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<h3>
Andrius Merkys pushed to branch master
at <a href="https://salsa.debian.org/java-team/openchemlib">Debian Java Maintainers / openchemlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/c748310021be5f55cab27dda4ebd1a5e0b1b3127">c7483100</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-14T08:24:53-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2022.1.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/da9e9df2e84003c7e8bc626adc0bff27833890c6">da9e9df2</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-14T08:25:04-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2022.1.0+dfsg'
Update to upstream version '2022.1.0+dfsg'
with Debian dir ef548b12bb364c21d8caa2976ef8cb50dadb8452</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/73e9db95770d79813a001d41465a0fa289f71d61">73e9db95</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-14T08:26:36-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bumping copyright years.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/4569bc2804db071f8f402d61d54cc259ee7da279">4569bc28</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-14T08:26:53-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog for 2022.1.0+dfsg-1 release
</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">
pom.xml
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<li class="file-stats">
<a href="#3f5337087ac5d25a71e6430314d07204f2471c0d">
src/main/java/com/actelion/research/chem/AbstractDepictor.java
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<li class="file-stats">
<a href="#c5295e693234df21de8d1950ded55cfb223e08f3">
src/main/java/com/actelion/research/chem/chemicalspaces/ChemicalSpaceCreator.java
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<li class="file-stats">
<a href="#8297ca073cc662966e0530ff788a1c96def3c515">
src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonCreator.java
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<li class="file-stats">
<a href="#2324bbf7db1501a1bb2aaae4a1db707a20b5f9b1">
src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java
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<li class="file-stats">
<a href="#fd33d2182c0e0f9cb9c01b5b6cd8a61b579abeb0">
src/main/java/com/actelion/research/chem/coords/InventorFragment.java
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<li class="file-stats">
<a href="#32943cdb0e248053d475693d07df3b36f28244bf">
src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java
</a>
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<li class="file-stats">
<a href="#53644f8fdeac019d663bcf78d973c6c33e7e0b47">
src/main/java/com/actelion/research/chem/descriptor/flexophore/example/MatchFlexophoreNodesMain.java
</a>
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<li class="file-stats">
<a href="#cf40108c840165d004c28f26bbfd06fa9b0a6a27">
src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
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<li class="file-stats">
<a href="#b913e9301eb349935afa9f9053995d0205bb3b8e">
src/main/java/com/actelion/research/chem/io/Mol2FileParser.java
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<li class="file-stats">
<a href="#22a48b6441e4880a80fbbf8c21720f71585f7170">
src/main/java/com/actelion/research/gui/JStructureView.java
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<li class="file-stats">
<a href="#5747d6186b6b4a54bba0c10bc9aa0e5835c7c31f">
src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">openchemlib (2022.1.0+dfsg-1) unstable; urgency=medium</span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 2022.1.0+dfsg</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Bumping copyright years.</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andrius Merkys <merkys@debian.org> Fri, 14 Jan 2022 08:26:48 -0500</span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">openchemlib (2021.12.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version 2021.12.0+dfsg</span>
</pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -5,11 +5,11 @@ Files-Excluded:</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> src/main/java/info</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Copyright: 1997-202<span class="idiff left right">1</span>, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Copyright: 1997-202<span class="idiff left right">2</span>, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Copyright: 2020-202<span class="idiff left right">1</span>, Andrius Merkys <merkys@debian.org></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Copyright: 2020-202<span class="idiff left right">2</span>, Andrius Merkys <merkys@debian.org></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Files: src/main/java/com/actelion/research/calc/statistics/median/MedianStatisticFunctions.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">@@ -49,7 +49,7 @@ Files: src/main/java/com/actelion/research/calc/statistics/median/MedianStatisti</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> src/main/java/com/actelion/research/gui/JEditableStructureView.java</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> src/main/java/com/actelion/research/gui/JStructureView.java</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> src/main/java/com/actelion/research/gui/StructureListener.java</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">Copyright: 1997-202<span class="idiff left right">1</span>, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Copyright: 1997-202<span class="idiff left right">2</span>, Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">License: BSD-3-clause</span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> (eg. 2016.4.1 for second release in Apr 2016)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"> --></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="xml"> <span class="nt" style="color: #000080;"><version></span>202<span class="idiff left">1</span>.1<span class="idiff right">2</span>.0<span class="nt" style="color: #000080;"></version></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="xml"> <span class="nt" style="color: #000080;"><version></span>202<span class="idiff left right">2</span>.1.0<span class="nt" style="color: #000080;"></version></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="xml"> <span class="nt" style="color: #000080;"><name></span>OpenChemLib<span class="nt" style="color: #000080;"></name></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="xml"> <span class="nt" style="color: #000080;"><description></span>Open Source Chemistry Library<span class="nt" style="color: #000080;"></description></span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,7 +195,7 @@</td>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="xml"> <span class="nt" style="color: #000080;"><connection></span>scm:git:git@github.com:Actelion/openchemlib.git<span class="nt" style="color: #000080;"></connection></span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="xml"> <span class="nt" style="color: #000080;"><developerConnection></span>scm:git:git@github.com:Actelion/openchemlib.git<span class="nt" style="color: #000080;"></developerConnection></span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="xml"> <span class="nt" style="color: #000080;"><url></span>https://github.com/Actelion/openchemlib<span class="nt" style="color: #000080;"></url></span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-202<span class="idiff left">1</span>.1<span class="idiff right">2</span>.0<span class="nt" style="color: #000080;"></tag></span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-202<span class="idiff left right">2</span>.1.0<span class="nt" style="color: #000080;"></tag></span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="xml"> <span class="nt" style="color: #000080;"></scm></span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="xml"> <span class="nt" style="color: #000080;"><distributionManagement></span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#3f5337087ac5d25a71e6430314d07204f2471c0d"><strong>src/main/java/com/actelion/research/chem/AbstractDepictor.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">@@ -162,7 +162,7 @@ public abstract class AbstractDepictor<T> {</td>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Rectangle2D</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Double</span> <span class="n" style="color: #333;">mBoundingRect</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;">Rectangle2D</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Double</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">DepictorTransformation</span> <span class="n" style="color: #333;">mTransformation</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Point2D</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Double</span> <span class="n" style="color: #333;">mChiralTextLocation</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAtomColor</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAtomColor</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">mAtomHiliteColor</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAtomText</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Point2D</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAlternativeCoords</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="n" style="color: #333;">mOverruleForeground</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mOverruleBackground</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mBondBGHiliteColor</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mBondFGHiliteColor</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">@@ -198,13 +198,6 @@ public abstract class AbstractDepictor<T> {</td>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/* @Deprecated</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> public void setDefaultColor(int c) {</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> mStandardForegroundColor = c;</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> updateBondHiliteColor();</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * If the foreground color is set, the molecule is drawn in the foreground</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * color except for non carbon atoms, which are drawn in atomicNo specific</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">@@ -235,6 +228,16 @@ public abstract class AbstractDepictor<T> {</td>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * If you want this tructure view to also draw an atom background with specific colors for every atom,</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * then you need to call this method before calling paint().</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param argb values with a==0 are not considered (may be null)</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setAtomHighlightColors</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;">argb</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java"> <span class="n" style="color: #333;">mAtomHiliteColor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argb</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setTransformation</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DepictorTransformation</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="java"> <span class="n" style="color: #333;">mTransformation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">;</span></span>
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<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="diff-line-num unfold js-unfold new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -561,6 +564,7 @@ public abstract class AbstractDepictor<T> {</td>
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561
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="java"></span>
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="java"> <span class="n" style="color: #333;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">COLOR_INITIALIZE</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// to initialize the color tracking mechanism</span></span>
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="java"></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="java"> <span class="n" style="color: #333;">hiliteAtomBackgrounds</span><span class="o" style="font-weight: 600;">();</span></span>
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="java"> <span class="n" style="color: #333;">hiliteExcludeGroups</span><span class="o" style="font-weight: 600;">();</span></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="java"> <span class="n" style="color: #333;">hiliteBondBackgrounds</span><span class="o" style="font-weight: 600;">();</span></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="java"> <span class="n" style="color: #333;">indicateQueryFeatures</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="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -593,7 +597,7 @@ public abstract class AbstractDepictor<T> {</td>
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593
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597
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<pre style="margin: 0;"> <span id="LC597" 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;">mDisplayMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cDModeNoImplicitAtomLabelColors</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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594
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomList</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="kc" style="font-weight: 600;">null</span></span>
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595
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</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="no" style="color: #008080;">ATOM_LABEL_COLOR</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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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="java"> <span class="n" style="color: #333;">setRGBColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getContrastColor</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">ATOM_LABEL_COLOR</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)]));</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="java"> <span class="n" style="color: #333;">setRGBColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getContrastColor</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">ATOM_LABEL_COLOR</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomicNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="java"> <span class="n" style="color: #333;">mpDrawAtom</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;">esrGroupMemberCount</span><span class="o" style="font-weight: 600;">);</span></span>
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602
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="java"> <span class="n" style="color: #333;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mStandardForegroundColor</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC603" 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="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -607,9 +611,10 @@ public abstract class AbstractDepictor<T> {</td>
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607
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="java"></span>
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="nf" style="color: #900; font-weight: 600;">getContrastColor</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;">rgb</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="nf" style="color: #900; font-weight: 600;">getContrastColor</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;">rgb</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">atom</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="n" style="color: #333;">bg</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mOverruleBackground</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;">mOverruleBackground</span></span>
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612
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<pre style="margin: 0;">-<span id="LC612" 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;">mCustomBackground</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;">mCustomBackground</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">WHITE</span><span class="o" style="font-weight: 600;">;</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" 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;">mAtomHiliteColor</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xFF000000</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 class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">])</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" 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;">mCustomBackground</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;">mCustomBackground</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">WHITE</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Color</span> <span class="n" style="color: #333;">fg</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;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rgb</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">ColorHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getContrastColor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fg</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bg</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC620" 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">@@ -666,6 +671,22 @@ public abstract class AbstractDepictor<T> {</td>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC674" 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;">hiliteAtomBackgrounds</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC675" 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;">mAtomHiliteColor</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span></span>
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<pre style="margin: 0;">+<span id="LC676" 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;">mAtomHiliteColor</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;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()))</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mTransformation</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getScaling</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAverageBondLength</span><span class="o" style="font-weight: 600;">();</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r</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;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" 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;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xFF000000</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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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="java"> <span class="n" style="color: #333;">setColor</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;">Color</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">]));</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="java"> <span class="n" style="color: #333;">fillCircle</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getAtomX</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)-</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">getAtomY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)-</span><span class="n" style="color: #333;">r</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>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC690" 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;">hiliteBondBackgrounds</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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691
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="java"> <span class="n" style="color: #333;">setLineWidth</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;">mpBondHiliteRadius</span><span class="o" style="font-weight: 600;">);</span></span>
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">DepictorLine</span> <span class="n" style="color: #333;">line</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;">DepictorLine</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="1592" style="width: 35px; color: rgba(0,0,0,0.3); 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="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1592,7 +1613,6 @@ public abstract class AbstractDepictor<T> {</td>
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1592
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1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mIsValidatingView</span><span class="o" style="font-weight: 600;">)</span></span>
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1593
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="java"> <span class="n" style="color: #333;">onDrawAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomLabel</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">getAtomX</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">getAtomY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">));</span></span>
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1594
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="java"></span>
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1595
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<pre style="margin: 0;">-<span id="LC1595" class="line" lang="java"></span>
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1596
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">propStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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1597
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1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1598
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<td class="new_line diff-line-num" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">valStr</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;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomCharge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1611,8 +1631,6 @@ public abstract class AbstractDepictor<T> {</td>
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1611
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<td class="new_line diff-line-num" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="java"> <span class="n" style="color: #333;">isoStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isoStr</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"!a"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1612
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<td class="new_line diff-line-num" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">queryFeatures</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFMoreNeighbours</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1613
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1633
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="java"> <span class="n" style="color: #333;">isoStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isoStr</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"s"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1614
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<td class="new_line diff-line-num old" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1614" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if ((queryFeatures & Molecule.cAtomQFNoMoreNeighbours) != 0)</span></span>
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1615
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<td class="new_line diff-line-num old" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1615" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// isoStr = append(isoStr, "!s");</span></span>
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1616
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1634
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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">queryFeatures</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFHydrogen</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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1617
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1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hydrogens</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">queryFeatures</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFHydrogen</span><span class="o" style="font-weight: 600;">);</span></span>
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1618
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1636
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<pre style="margin: 0;"> <span id="LC1636" 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;">hydrogens</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;">cAtomQFNot1Hydrogen</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;">cAtomQFNot2Hydrogen</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;">cAtomQFNot3Hydrogen</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="1766" style="width: 35px; color: rgba(0,0,0,0.3); 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="1784" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1766,11 +1784,6 @@ public abstract class AbstractDepictor<T> {</td>
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<td class="old_line diff-line-num" data-linenumber="1766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1766
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1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hydrogensToAdd</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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1767
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1785
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<pre style="margin: 0;"> <span id="LC1785" 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;">mDisplayMode</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cDModeNoImplicitHydrogen</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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1768
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1786
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<pre style="margin: 0;"> <span id="LC1786" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFragment</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="1769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1769
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<td class="new_line diff-line-num old" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1769" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/* if ((mMol.getAtomicNo(atom) != 6</span></span>
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1770
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<td class="new_line diff-line-num old" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1770" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> || !mAtomIsConnected[atom]</span></span>
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1771
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<pre style="margin: 0;">-<span id="LC1771" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> || mMol.getAtomCharge(atom) != 0</span></span>
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1772
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<pre style="margin: 0;">-<span id="LC1772" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> || mMol.getAtomRadical(atom) != 0)</span></span>
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1773
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<pre style="margin: 0;">-<span id="LC1773" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> && (mMol.getAtomQueryFeatures(atom) & Molecule.cAtomQFNoMoreNeighbours) != 0)*/</span></span>
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtomQueryFeatures</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cAtomQFNoMoreNeighbours</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC1788" class="line" lang="java"> <span class="n" style="color: #333;">hydrogensToAdd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getImplicitHydrogens</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC1789" 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/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#c5295e693234df21de8d1950ded55cfb223e08f3"><strong>src/main/java/com/actelion/research/chem/chemicalspaces/ChemicalSpaceCreator.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">@@ -82,13 +82,13 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">create</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Reaction</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">allSynthonTransformations</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</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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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="n" style="color: #333;">generateSynthonTransformations</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">allSynthonTransformations</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ConcurrentMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">processedToOrigIDCode</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;">ConcurrentHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ConcurrentMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333;">reactionsWithSynthons</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;">ConcurrentHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>>>();</span> </span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">processBuildingBlocks</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;">bbs</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">processedToOrigIDCode</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">functionalizations</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">fps</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;">ConcurrentHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]>();</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">calcFragFPs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">processedToOrigIDCode</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">fps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Reaction</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">allSynthonTransformations</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;">ConcurrentHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</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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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">generateSynthonTransformations</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">allSynthonTransformations</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="n" style="color: #333;">generateSynthons</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">processedToOrigIDCode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reactionsWithSynthons</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">fps</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">allSynthonTransformations</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">generateCombinatoriaLibraries</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactionsWithSynthons</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allSynthonTransformations</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java"> <span class="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">@@ -225,8 +225,6 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="java"> <span class="n" style="color: #333;">processedToOrigIDCode</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">processedIDcode</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span> </span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//for (String processedIDcode : processedToOrigIDCode.keySet()) {</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//String processedIDcode= processedToOrigIDCode.get(idcode);</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IDCodeParser</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getCompactMolecule</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">processedIDcode</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fps</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;">processedIDcode</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="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -309,7 +307,7 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="java"> <span class="n" style="color: #333;">functionalizations</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;">rxn</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC309" 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;">Long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="java"> <span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">parallelS</span>tream</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java"> <span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">s</span>tream</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC311" 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;">reaction</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IDCodeParser</span> <span class="n" style="color: #333;">parser</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;">IDCodeParser</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">@@ -342,16 +340,16 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="java"> <span class="n" style="color: #333;">precursorLibs</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;">precursorLib</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">synthonTransformation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">synthonTransformations</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;">libraryReaction</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;">libReactantID</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="java"> <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="n" style="color: #333;">synthonTransformation</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProduct</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</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="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//offset is required to correctly mutate connector atoms</span></span></span>
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<pre style="margin: 0;"> <span id="LC344" 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;">a</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;">a</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC345" 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;">getAtomicNo</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;">92</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="java"> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC351" 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;">Reaction</span> <span class="n" style="color: #333;">reaction<span class="idiff left right">2</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC352" 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;">reaction<span class="idiff left right">2</span></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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> </span>
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<pre style="margin: 0;">+<span id="LC349" 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;">Reaction</span> <span class="n" style="color: #333;">reaction<span class="idiff left">Prec</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// precursor reaction</span></span></span>
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<pre style="margin: 0;">+<span id="LC350" 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;">reaction<span class="idiff left right">Prec</span></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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> </span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">precursorReaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reaction<span class="idiff left right">2</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">precursorReaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reaction<span class="idiff left right">Prec</span></span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC354" 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;">reactantID</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;">reactantID</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">reactionsWithSynthons</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;">precursorReaction</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;">reactantID</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC355" 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;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">libSynthons</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 match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -359,18 +357,17 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="java"> <span class="n" style="color: #333;">precursorName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">precursorReaction</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;">reactantID</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="java"> <span class="n" style="color: #333;">precursorLib</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">precursorName</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">libSynthons</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">dummyReactants</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">-<span id="LC362" 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;">l</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;">l</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">reaction<span class="idiff left right">2</span></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;">l</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC360" 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;">l</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;">l</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">reaction<span class="idiff left right">Prec</span></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;">l</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC361" 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;">l</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">reactantID</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC363" 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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<pre style="margin: 0;">-<span id="LC366" class="line" lang="java"> <span class="n" style="color: #333;">dummyReactants</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">reaction<span class="idiff left right">2</span></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;">l</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="java"> <span class="n" style="color: #333;">dummyReactants</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">reaction<span class="idiff left right">Prec</span></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;">l</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC367" 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;">reactionsWithSynthons</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;">precursorReaction</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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<pre style="margin: 0;"> <span id="LC368" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">precursorSynthons</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="java"> <span class="n" style="color: #333;">libSynthons</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;">precursorSynthons</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">twoConnectorSynthons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libSynthons</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;">reactantID</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</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="n" style="color: #333;">reactionsWithSynthons</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;">precursorReaction</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;">reactantID</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">@@ -378,7 +375,7 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">bb</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">synthon</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="java"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">synthon</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactedBB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dummyReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bb</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">reaction<span class="idiff left right">2</span></span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dummyReactants</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">reactantID</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">reactedBB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dummyReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bb</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">reaction<span class="idiff left right">Prec</span></span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">dummyReactants</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">reactantID</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactedBB</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we create candidate products by a "dummy reaction" and see if it still matches the substructure query of rxn1</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">@@ -392,7 +389,7 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC390" 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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<pre style="margin: 0;"> <span id="LC391" 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;">Reaction</span> <span class="n" style="color: #333;">functionalization</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">functionalizations</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC395" 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;">functionalizations</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reaction<span class="idiff left right">2</span></span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC392" 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;">functionalizations</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reaction<span class="idiff left right">Prec</span></span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//don't couple two functionalization reactions</span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SSSearcher</span> <span class="n" style="color: #333;">ssearcher</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;">SSSearcher</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="java"> <span class="n" style="color: #333;">ssearcher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setFragment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">functionalization</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="mi" style="color: #099;">0</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">@@ -409,8 +406,7 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC406" 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;">prod</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="java"> <span class="n" style="color: #333;">mutateConnectorAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">prod</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//for(int j=0;j<reactantID;j++) </span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// mutateConnectorAtoms(prod,offset); //mutate again, to prevent same linker atoms appearing in A and B (C) parts of same library</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">transformedSynthon</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transformToSynthon</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">synthonTransformation</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">prod</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC411" 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;">precursorLib</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">precursorName</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC412" 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;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">libSynthons2</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 match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -431,7 +427,6 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// if the BB that is used in the precursor step also matches any role of the second reaction, it is excluded (otherwise multiple products may be formed)</span></span>
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<pre style="margin: 0;"> <span id="LC431" 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;">reactionsWithSynthons</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;">precursorReaction</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 class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//get synthons from rxn1 that are compatible with the two-connector synthon</span></span>
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<pre style="margin: 0;"> <span id="LC432" 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;">j</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">reactantID</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">@@ -451,11 +446,9 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC447" 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;">compatible</span><span class="o" style="font-weight: 600;">)</span> <span class="c1" style="color: #998; font-style: italic;">//matches also role from second reaction --> don't add to library</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="java"> <span class="n" style="color: #333;">mutateConnectorAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mutatedSynthon</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//for(int k=0;k<reactantID;k++) </span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//mutateConnectorAtoms(mutatedSynthon,offset); //mutate again, to prevent same linker atoms appearing in A and B (C) parts of same library</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="java"> <span class="n" style="color: #333;">mutatedSynthons</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mutatedSynthon</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">compatibleSynthons</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;">s</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="java"> <span class="n" style="color: #333;">libSynthons</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 class="na" style="color: #008080;">putAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mutatedSynthons</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">@@ -470,9 +463,8 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="java"> <span class="n" style="color: #333;">combiLibrary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cleanup</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="java"> <span class="n" style="color: #333;">sizes</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;">combiLibrary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSize</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="java"> <span class="n" style="color: #333;">combiLibrary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">generateRandomProducts</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">300</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">productsWithBBs</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">productsWithReactions</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"generated"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" compounds"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="java"> <span class="n" style="color: #333;">combiLibrary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">generateRandomProducts</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">productsWithBBs</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">productsWithReactions</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC468" 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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<pre style="margin: 0;"> <span id="LC469" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="java"> <span class="n" style="color: #333;">writeCombinatorialLibrary</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">combiLibrary</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">@@ -743,10 +735,12 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="java"> <span class="n" style="color: #333;">toRemove</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">getSize</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">sizeOneStep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// first calculate size of the single-step space</span></span>
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<pre style="margin: 0;"> <span id="LC744" 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;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</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="n" style="color: #333;">bbSynthons</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="java"> <span class="n" style="color: #333;">sizeOneStep</span><span class="o" style="font-weight: 600;">*=(</span><span class="kt" style="color: #458; font-weight: 600;">long</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="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC746" 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">@@ -780,12 +774,17 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">generateRandomProducts</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;">nProducts</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">productsWithBBs</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC783" 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;">String</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">productsWithReactions</span> <span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rnd</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;">Random</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IDCodeParser</span> <span class="n" style="color: #333;">parser</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;">IDCodeParser</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nProducts</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getSize</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">nProducts</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC788" 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;">StereoMolecule</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="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;"> <span id="LC789" 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;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;"> <span id="LC790" 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;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">reactions</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 match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -794,7 +793,8 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="java"> <span class="n" style="color: #333;">reactions</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;">reaction</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">());</span></span>
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<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;">reaction</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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<pre style="margin: 0;"> <span id="LC795" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextInt</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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797
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<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;">r</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="c1" style="color: #998; font-style: italic;">//pick commercial bb</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333;">libs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">precursorLibs</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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<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;">libs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()<</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</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="c1" style="color: #998; font-style: italic;">//pick commercial bb</span></span>
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798
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798
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<pre style="margin: 0;"> <span id="LC798" 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;">bbSynthons</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 class="na" style="color: #008080;">size</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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799
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">;</span></span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bbSynthons</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 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="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -809,9 +809,6 @@ public class ChemicalSpaceCreator {</td>
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">//create random virtual bb</span></span>
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pick random precursor reaction</span></span>
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<pre style="margin: 0;"> <span id="LC811" 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;">StereoMolecule</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">precursors</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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812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333;">libs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">precursorLibs</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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<pre style="margin: 0;">-<span id="LC813" 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;">libs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()<</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactionNr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">libs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC813" 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;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">keys</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 class="n" style="color: #333;">libs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC814" 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;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">lib</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">libs</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;">keys</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;">reactionNr</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">@@ -830,31 +827,36 @@ public class ChemicalSpaceCreator {</td>
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="java"> <span class="n" style="color: #333;">preCoupledSynthons</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="nc" style="color: #458; font-weight: 600;">SynthonReactor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">react</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">precursors</span><span class="o" style="font-weight: 600;">));</span></span>
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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832
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="java"> </span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="java"> <span class="n" style="color: #333;">e</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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831
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<pre style="margin: 0;">+<span id="LC831" 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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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">count</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++;</span></span></span>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC837" 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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838
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<pre style="margin: 0;"> <span id="LC838" 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="nc" style="color: #458; font-weight: 600;">SynthonReactor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">react</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">preCoupledSynthons</span><span class="o" style="font-weight: 600;">);</span></span>
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841
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839
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<pre style="margin: 0;"> <span id="LC839" 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;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bbIDCodes</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="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">map</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">()).</span><span class="na" style="color: #008080;">collect</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Collectors</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toList</span><span class="o" style="font-weight: 600;">());</span></span>
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840
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<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;">productsWithSynthons</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">containsKey</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;">getIDCode</span><span class="o" style="font-weight: 600;">()))</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" 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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842
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="java"> <span class="n" style="color: #333;">productsWithSynthons</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">bbIDCodes</span><span class="o" style="font-weight: 600;">);</span></span>
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843
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="java"> <span class="n" style="color: #333;">productsWithBBs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">bbs</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="java"> <span class="n" style="color: #333;">productsWithReactions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIDCode</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">reactions</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="java"> <span class="n" style="color: #333;">e</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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<pre style="margin: 0;"> <span id="LC860" 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;">matchesReactionRole</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">SSSearcherWithIndex</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">searchers</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;">component</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;">reactant</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isMatch</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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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#8297ca073cc662966e0530ff788a1c96def3c515"><strong>src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonCreator.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">@@ -13,6 +13,7 @@ import java.util.Map;</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Set</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Molecule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.RingCollection</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.StereoMolecule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.coords.CoordinateInventor</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.RXNFileCreator</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">@@ -21,6 +22,12 @@ import com.actelion.research.chem.reaction.Reaction;</td>
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<pre style="margin: 0;"> <span id="LC22" 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;">SynthonCreator</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * only works for reactions with a single product</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param rxn</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws Exception</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC31" 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;">Reaction</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">create</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProducts</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"only reactions with one product are supported"</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">@@ -41,219 +48,112 @@ public class SynthonCreator {</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//find bonds in products that are formed between a) atoms from different reactants or b) between an unmapped and a mapped atom</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//in a properly mapped reaction, unmapped atoms stem from a reagent or solvent</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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;">p</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;">p</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProducts</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" 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="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC46" 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;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bondsToCut</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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;">b</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;">b</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;">getBonds</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondAtom1</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondAtom2</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedBondAtom1</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondAtom1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedBondAtom2</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondAtom2</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mappedBondAtom1</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC53" 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;">mappedBondAtom2</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="k" style="font-weight: 600;">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;">mappedBondAtom2</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="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="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProduct</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//detect homogeneous rings: homogeneous rings are rings that either consist of only one reactant, or </span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//one reactant and unmapped (reagent) atoms. Bonds in homogeneous rings should not be cut!</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RingCollection</span> <span class="n" style="color: #333;">rc</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;">getRingSet</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="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;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">homogeneousRingBonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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;">ringNo</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;">ringNo</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSize</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">ringNo</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Set</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ringReactant</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;">HashSet</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">+<span id="LC58" 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;">atoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRingAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringNo</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="k" style="font-weight: 600;">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;">a</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">atoms</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedA</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" 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;">mappedA</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC63" 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;">mappedAtomToReactant</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;">mappedBondAtom1</span><span class="o" style="font-weight: 600;">)!=</span><span class="n" style="color: #333;">mappedAtomToReactant</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;">mappedBondAtom2</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mappedAtomToReactant</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;">mappedA</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"> <span class="n" style="color: #333;">ringReactant</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;">reactant</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">decomposedProduct</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 class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC70" 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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<pre style="margin: 0;">-<span id="LC71" 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;">cutBond</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bondsToCut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//first check if cutting this bond would result in isolating a fragment that is made of nonmapped atoms --> stem from a reagent</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//we want to assign these atoms to one of the synthons, so such a cut is forbidden</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">tmpMol</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 class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</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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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</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;">cBondTypeDeleted</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">deleteMarkedAtomsAndBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tmpFrags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFragments</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">acceptCut</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC80" 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;">StereoMolecule</span> <span class="n" style="color: #333;">tmpFrag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tmpFrags</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="n" style="color: #333;">tmpFrag</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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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC83" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tmpFrag</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="n" style="color: #333;">mapSum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">tmpFrag</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;">a</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapSum</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="n" style="color: #333;">acceptCut</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">acceptCut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</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;">cBondTypeDeleted</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connector1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">92</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>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connector2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">92</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>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBond1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">connector1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newBond1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bondType</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<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;">newBond2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connector2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newBond2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bondType</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> </span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">1</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;">//homogeneous ring!</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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;">ringBonds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRingBonds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringNo</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ringBonds</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">homogeneousRingBonds</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;">e</span><span class="o" style="font-weight: 600;">));</span></span>
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103
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">deleteMarkedAtomsAndBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">frags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFragments</span><span class="o" style="font-weight: 600;">();</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" 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;">StereoMolecule</span> <span class="n" style="color: #333;">frag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">frags</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CoordinateInventor</span> <span class="n" style="color: #333;">inventor</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;">CoordinateInventor</span><span class="o" style="font-weight: 600;">();</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">inventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setRandomSeed</span><span class="o" style="font-weight: 600;">(</span><span class="mh" style="color: #099;">0x1234567890</span><span class="no" style="color: #008080;">L</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// create reproducible coordinates</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">inventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">invent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">frag</span><span class="o" style="font-weight: 600;">);</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">reaction</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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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactantID</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">frag</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">frag</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;">a</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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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">reactantID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mappedAtomToReactant</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;">frag</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;">a</span><span class="o" style="font-weight: 600;">));</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> </span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" 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;">reactantID</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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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"could not process reaction"</span><span class="o" style="font-weight: 600;">);</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> <span class="n" style="color: #333;">frag</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">reaction</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;">rxn</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;">reactantID</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">reaction</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;">frag</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">synthonTransformations</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantID</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Writer writer = new BufferedWriter(new FileWriter(rxn.getName() + "_" + i + ".rxn"));</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//new RXNFileCreator(reaction).writeRXNfile(writer);</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//writer.close();</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">synthonTransformations</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * does not allow cuts through ring bonds</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param rxn</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws Exception</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" 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;">Reaction</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">createStrict</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProducts</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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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"only reactions with one product are supported"</span><span class="o" style="font-weight: 600;">);</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">synthonTransformations</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 class="n" style="color: #333;">rxn</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>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mappedAtomToReactant</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">>();</span> <span class="c1" style="color: #998; font-style: italic;">//stores the information on which mapped atom in the product is contributed by which reactant</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" 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;">r</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;">r</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactants</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReactants</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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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"cannot create Synthons for reactions with one reactant"</span><span class="o" style="font-weight: 600;">);</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" 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;">rxn</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;">r</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" 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;">a</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;">a</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactantMapNo</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;">a</span><span class="o" style="font-weight: 600;">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" 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;">reactantMapNo</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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160
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<pre style="margin: 0;">-<span id="LC160" 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 old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> <span class="n" style="color: #333;">mappedAtomToReactant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reactantMapNo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">);</span></span>
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163
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<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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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//find bonds in products that are formed between a) atoms from different reactants or b) between an unmapped and a mapped atom</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//in a properly mapped reaction, unmapped atoms stem from a reagent or solvent</span></span>
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<pre style="margin: 0;">-<span id="LC168" 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;">p</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;">p</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProducts</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC169" 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="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProduct</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC170" 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;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bondsToCut</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;">-<span id="LC171" 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;">b</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;">b</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;">getBonds</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondAtom1</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondAtom2</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedBondAtom1</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondAtom1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedBondAtom2</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondAtom2</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mappedBondAtom1</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC177" 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;">mappedBondAtom2</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> </span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <span class="k" style="font-weight: 600;">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;">mappedBondAtom2</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" 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;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bondsToCut</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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73
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<pre style="margin: 0;">+<span id="LC73" 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;">b</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;">b</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;">getBonds</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">homogeneousRingBonds</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">))</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" 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="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondAtom1</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondAtom2</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;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b</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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedBondAtom1</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondAtom1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mappedBondAtom2</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;">getAtomMapNo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondAtom2</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<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;">mappedBondAtom1</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="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">
81
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<pre style="margin: 0;">+<span id="LC81" 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;">mappedBondAtom2</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="c1" style="color: #998; font-style: italic;">// both atoms unmapped</span></span>
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185
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82
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<pre style="margin: 0;"> <span id="LC82" 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 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">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" 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;">mappedAtomToReactant</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;">mappedBondAtom1</span><span class="o" style="font-weight: 600;">)!=</span><span class="n" style="color: #333;">mappedAtomToReactant</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;">mappedBondAtom2</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="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//bond between a mapped and an unmapped atom</span></span>
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188
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="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;">mappedBondAtom2</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="c1" style="color: #998; font-style: italic;">//bond between a mapped and an umapped atom</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="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;">mappedAtomToReactant</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;">mappedBondAtom1</span><span class="o" style="font-weight: 600;">)!=</span><span class="n" style="color: #333;">mappedAtomToReactant</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;">mappedBondAtom2</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;">//atoms from two different reactants</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="n" style="color: #333;">bondsToCut</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;">b</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">decomposedProduct</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 class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC194" 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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<pre style="margin: 0;">-<span id="LC195" 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;">cutBond</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bondsToCut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//first check if cutting this bond would result in isolating a fragment that is made of nonmapped atoms --> stem from a reagent</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//we want to assign these atoms to one of the synthons, so such a cut is forbidden</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">tmpMol</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 class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</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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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</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;">cBondTypeDeleted</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">deleteMarkedAtomsAndBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tmpFrags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFragments</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">acceptCut</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC204" 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;">StereoMolecule</span> <span class="n" style="color: #333;">tmpFrag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tmpFrags</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"> <span class="n" style="color: #333;">tmpFrag</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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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC207" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tmpFrag</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java"> <span class="n" style="color: #333;">mapSum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">tmpFrag</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;">a</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapSum</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java"> <span class="n" style="color: #333;">acceptCut</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">decomposedProduct</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 class="n" style="color: #333;">product</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<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;">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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99
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<pre style="margin: 0;">+<span id="LC99" 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;">cutBond</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bondsToCut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//first check if cutting this bond would result in isolating a fragment that is made of nonmapped atoms --> stem from a reagent</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//we want to assign these atoms to one of the synthons, so such a cut is forbidden</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">tmpMol</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 class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</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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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</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;">cBondTypeDeleted</span><span class="o" style="font-weight: 600;">);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">deleteMarkedAtomsAndBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tmpFrags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFragments</span><span class="o" style="font-weight: 600;">();</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">acceptCut</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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108
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<pre style="margin: 0;">+<span id="LC108" 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;">StereoMolecule</span> <span class="n" style="color: #333;">tmpFrag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tmpFrags</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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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">tmpFrag</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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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapSum</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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111
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<pre style="margin: 0;">+<span id="LC111" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tmpFrag</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">mapSum</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">tmpFrag</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;">a</span><span class="o" style="font-weight: 600;">);</span></span>
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214
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC215" 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;">acceptCut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</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;">cBondTypeDeleted</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connector1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">92</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>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connector2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">92</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>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBond1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">connector1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newBond1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bondType</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBond2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connector2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newBond2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bondType</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapSum</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">acceptCut</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">deleteMarkedAtomsAndBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">frags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFragments</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC231" 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;">StereoMolecule</span> <span class="n" style="color: #333;">frag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">frags</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CoordinateInventor</span> <span class="n" style="color: #333;">inventor</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;">CoordinateInventor</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="java"> <span class="n" style="color: #333;">inventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setRandomSeed</span><span class="o" style="font-weight: 600;">(</span><span class="mh" style="color: #099;">0x1234567890</span><span class="no" style="color: #008080;">L</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// create reproducible coordinates</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="java"> <span class="n" style="color: #333;">inventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">invent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">frag</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">reaction</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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<pre style="margin: 0;">-<span id="LC236" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactantID</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC237" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">frag</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">frag</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;">a</span><span class="o" style="font-weight: 600;">)!=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="java"> <span class="n" style="color: #333;">reactantID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mappedAtomToReactant</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;">frag</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;">a</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="java"> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" 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;">acceptCut</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bondType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cutBond</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;">cBondTypeDeleted</span><span class="o" style="font-weight: 600;">);</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connector1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">92</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>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connector2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">92</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>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBond1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">connector1</span><span class="o" style="font-weight: 600;">);</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newBond1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bondType</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newBond2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">connector2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cutBond</span><span class="o" style="font-weight: 600;">));</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newBond2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bondType</span><span class="o" style="font-weight: 600;">);</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">deleteMarkedAtomsAndBonds</span><span class="o" style="font-weight: 600;">();</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">frags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decomposedProduct</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFragments</span><span class="o" style="font-weight: 600;">();</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" 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;">StereoMolecule</span> <span class="n" style="color: #333;">frag</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">frags</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CoordinateInventor</span> <span class="n" style="color: #333;">inventor</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;">CoordinateInventor</span><span class="o" style="font-weight: 600;">();</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> <span class="n" style="color: #333;">inventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setRandomSeed</span><span class="o" style="font-weight: 600;">(</span><span class="mh" style="color: #099;">0x1234567890</span><span class="no" style="color: #008080;">L</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// create reproducible coordinates</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">inventor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">invent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">frag</span><span class="o" style="font-weight: 600;">);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Reaction</span> <span class="n" style="color: #333;">reaction</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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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">reactantID</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">frag</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;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" 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;">frag</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;">a</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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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="n" style="color: #333;">reactantID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mappedAtomToReactant</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;">frag</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;">a</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC243" 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;">reactantID</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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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"could not process reaction"</span><span class="o" style="font-weight: 600;">);</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="java"> <span class="n" style="color: #333;">frag</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="java"> <span class="n" style="color: #333;">reaction</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;">rxn</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;">reactantID</span><span class="o" style="font-weight: 600;">));</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="java"> <span class="n" style="color: #333;">reaction</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;">frag</span><span class="o" style="font-weight: 600;">);</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="java"> <span class="n" style="color: #333;">synthonTransformations</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantID</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">;</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Writer writer = new BufferedWriter(new FileWriter(rxn.getName() + "_" + i + ".rxn"));</span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//new RXNFileCreator(reaction).writeRXNfile(writer);</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//writer.close();</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" 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;">reactantID</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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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Exception</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"could not process reaction"</span><span class="o" style="font-weight: 600;">);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="n" style="color: #333;">frag</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ensureHelperArrays</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cHelperCIP</span><span class="o" style="font-weight: 600;">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="n" style="color: #333;">reaction</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;">rxn</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;">reactantID</span><span class="o" style="font-weight: 600;">));</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> <span class="n" style="color: #333;">reaction</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;">frag</span><span class="o" style="font-weight: 600;">);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java"> <span class="n" style="color: #333;">synthonTransformations</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">reactantID</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Writer</span> <span class="n" style="color: #333;">writer</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;">BufferedWriter</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;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxn</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">()</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;">reactantID</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rxn"</span><span class="o" style="font-weight: 600;">));</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java"> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RXNFileCreator</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reaction</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">writeRXNfile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">);</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java"></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> </span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">synthonTransformations</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="264" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -264,7 +164,6 @@ public class SynthonCreator {</td>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="java"> </span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="java"> </span>
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268
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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269
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> public static void main(String[] args) {</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> List<Reaction> htmcReactions = ReactionList.INSTANCE.getReactionsHTMC();</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#2324bbf7db1501a1bb2aaae4a1db707a20b5f9b1"><strong>src/main/java/com/actelion/research/chem/coords/CoordinateInventor.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">@@ -108,12 +108,13 @@ public class CoordinateInventor {</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * By providing a custom template list containing substructures with predefined atom</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * coordinates, any occurence of any of these substructures will receive the</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * relative atom coordinates of the provided template, unless the substructure</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * shares more than one atom with a previously found substructure or the substructure</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * shares more than one atom with the non marked atoms and mode is</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MODE_????_MARKED_ATOM_COORDS.</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * A custom template list contains substructures with predefined atom coordinates.</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * When such a list is provided, and if a molecules contains one of the list's substructures,</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * then the matching atoms will receive the relative atom coordinates of the provided template,</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * unless the substructure shares two or more atoms with another earlier found template or</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * if mode is MODE_????_MARKED_ATOM_COORDS and the substructure match contains two or more</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * non-marked (and therefore untouchable) atoms. If a template substructure contains an E- or Z-</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * double bound, then the query feature 'match EZ-parity' should be set.</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param templateList</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setCustomTemplateList</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;">InventorTemplate</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">templateList</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#fd33d2182c0e0f9cb9c01b5b6cd8a61b579abeb0"><strong>src/main/java/com/actelion/research/chem/coords/InventorFragment.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">@@ -195,7 +195,8 @@ public class InventorFragment {</td>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">coreOnSide</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">coreOffSide</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC197" 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;">mGlobalAtom</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 class="o" style="font-weight: 600;">{</span></span>
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<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;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isMarkedAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mGlobalAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mGlobalAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mMol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isMarkedAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">atom1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">atom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">atom2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isOnSide</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mGlobalAtom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]])</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="n" style="color: #333;">coreOnSide</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#32943cdb0e248053d475693d07df3b36f28244bf"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.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">@@ -511,6 +511,56 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp</td>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param solution a valid solution for IMolDistHis base and IMolDistHis query. Query and base must be set before</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * starting the similarity calculation.</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param indexHeap heap index of the node for which the histogram similarities to all other nodes will be calculated.</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * indexHeap is the index from the list of matching query and base nodes.</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return histogram similarity for a single node. Calculated as average from the sum of histogram similarities.</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">getSimilarityHistogramsForNode</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SolutionCompleteGraph</span> <span class="n" style="color: #333;">solution</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;">indexHeap</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">heap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSizeHeap</span><span class="o" style="font-weight: 600;">();</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="java"></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the query must hit with all pharmacophore nodes</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" 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;">modeQuery</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" 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;">nodesQuery</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">heap</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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533
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumPairwiseMapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexNode1Query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIndexQueryFromHeap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexHeap</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexNode1Base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIndexCorrespondingBaseNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexNode1Query</span><span class="o" style="font-weight: 600;">);</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC540" 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;">heap</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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541
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<pre style="margin: 0;">+<span id="LC541" 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;">indexHeap</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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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexNode2Query</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIndexQueryFromHeap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexNode2Base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIndexCorrespondingBaseNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexNode2Query</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">simHists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSimilarityHistogram</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexNode1Query</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexNode2Query</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexNode1Base</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexNode2Base</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="java"> <span class="n" style="color: #333;">sumPairwiseMapping</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">simHists</span><span class="o" style="font-weight: 600;">;</span></span>
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551
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552
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<pre style="margin: 0;">+<span id="LC552" 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;">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"scorePairwiseMapping "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">simHists</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mappings</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">heap</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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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">avrPairwiseMapping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sumPairwiseMapping</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">mappings</span><span class="o" style="font-weight: 600;">;</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">avrPairwiseMapping</span><span class="o" style="font-weight: 600;">;</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">getDeltaNanoQueryBlur</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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515
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">deltaNanoQueryBlur</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC566" 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">@@ -835,12 +885,10 @@ public class ObjectiveBlurFlexophoreHardMatchUncovered implements IObjectiveComp</td>
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">simHists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSimilarityHistogram</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexNode1Query</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexNode2Query</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexNode1Base</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexNode2Base</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC838" 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;">simHists</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">){</span></span>
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ObjectiveFlexophoreHardMatchUncovered getScorePairwiseMapping(int indexNode1Query, int indexNode2Query, int indexNode1Base, int indexNode2Base)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Sim hists = 0"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if(simHists==0){</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.out.println("ObjectiveFlexophoreHardMatchUncovered getScorePairwiseMapping(int indexNode1Query, int indexNode2Query, int indexNode1Base, int indexNode2Base)");</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.out.println("Sim hists = 0");</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC893" 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;">verbose</span><span class="o" style="font-weight: 600;">){</span></span>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"simHists "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">simHists</span><span class="o" style="font-weight: 600;">));</span></span>
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<li id="53644f8fdeac019d663bcf78d973c6c33e7e0b47">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#53644f8fdeac019d663bcf78d973c6c33e7e0b47"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/example/MatchFlexophoreNodesMain.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">@@ -7,8 +7,13 @@ import com.actelion.research.chem.descriptor.DescriptorHandlerFlexophore;</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor.flexophore.ModelSolutionSimilarity</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor.flexophore.MolDistHistViz</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor.flexophore.PPNodeViz</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor.flexophore.completegraphmatcher.ObjectiveBlurFlexophoreHardMatchUncovered</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.gui.table.ChemistryRenderPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.ArrayUtils</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.Formatter</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC18" 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;">MatchFlexophoreNodesMain</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -26,45 +31,61 @@ public class MatchFlexophoreNodesMain {</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="java"> <span class="n" style="color: #333;">pairMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">idcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">idcodeQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pairMatch</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;">idcodeQuery</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pairMatch</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 class="idiff left right">Base</span></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;">idcodeQuery</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerFlexophore</span> <span class="n" style="color: #333;">dhFlexophore</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;">DescriptorHandlerFlexophore</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ObjectiveBlurFlexophoreHardMatchUncovered</span> <span class="n" style="color: #333;">objectiveBlurFlexophoreHardMatchUncovered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dhFlexophore</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getObjectiveCompleteGraph</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IDCodeParser</span> <span class="n" style="color: #333;">parser</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;">IDCodeParser</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MolDistHistViz</span> <span class="n" style="color: #333;">mdh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dhFlexophore</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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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MolDistHistViz</span> <span class="n" style="color: #333;">mdhvBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dhFlexophore</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">idcodeBase</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Num pp nodes base "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mdh</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNumPPNodes</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MolDistHistViz</span> <span class="n" style="color: #333;">mdhQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dhFlexophore</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">idcodeQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Num pp nodes query "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mdhQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNumPPNodes</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdh</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Num pp nodes base "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mdhvBase</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNumPPNodes</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ModelSolutionSimilarity</span> <span class="n" style="color: #333;">modelSolutionSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dhFlexophore</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBestMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdh</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mdhQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MolDistHistViz</span> <span class="n" style="color: #333;">mdhvQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dhFlexophore</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">idcodeQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Num pp nodes query "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mdhvQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNumPPNodes</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhvBase</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhvQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ModelSolutionSimilarity</span> <span class="n" style="color: #333;">modelSolutionSimilarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dhFlexophore</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBestMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhvBase</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mdhvQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">heap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelSolutionSimilarity</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSizeHeap</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// System.out.println(Formatter.format3(sim) + "\t" + Formatter.format3(simDH));</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// System.out.println(Formatter.format3(sim) +"\t"+ Formatter.format3(simNormalized));</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="n" style="color: #333;">objectiveBlurFlexophoreHardMatchUncovered</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhvBase</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="n" style="color: #333;">objectiveBlurFlexophoreHardMatchUncovered</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setQuery</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhvQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"> <span class="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;">heap</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelSolutionSimilarity</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIndexQueryFromHeap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indexBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modelSolutionSimilarity</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getIndexBaseFromHeap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PPNodeViz</span> <span class="n" style="color: #333;">ppv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mdh</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexBase</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PPNodeViz</span> <span class="n" style="color: #333;">ppvQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mdhQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppv</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PPNodeViz</span> <span class="n" style="color: #333;">ppvBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mdhvBase</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexBase</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC70" 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;">arrAtomIndexBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toIntArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppvBase</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getListIndexOriginalAtoms</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PPNodeViz</span> <span class="n" style="color: #333;">ppvQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mdhvQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexQuery</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC74" 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;">arrAtomIndexQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toIntArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppvQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getListIndexOriginalAtoms</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppvBase</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ppvQuery</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// System.out.println(Formatter.format3((double)ppv.getSimilarityMappingNodes()) + "\t" + Formatter.format3((double)ppvQuery.getSimilarityMappingNodes()));</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format3</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;">modelSolutionSimilarity</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarityNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexQuery</span><span class="o" style="font-weight: 600;">)));</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">simHistogram</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">objectiveBlurFlexophoreHardMatchUncovered</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarityHistogramsForNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">modelSolutionSimilarity</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Node similarity "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format3</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;">modelSolutionSimilarity</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarityNode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indexQuery</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", histogram similarity "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format3</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;">simHistogram</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Un-normalized similarity "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format3</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">modelSolutionSimilarity</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>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#cf40108c840165d004c28f26bbfd06fa9b0a6a27"><strong>src/main/java/com/actelion/research/chem/io/CompoundTableConstants.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">@@ -181,6 +181,7 @@ public interface CompoundTableConstants {</td>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnProperty3DFragmentSplit</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"split3D"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// if "true": unconnected fragments of 3D-structure are shown as differently colored V3DMolecules</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyCommentUploadStatus</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"commentUploadStatus"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyCommentDepartment</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"commentDepartment"</span><span class="o" style="font-weight: 600;">;</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cColumnPropertyCalculated</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"calculated"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//for columns that can be calculated by a task</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cSuperposeValueReferenceRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"refRow"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// "reference" or null</span></span>
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186
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">cSuperposeAlignValueShape</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"shape"</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// "reference" or null</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#b913e9301eb349935afa9f9053995d0205bb3b8e"><strong>src/main/java/com/actelion/research/chem/io/Mol2FileParser.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">@@ -4,31 +4,14 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.*</span><span class="o" style="font-weight: 600;">;</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.LineNumberReader</span><span class="o" style="font-weight: 600;">;</span></span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.Reader</span><span class="o" style="font-weight: 600;">;</span></span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.Writer</span><span class="o" style="font-weight: 600;">;</span></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.DecimalFormat</span><span class="o" style="font-weight: 600;">;</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.NumberFormat</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Collections</span><span class="o" style="font-weight: 600;">;</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Map</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Set</span><span class="o" style="font-weight: 600;">;</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.StringTokenizer</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.TreeMap</span><span class="o" style="font-weight: 600;">;</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"></span>
</pre>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.AromaticityResolver</span><span class="o" style="font-weight: 600;">;</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Canonizer</span><span class="o" style="font-weight: 600;">;</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.ExtendedMolecule</span><span class="o" style="font-weight: 600;">;</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Molecule3D</span><span class="o" style="font-weight: 600;">;</span></span>
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27
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<td class="new_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.Molecule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.SmilesCreator</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.StereoMolecule</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.pdb.converter.BondsCalculator</span><span class="o" style="font-weight: 600;">;</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.AbstractParser</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC17" 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">@@ -87,8 +70,7 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC70" 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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBonds</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBondOrder</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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bondMap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]));</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> else {</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> //Use BondsCalculator.aromatize</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +87,6 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAllAtomFlag</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule3D</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">LIGAND</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">res</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;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC92" 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;">assignCharges</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Molecule3D</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,9 +121,7 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getChargeType</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;">type</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"> </span>
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<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;">hmIndex_CHARGETYPE</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">){</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">hmIndex_CHARGETYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">hmIndex_CHARGETYPE</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iNO_CHARGES</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sNO_CHARGES</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">hmIndex_CHARGETYPE</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iDEL_RE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sDEL_RE</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="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -163,8 +142,7 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @see com.actelion.research.chem.parsers.AbstractParser#parse(java.io.Reader,</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * com.actelion.research.chem.Molecule3D)</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @see com.actelion.research.chem.io.AbstractParser#loadGroup(String, java.io.Reader, int, int)</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</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;">Molecule3D</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">loadGroup</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;">fileName</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Reader</span> <span class="n" style="color: #333;">in</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;">from</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;">to</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -303,11 +281,8 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC281" 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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<pre style="margin: 0;"> <span id="LC282" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">RuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown bond type "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">order</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">@@ -356,9 +331,7 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">save</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;">Molecule3D</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mols</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;">chargeType</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Writer</span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">DecimalFormat</span> <span class="n" style="color: #333;">df</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;">DecimalFormat</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0.0000"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC335" 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;">Molecule3D</span> <span class="n" style="color: #333;">mol</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mols</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//Count the number of bonds and atoms (except lone pairs)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -373,8 +346,7 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC346" 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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBondAtom</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">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="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="java"> <span class="n" style="color: #333;">nBonds</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Write the molecule</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="java"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"@<TRIPOS>MOLECULE"</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">NEWLINE</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="java"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</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;">getName</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">NEWLINE</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">@@ -423,10 +395,8 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="java"> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">NEWLINE</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC402" 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;">Molecule3D</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">res</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;">Mol2FileParser</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">loadGroup</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"c:/mopac11971.mol2"</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">@@ -434,7 +404,4 @@ public class Mol2FileParser extends AbstractParser {</td>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"models="</span> <span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">res</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="s" style="color: #d14;">" atm="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">res</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="mi" style="color: #099;">0</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 class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">res</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//new Mol2FileParser().save(res.get(0), "c:/t.mol2");</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="22a48b6441e4880a80fbbf8c21720f71585f7170">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#22a48b6441e4880a80fbbf8c21720f71585f7170"><strong>src/main/java/com/actelion/research/gui/JStructureView.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">@@ -65,6 +65,7 @@ public class JStructureView extends JComponent implements ActionListener,MouseLi</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mAllowedDragAction</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mAllowedDropAction</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">mWarningMessage</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">JStructureView</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,6 +217,15 @@ public class JStructureView extends JComponent implements ActionListener,MouseLi</td>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">mAllowFragmentStatusChangeOnPasteOrDrop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allow</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * If you want this tructure view to also draw an atom background with specific colors for every atom,</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * then you need to call this method before or just after one of the structureChanged() calls.</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param argb values with a==0 are not considered (may be null)</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setAtomHighlightColors</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;">argb</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java"> <span class="n" style="color: #333;">mAtomHiliteColor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argb</span><span class="o" style="font-weight: 600;">;</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java"></span>
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219
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">canDrop</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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220
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mIsEditable</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isEnabled</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;">mIsDraggingThis</span><span class="o" style="font-weight: 600;">;</span></span>
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221
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231
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<pre style="margin: 0;"> <span id="LC231" 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="267" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -257,6 +267,7 @@ public class JStructureView extends JComponent implements ActionListener,MouseLi</td>
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257
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="java"> <span class="n" style="color: #333;">mDepictor</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;">GenericDepictor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDisplayMol</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="java"> <span class="n" style="color: #333;">mDepictor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setDisplayMode</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mDisplayMode</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="java"> <span class="n" style="color: #333;">mDepictor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomText</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAtomText</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="java"> <span class="n" style="color: #333;">mDepictor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomHighlightColors</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mAtomHiliteColor</span><span class="o" style="font-weight: 600;">);</span></span>
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260
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC272" 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;">isEnabled</span><span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="java"> <span class="n" style="color: #333;">mDepictor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setOverruleColor</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ColorHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getContrastColor</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Color</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">GRAY</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bg</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">bg</span><span class="o" style="font-weight: 600;">);</span></span>
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<li id="5747d6186b6b4a54bba0c10bc9aa0e5835c7c31f">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/eaa5350449d28a28c22c3592b6579017ac1b6822...4569bc2804db071f8f402d61d54cc259ee7da279#5747d6186b6b4a54bba0c10bc9aa0e5835c7c31f"><strong>src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -153,7 +153,6 @@ public class CompleteGraphMatcher<T extends ICompleteGraph> {</td>
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153
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">initSearch</span><span class="o" style="font-weight: 600;">();</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="java"></span>
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155
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<pre style="margin: 0;"> <span id="LC155" 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;">nodesBase</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;">nodesQuery</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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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SolutionCompleteGraph</span> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">liliSolution</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="mi" style="color: #099;">1</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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156
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<pre style="margin: 0;"> <span id="LC156" 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;">objectiveCompleteGraph</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarityNodes</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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158
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sim</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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