weight: 600;">);</span></span>
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172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right addition">Copy from generic</span> product"</span><span class="o" style="font-weight: 600;">);</span></span>
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173
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173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="java"> <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Keep reactant configuration"</span><span class="o" style="font-weight: 600;">);</span></span>
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174
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="java"> <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Invert reactant configuration"</span><span class="o" style="font-weight: 600;">);</span></span>
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175
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175
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">mChoiceReactionParityHint</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addItem</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Racemise configuration"</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/commit/b7b040369c116f28ee63fc223e33bd2cd7e5a1ad#98ac8c26d9087ed4dfec10db567462ed5ca7be22"><strong>src/main/java/com/actelion/research/util/BrowserControl.java</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.util</span><span class="o" style="font-weight: 600;">;</span></span>
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>
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3
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.net.URI</span><span class="o" style="font-weight: 600;">;</span></span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.net.URISyntaxException</span><span class="o" style="font-weight: 600;">;</span></span>
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7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="java"></span>
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BrowserControl</span> <span class="o" style="font-weight: 600;">{</span></span>
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +24,19 @@ public class BrowserControl {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Platform</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isMacintosh</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="java"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">OSX_PATH</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Runtime</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRuntime</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">exec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC24" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isDesktopSupported</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Desktop</span> <span class="n" style="color: #333;">desktop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getDesktop</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isSupported</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Action</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">BROWSE</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="java"> <span class="n" style="color: #333;">desktop</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">browse</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="no" style="color: #008080;">URI</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">URISyntaxException</span> <span class="n" style="color: #333;">use</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="java"> <span class="n" style="color: #333;">use</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>
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36
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37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/* else {</span></span>
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40
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> // Under Unix, Netscape has to be running for the "-remote"</span></span>
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26
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41
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> // command to work. So, we try sending the command and</span></span>
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42
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> // check for an exit value. If the exit command is 0,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +59,7 @@ public class BrowserControl {</td>
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59
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> + "'");</span></span>
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60
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> System.err.println("Caught: " + x);</span></span>
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61
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> }<span class="idiff left right addition">*/</span></span></span>
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48
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63
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">IOException</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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49
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64
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// couldn't exec browser</span></span>
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50
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65
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Could not invoke browser, command="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,8 +85,8 @@ public class BrowserControl {</td>
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70
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85
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">UNIX_PATH</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"firefox"</span><span class="o" style="font-weight: 600;">;</span></span>
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71
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86
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="java"></span>
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72
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// The flag to display a url.</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">UNIX_PARAM_START</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-remote \"openURL("</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
74
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<td class="new_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC74" class="line" lang="java"><span class="idiff left right deletion"> </span> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">UNIX_PARAM_END</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">")\""</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC88" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span> private static final String UNIX_PARAM_START = "-remote \"openURL(";</span></span>
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<td class="old_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC89" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span> private static final String UNIX_PARAM_END = ")\"";</span></span>
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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
75
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90
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="java"></span>
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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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91
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// The open command MacOSX.</span></span>
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<td class="old_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
77
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92
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">OSX_PATH</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"open"</span><span class="o" style="font-weight: 600;">;</span></span>
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