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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/8089473afb60abe4596694df2be2f540fce06bc5">8089473a</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2020-11-23T05:39:28-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020.11.3+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/a3158be613f71380833b8cddeb32e640be5f5f28">a3158be6</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2020-11-23T05:39:53-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2020.11.3+dfsg'
Update to upstream version '2020.11.3+dfsg'
with Debian dir ec15fca024802554cd07ee307c7edcf673b180b0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/be42eb61ce2839e41cfff2585d2ba329847ce1b2">be42eb61</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2020-11-23T05:40:48-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing javafx.patch.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/7c444c4785444f0986e5bcd13b080f0dd0e45eac">7c444c47</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2020-11-23T05:41:07-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog for 2020.11.3+dfsg-1 release
</pre>
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<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#86f5ff6c6075c2da045f28d3e5f76380f5c1292e">
debian/patches/javafx.patch
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<li class="file-stats">
<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">
pom.xml
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<li class="file-stats">
<a href="#a1ec33c7804dfaa6cf903376c9e2af00e9a9a224">
src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
</a>
</li>
<li class="file-stats">
<a href="#7591869d39cf992c9eaa2bbe2598c5927a014b3b">
src/main/java/com/actelion/research/chem/Molecule.java
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<li class="file-stats">
<a href="#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3">
src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java
</a>
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<li class="file-stats">
<a href="#848ff0a267a24996442ab1f307aef324a7e6e5ea">
src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHistHelper.java
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<li class="file-stats">
<a href="#5a4e816ea63ec2b90fb4deb3681f880d4a21988b">
src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveFlexophoreHardMatchUncovered.java
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<li class="file-stats">
<a href="#0a63218c74989067a660fa50ae242a235586f8ac">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.java
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<li class="file-stats">
<a href="#b0cbe5340e4699fb85c32e35097b39fa252b8b72">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreGenerator.java
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<li class="file-stats">
<a href="#1a2948d1808e5bf4b5ae448818a4c444d9b4870a">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">openchemlib (2020.11.3+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" 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>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 2020.11.3+dfsg</span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Refreshing javafx.patch.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" 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> Mon, 23 Nov 2020 05:41:04 -0500</span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">openchemlib (2020.11.2+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Switching back to watching tags.</span>
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<li id="86f5ff6c6075c2da045f28d3e5f76380f5c1292e">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#86f5ff6c6075c2da045f28d3e5f76380f5c1292e"><strong>debian/patches/javafx.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pom.xml</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">@@ -101,6 +101,21 @@</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> <version>4.<span class="idiff left right">9</span></version></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> <version>4.<span class="idiff left right">13.1</span></version></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> <scope>test</scope></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <dependency></span></span>
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<li id="442292b8a7efeabbe4cc176709b833b1792140ec">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</strong></a>
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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>2020.11.<span class="idiff left right">2</span><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>2020.11.<span class="idiff left right">3</span><span class="nt" style="color: #000080;"></version></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="xml"></span>
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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">@@ -98,7 +98,7 @@</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="xml"> <span class="nt" style="color: #000080;"><dependency></span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="xml"> <span class="nt" style="color: #000080;"><groupId></span>junit<span class="nt" style="color: #000080;"></groupId></span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="xml"> <span class="nt" style="color: #000080;"><artifactId></span>junit<span class="nt" style="color: #000080;"></artifactId></span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="xml"> <span class="nt" style="color: #000080;"><version></span>4.<span class="idiff left right">9</span><span class="nt" style="color: #000080;"></version></span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="xml"> <span class="nt" style="color: #000080;"><version></span>4.<span class="idiff left right">13.1</span><span class="nt" style="color: #000080;"></version></span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="xml"> <span class="nt" style="color: #000080;"><scope></span>test<span class="nt" style="color: #000080;"></scope></span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="xml"> <span class="nt" style="color: #000080;"></dependency></span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="xml"> <span class="nt" style="color: #000080;"></dependencies></span></span>
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<pre style="margin: 0;"> <span id="LC189" 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="LC190" 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="LC191" 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="LC192" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-2020.11.<span class="idiff left right">2</span><span class="nt" style="color: #000080;"></tag></span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-2020.11.<span class="idiff left right">3</span><span class="nt" style="color: #000080;"></tag></span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="xml"> <span class="nt" style="color: #000080;"></scm></span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC195" 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/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#a1ec33c7804dfaa6cf903376c9e2af00e9a9a224"><strong>src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.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">@@ -936,7 +936,7 @@ public class IDCodeParserWithoutCoordinateInvention {</td>
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="java"></span>
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938
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<pre style="margin: 0;"> <span id="LC938" 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;">parseMapping</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mapping</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;">mappingStart</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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939
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapping</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;">mapping</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;">mappingStart</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapping</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;">mapping</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;">mappingStart</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mapping</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">mappingStart</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mh" style="color: #099;"><span class="idiff right">0x40</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC940" 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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941
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="java"> <span class="n" style="color: #333;">decodeBitsStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mapping</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mappingStart</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#7591869d39cf992c9eaa2bbe2598c5927a014b3b"><strong>src/main/java/com/actelion/research/chem/Molecule.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">@@ -2446,7 +2446,7 @@ public class Molecule implements Serializable {</td>
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<pre style="margin: 0;"> <span id="LC2446" 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;">original</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="LC2447" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">original</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 class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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2448
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<pre style="margin: 0;"> <span id="LC2448" class="line" lang="java"> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">original</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;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC2449" 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;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">original</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">],</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">copy</span><span 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;">original</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;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC2449" 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;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">original</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">],</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">original</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;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC2450" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC2451" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC2452" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">copy</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">@@ -2456,7 +2456,7 @@ public class Molecule implements Serializable {</td>
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<pre style="margin: 0;"> <span id="LC2456" 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;">original</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="LC2457" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">original</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 class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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2458
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2458
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<pre style="margin: 0;"> <span id="LC2458" class="line" lang="java"> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">original</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;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC2459" 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;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">original</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">],</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">copy</span><span 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;">original</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;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC2459" 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;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">original</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">],</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">original</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;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC2460" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC2461" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC2462" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3"><strong>src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -146,7 +146,7 @@ public class PheSAAlignmentOptimizer {</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bestTransformPMI</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MolecularVolume</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bestPairPMI</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;">MolecularVolume</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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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bestScoreTriangle</span><span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span><span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<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;">bestScoreTriangle</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"> <span class="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestScoreTriangle</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">similarity</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;">result</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">triangleRes</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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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#848ff0a267a24996442ab1f307aef324a7e6e5ea"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHistHelper.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">@@ -36,6 +36,28 @@ import java.util.List;</td>
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<pre style="margin: 0;"> <span id="LC36" 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="LC37" 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;">DistHistHelper</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="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;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getMedianBin</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">a</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="LC41" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">medianBin</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="LC42" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum</span> <span 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="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;">byte</span> <span class="n" style="color: #333;">b</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="LC45" class="line" lang="java"> <span class="n" style="color: #333;">sum</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="LC46" class="line" lang="java"> <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="n" style="color: #333;">sum</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="LC48" class="line" lang="java"></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;">s2</span><span 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="LC50" 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;">a</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="LC51" class="line" lang="java"> <span class="n" style="color: #333;">s2</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;">i</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;">s2</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">sum</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="n" style="color: #333;">medianBin</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="LC54" 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="LC55" class="line" lang="java"> <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="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">medianBin</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC61" 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;">RangeStatistics</span> <span class="nf" style="color: #900; font-weight: 600;">getRangeStatistics</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MolDistHist</span> <span class="n" style="color: #333;">mdh</span><span class="o" style="font-weight: 600;">){</span></span>
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62
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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="nc" style="color: #458; font-weight: 600;">RangeStatistics</span> <span class="n" style="color: #333;">rangeStatisticsTotal</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;">RangeStatistics</span><span class="o" style="font-weight: 600;">();</span></span>
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<li id="5a4e816ea63ec2b90fb4deb3681f880d4a21988b">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#5a4e816ea63ec2b90fb4deb3681f880d4a21988b"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveFlexophoreHardMatchUncovered.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">@@ -421,6 +421,15 @@ public class ObjectiveFlexophoreHardMatchUncovered implements IObjectiveComplete</td>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="java"> </span>
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422
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<pre style="margin: 0;"> <span id="LC422" 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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423
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="java"></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" 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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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="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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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="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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429
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<pre style="margin: 0;">+<span id="LC429" 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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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC433" 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="LC434" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// double productPairwiseMapping = 0;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -462,7 +471,7 @@ public class ObjectiveFlexophoreHardMatchUncovered implements IObjectiveComplete</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ratioNodesMatchBase</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;">heap</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="o" style="font-weight: 600;">/</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="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">heap</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>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="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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<pre style="margin: 0;">-<span id="LC465" class="line" lang="java"> <span class="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">avrPairwiseMappingScaled</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coverageQuery</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ratioNodesMatchQuery</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="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">avrPairwiseMappingScaled</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coverageQuery</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left">coverageQuery</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ratioNodesMatchQuery</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ratioNodesMatchQuery</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="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="LC476" class="line" lang="java"> <span class="n" style="color: #333;">similarity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">avrPairwiseMappingScaled</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ratioNodesMatchQuery</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ratioNodesMatchBase</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#0a63218c74989067a660fa50ae242a235586f8ac"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.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">@@ -27,10 +27,14 @@ public class ConstantsFlexophoreGenerator {</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Filter for sliding window to blurr distance histograms</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;"> * 07.04.2020</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;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// public static final double [] FILTER</span> = {0.25,0.5,0.25};</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"> <span class="kd" style="font-weight: 600;"><span class="idiff left">public</span></span><span class="idiff"> </span><span class="kd" style="font-weight: 600;"><span class="idiff">static</span></span><span class="idiff"> </span><span class="kd" style="font-weight: 600;"><span class="idiff">final</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">FILTER_SUB</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span><span class="mf" style="color: #099;">0.25</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">0.25</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="c1" style="color: #998; font-style: italic;">// public static final double [] FILTER = {0.125, 0.25,0.25,0.25, 0.125};</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// public static final double [] FILTER = {0.06, 0.125, 0.19,0.25,0.19, 0.125, 0.06};</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC35" 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="LC36" 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="LC37" 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="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[]</span> <span class="no" style="color: #008080;">FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span><span class="mf" style="color: #099;">0.125</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.125</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.125</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">0.25</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">0.125</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.125</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.125</span><span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#b0cbe5340e4699fb85c32e35097b39fa252b8b72"><strong>src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreGenerator.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">@@ -15,7 +15,6 @@ import java.util.List;</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This software is the proprietary information of Actelion Pharmaceuticals, Ltd.</span></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;"> * Use is subject to license terms.</p></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;"> * @author Modest von Korff</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @version 1.0</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Oct 12, 2012 MvK: Start implementation</span></span>
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<pre style="margin: 0;"> <span id="LC19" 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="LC20" 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;">SubFlexophoreGenerator</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">@@ -154,9 +153,7 @@ public class SubFlexophoreGenerator {</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC154" 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;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minNumPPPoints</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxNumPPPointsReal</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">size</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="LC155" 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;">MolDistHistViz</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">liMDHVSub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">generateSubPharmacophores</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mdhv</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">liHsMolDistHistViz</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;">size</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">liMDHVSub</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> <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>
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<pre style="margin: 0;"> <span id="LC159" 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;">MolDistHistViz</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">liMDHVSubAll</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="nc" style="color: #458; font-weight: 600;">MolDistHistViz</span><span class="o" style="font-weight: 600;">>();</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/f806013184f6b0a9b9f665fc0d4938a684735cc7...7c444c4785444f0986e5bcd13b080f0dd0e45eac#1a2948d1808e5bf4b5ae448818a4c444d9b4870a"><strong>src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.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">@@ -68,7 +68,7 @@ public class PharmacophoreCalculator {</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">interactionClass</span><span 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="LC69" 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="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span 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;">i</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">neighbours</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBondOrder</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="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="nc" style="color: #458; font-weight: 600;">AtomFunctionAnalyzer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAcidicOxygen</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;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="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;">i</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">neighbours</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBondOrder</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="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="nc" style="color: #458; font-weight: 600;">AtomFunctionAnalyzer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAcidicOxygen</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;">i</span><span class="o" style="font-weight: 600;">)</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">mol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">getAtomCharge</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)==-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff right"> </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="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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="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;">a1</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">||</span> <span class="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;">a1</span><span class="o" style="font-weight: 600;">)==</span><span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span> </span>
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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="n" style="color: #333;">aa1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span 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="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,6 +76,7 @@ public class PharmacophoreCalculator {</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="n" style="color: #333;">aa1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtom</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">neighbourList</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;">aa1</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;">AcceptorPoint</span> <span class="n" style="color: #333;">ap</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;">AcceptorPoint</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;">i</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">neighbourList</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">interactionClass</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="LC79" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="n" style="color: #333;">ppPoints</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;">ap</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="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;">neighbourList2</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="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="LC82" 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;">neighbour</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">neighbourList</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">@@ -83,6 +84,7 @@ public class PharmacophoreCalculator {</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java"> <span class="n" style="color: #333;">ap</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;">AcceptorPoint</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;">i</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">neighbourList2</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">interactionClass</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="LC86" class="line" lang="java"> <span class="n" style="color: #333;">ppPoints</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;">ap</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>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <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;">else</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;">AcceptorPoint</span> <span class="n" style="color: #333;">ap</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;">AcceptorPoint</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;">i</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">neighbourList</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">interactionClass</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">@@ -93,6 +95,7 @@ public class PharmacophoreCalculator {</td>
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<pre style="margin: 0;"> <span id="LC95" 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="LC96" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">AcceptorPoint</span> <span class="n" style="color: #333;">ap</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;">AcceptorPoint</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;">i</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">neighbourList</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">interactionClass</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;">ppPoints</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;">ap</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java"> <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="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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