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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/3d4bbf950a6711a7db54a882784d78f4ad2eb5dd">3d4bbf95</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2021-01-19T03:37:17-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.1.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/d560b7b29d39362efddf121a516ccedc2c14bf1c">d560b7b2</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2021-01-19T03:37:26-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2021.1.1+dfsg'
Update to upstream version '2021.1.1+dfsg'
with Debian dir 5dc01784eb206d0797abaaced8684d8cb2f34036</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/6d18c203b1db56292b85a73ba5d60de0c9a1b16c">6d18c203</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2021-01-19T03:40:24-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating copyright years.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/6479ea7ed19dedf17fe8ee9bf03268d76dd07738">6479ea7e</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2021-01-19T03:41:14-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog for 2021.1.1+dfsg-1 release
</pre>
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<h4>14 changed files:</h4>
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<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="#24b35affedf264aaec6df0bd309ea65d03428712">
src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java
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<li class="file-stats">
<a href="#e7671dc46f3e70e56af6a03b98490361bbda252a">
src/main/java/com/actelion/research/calc/Matrix.java
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<li class="file-stats">
<a href="#ccb8da0cdb5f4e8eed3dc4d22c1c5c87e987a8ac">
src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedCFp.java
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<a href="#e16f6d2de98a0d66ea41fdde47b8ed3451728bf8">
<span class="deleted-file">
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src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedPharmSphere.java
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<a href="#4e2d9b56ee5e6cfbdc91257503f8c30f1071d7ad">
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−
src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerPharmPath.java
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<li class="file-stats">
<a href="#ed22655495db08a2aca5f09f76905385ae99687a">
src/main/java/com/actelion/research/chem/descriptor/FingerPrintGenerator.java
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<li class="file-stats">
<a href="#799dbb15966654dfe6c09e7675f2260997c84d43">
<span class="deleted-file">
−
src/main/java/com/actelion/research/chem/descriptor/FingerPrintGeneratorPharmGraph.java
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<li class="file-stats">
<a href="#eb906fd58f60b7b86b0fb0d40ae47f3639d5a510">
src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java
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<li class="file-stats">
<a href="#7b32aee2bd2c1c0fe6cea4b3b6604cb7c21864dd">
src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileParser.java
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<li class="file-stats">
<a href="#e44318dc5e713fcc04825cb6ce1158d655b25241">
src/main/java/com/actelion/research/chem/io/pdb/parser/Residue.java
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<li class="file-stats">
<a href="#b79ed66de0dd694eb9d9001763bf57deb57a6bdf">
src/main/java/com/actelion/research/gui/JChemistryView.java
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">openchemlib (2021.1.1+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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<td class="diff-line-num new new_line" 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 2021.1.1+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"></span>
</pre>
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<td class="diff-line-num new new_line" 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"> -- Andrius Merkys <merkys@debian.org> Tue, 19 Jan 2021 03:41:04 -0500</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"></span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">openchemlib (2021.1.0+dfsg-2) unstable; urgency=medium</span>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="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"> * Not running autopkgtest on armhf and i386 due to missing libopenjfx-jni.</span>
</pre>
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<br>
</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Copyright: 1997-2021, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, CH-412</td>
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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: 2021, Andrius Merkys <merkys@debian.org></span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Copyright: 202<span class="idiff left right">0-202</span>1, 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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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#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>2021.1.<span class="idiff left right">0</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>2021.1.<span class="idiff left right">1</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">@@ -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-2021.1.<span class="idiff left right">0</span><span class="nt" style="color: #000080;"></tag></span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="xml"> <span class="nt" style="color: #000080;"><tag></span>openchemlib-2021.1.<span class="idiff left right">1</span><span class="nt" style="color: #000080;"></tag></span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="xml"> <span class="nt" style="color: #000080;"></scm></span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="xml"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="xml"> <span class="nt" style="color: #000080;"><distributionManagement></span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#24b35affedf264aaec6df0bd309ea65d03428712"><strong>src/main/java/com/actelion/research/calc/ArrayUtilsCalc.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">@@ -178,33 +178,42 @@ public class ArrayUtilsCalc {</td>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kt" style="color: #458; font-weight: 600;">var</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java"> <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="LC181" 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="nf" style="color: #900; font-weight: 600;">getVariance</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;">arr</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</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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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getMean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</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="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;">arr</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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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</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;">mean</span><span class="o" style="font-weight: 600;">)*(</span><span class="n" style="color: #333;">arr</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;">mean</span><span class="o" style="font-weight: 600;">);</span></span>
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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="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="kt" style="color: #458; font-weight: 600;">var</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 class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kt" style="color: #458; font-weight: 600;">var</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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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java"></span>
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182
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191
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<pre style="margin: 0;"> <span id="LC191" 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="nf" style="color: #900; font-weight: 600;">getStandardDeviation</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;">arr</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> </span>
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184
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</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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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> </span>
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186
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getMean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</span><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>
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188
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194
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<pre style="margin: 0;"> <span id="LC194" 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;">arr</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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189
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</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;">mean</span><span class="o" style="font-weight: 600;">)*(</span><span class="n" style="color: #333;">arr</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;">mean</span><span class="o" style="font-weight: 600;">);</span></span>
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190
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sdv</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;">sqrt</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 class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sdv</span><span class="o" style="font-weight: 600;">;</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"> <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>
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201
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<pre style="margin: 0;"> <span id="LC201" 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="nf" style="color: #900; font-weight: 600;">getMean</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;">arr</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>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</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="LC200" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC203" 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;">arr</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="LC204" 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;">arr</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="LC205" class="line" lang="java"> <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>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">arr</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="LC207" class="line" lang="java"> <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>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC209" 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="nf" style="color: #900; font-weight: 600;">getMean</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;">arr</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="LC210" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</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="LC211" 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;">arr</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="LC212" 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;">arr</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="LC213" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">arr</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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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java"></span>
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208
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217
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<pre style="margin: 0;"> <span id="LC217" 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;">ModelMedianDouble</span> <span class="nf" style="color: #900; font-weight: 600;">getMedian</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;">arr</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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209
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java"> </span>
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210
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219
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<pre style="margin: 0;"> <span id="LC219" 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;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arr</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="705" style="width: 35px; color: rgba(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="714" style="width: 35px; color: rgba(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">@@ -705,6 +714,7 @@ public class ArrayUtilsCalc {</td>
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">;</span></span>
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706
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="java"></span>
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708
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</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;">toArray</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;">list</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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709
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">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;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">list</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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710
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720
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<pre style="margin: 0;"> <span id="LC720" 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;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="760" style="width: 35px; color: rgba(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">@@ -750,6 +760,7 @@ public class ArrayUtilsCalc {</td>
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750
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">;</span></span>
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="java"></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="java"></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</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;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">toList</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;">a</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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754
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765
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<pre style="margin: 0;"> <span id="LC765" 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;">a</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="LC766" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#e7671dc46f3e70e56af6a03b98490361bbda252a"><strong>src/main/java/com/actelion/research/calc/Matrix.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">@@ -35,6 +35,7 @@ package com.actelion.research.calc;</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.DoubleVec</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.convert.String2DoubleArray</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.datamodel.IntegerDouble</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.datamodel.ScorePoint</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.awt.*</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -538,12 +539,20 @@ public class Matrix {</td>
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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="kd" style="font-weight: 600;">public</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;">getColAsFloat</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;">iCol</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="LC541" class="line" lang="java"> <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;">arr</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;">float</span> <span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rows</span><span class="o" style="font-weight: 600;">()];</span></span>
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<pre style="margin: 0;">-<span id="LC541" 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 class="idiff left">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></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">ii</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">rows</span></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 right">i</span>i</span><span class="o" style="font-weight: 600;">++){</span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="java"> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i<span class="idiff left">i</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="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>i</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">iCol</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">+<span id="LC542" 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 class="idiff left">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></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">i</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">rows</span></span><span class="o" style="font-weight: 600;"><span class="idiff">();</span></span><span class="idiff right"> </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="LC543" class="line" lang="java"> <span class="n" style="color: #333;">arr</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="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="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">[</span></span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">iCol</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arr</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</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;">getColAsInt</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;">iCol</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="LC549" 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;">arr</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;">rows</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="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;">rows</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="LC551" class="line" lang="java"> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)(</span><span class="n" style="color: #333;">data</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;">iCol</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>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arr</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>
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<pre style="margin: 0;"> <span id="LC556" 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="LC557" 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="LC558" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param vecIndices</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3031" style="width: 35px; color: rgba(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">@@ -3031,6 +3040,35 @@ public class Matrix {</td>
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<pre style="margin: 0;"> <span id="LC3040" class="line" lang="java"> <span class="no" style="color: #008080;">OUT_SEPARATOR_ROW</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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3041
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<pre style="margin: 0;"> <span id="LC3041" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC3042" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC3043" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC3044" 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;">shuffleRows</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="LC3045" 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="LC3046" 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;">rows</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC3047" 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="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="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="LC3048" class="line" lang="java"> <span class="n" style="color: #333;">swapRows</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;">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;">i</span><span class="o" style="font-weight: 600;">));</span></span>
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3049
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<pre style="margin: 0;">+<span id="LC3049" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3050
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<pre style="margin: 0;">+<span id="LC3050" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3051
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<pre style="margin: 0;">+<span id="LC3051" class="line" lang="java"></span>
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3052
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<pre style="margin: 0;">+<span id="LC3052" 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;">swapRows</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="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="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3053
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<pre style="margin: 0;">+<span id="LC3053" 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;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</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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3054
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<pre style="margin: 0;">+<span id="LC3054" class="line" lang="java"> <span class="n" style="color: #333;">data</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;">data</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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3055
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<pre style="margin: 0;">+<span id="LC3055" class="line" lang="java"> <span class="n" style="color: #333;">data</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;">t</span><span class="o" style="font-weight: 600;">;</span></span>
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3056
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<pre style="margin: 0;">+<span id="LC3056" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3057
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<pre style="margin: 0;">+<span id="LC3057" class="line" lang="java"></span>
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3058
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<pre style="margin: 0;">+<span id="LC3058" 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;">sortRows</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;">col</span><span class="o" style="font-weight: 600;">){</span></span>
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3059
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<pre style="margin: 0;">+<span id="LC3059" 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;">rows</span><span class="o" style="font-weight: 600;">();</span></span>
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3060
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<pre style="margin: 0;">+<span id="LC3060" 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;">IntegerDouble</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">li</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;">r</span><span class="o" style="font-weight: 600;">);</span></span>
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3061
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<pre style="margin: 0;">+<span id="LC3061" 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;">r</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3062
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<pre style="margin: 0;">+<span id="LC3062" class="line" lang="java"> <span class="n" style="color: #333;">li</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="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntegerDouble</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;">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="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">)));</span></span>
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3063
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<pre style="margin: 0;">+<span id="LC3063" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3064
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<pre style="margin: 0;">+<span id="LC3064" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">li</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntegerDouble</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getComparatorDouble</span><span class="o" style="font-weight: 600;">());</span></span>
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3065
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<pre style="margin: 0;">+<span id="LC3065" 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;">dataSorted</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">][];</span></span>
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3066
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<pre style="margin: 0;">+<span id="LC3066" 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;">r</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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3067
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<pre style="margin: 0;">+<span id="LC3067" class="line" lang="java"> <span class="n" style="color: #333;">dataSorted</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;">data</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">li</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;">getInt</span><span class="o" style="font-weight: 600;">()];</span></span>
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3068
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<pre style="margin: 0;">+<span id="LC3068" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3069
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<pre style="margin: 0;">+<span id="LC3069" class="line" lang="java"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataSorted</span><span class="o" style="font-weight: 600;">;</span></span>
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3070
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<pre style="margin: 0;">+<span id="LC3070" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC3071" class="line" lang="java"></span>
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3072
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<pre style="margin: 0;"> <span id="LC3072" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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3035
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3073
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<pre style="margin: 0;"> <span id="LC3073" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Get the standard scores, also known as z-scores.</span></span>
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3036
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3074
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<pre style="margin: 0;"> <span id="LC3074" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return matrux with standardized values.</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#ccb8da0cdb5f4e8eed3dc4d22c1c5c87e987a8ac"><strong>src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedCFp.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -104,7 +104,7 @@ public class DescriptorHandlerHashedCFp extends AbstractDescriptorHandlerFP<Ster</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newMax</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>
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<pre style="margin: 0;"> <span id="LC105" 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="n" style="color: #333;">min</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;">max</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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106
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<pre style="margin: 0;"> <span id="LC106" 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;">atomList</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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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="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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">);</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<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="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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)</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">mol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">getMetalBondedConnAtoms</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">atom</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" 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;">atomMask</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">atomMask</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#e16f6d2de98a0d66ea41fdde47b8ed3451728bf8"><strong>src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerHashedPharmSphere.java</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 1997 - 2016</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Actelion Pharmaceuticals Ltd.</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Gewerbestrasse 16</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* CH-4123 Allschwil, Switzerland</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* All rights reserved.</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Redistribution and use in source and binary forms, with or without</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* modification, are permitted provided that the following conditions are met:</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 1. Redistributions of source code must retain the above copyright notice, this</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* list of conditions and the following disclaimer.</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 2. Redistributions in binary form must reproduce the above copyright notice,</span></span>
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15
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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 list of conditions and the following disclaimer in the documentation</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* and/or other materials provided with the distribution.</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 3. Neither the name of the the copyright holder nor the</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* names of its contributors may be used to endorse or promote products</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* derived from this software without specific prior written permission.</span></span>
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<pre style="margin: 0;">-<span id="LC20" 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="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR</span></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;">* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES</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;">* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;</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;">* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND</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;">* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</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;">* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</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;">* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></span>
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<pre style="margin: 0;">-<span id="LC31" 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="LC32" 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="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor</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>
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<pre style="margin: 0;">-<span id="LC36" 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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<pre style="margin: 0;">-<span id="LC37" 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="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.SSSearcherWithIndex</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 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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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.BurtleHasher</span><span class="o" style="font-weight: 600;">;</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.util.datamodel.IntVec</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerHashedPharmSphere</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractDescriptorHandlerFP</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="o" style="font-weight: 600;">{</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="no" style="color: #008080;">CORRECTION_FACTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.6</span><span class="o" style="font-weight: 600;">;</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerHashedPharmSphere</span> <span class="n" style="color: #333;">sDefaultInstance</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>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">SPHERE_COUNT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">HASH_BITS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">HASH_INIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">13</span><span class="o" style="font-weight: 600;">;</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">DESCRIPTOR_SIZE</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="no" style="color: #008080;">HASH_BITS</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC55" 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;">DescriptorHandlerHashedPharmSphere</span> <span class="nf" style="color: #900; font-weight: 600;">getDefaultInstance</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="LC56" class="line" lang="java"> <span class="kd" style="font-weight: 600;">synchronized</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerHashedPharmSphere</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">class</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sDefaultInstance</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="LC58" class="line" lang="java"> <span class="n" style="color: #333;">sDefaultInstance</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;">DescriptorHandlerHashedPharmSphere</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 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;">return</span> <span class="n" style="color: #333;">sDefaultInstance</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>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorInfo</span> <span class="nf" style="color: #900; font-weight: 600;">getInfo</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="LC65" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorConstants</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DESCRIPTOR_HashedCFp</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="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="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getVersion</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;">return</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorConstants</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DESCRIPTOR_HashedCFp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">version</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>
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<pre style="margin: 0;">-<span id="LC72" 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="LC73" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This descriptor requires proper up/down bonds, because it encodes stereo parities.</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;"> * If a passed molecule is generated from idcode parsing, make sure that coordinates</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;"> * and up/down/bonds are available, i.e. that the IDCodeParser was instantiated with</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;"> * the respective option.</span></span>
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<pre style="margin: 0;">-<span id="LC77" 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="LC78" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">createDescriptor</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC81" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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;">cHelperRings</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="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">fragment</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;">mol</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="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllBonds</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// byte[] descriptor = new byte[DESCRIPTOR_SIZE];</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">DESCRIPTOR_SIZE</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="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="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntVec</span> <span class="n" style="color: #333;">iv</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;">IntVec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">len</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">atomList</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">atomMask</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">()];</span></span>
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<pre style="margin: 0;">-<span id="LC91" 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;">rootAtom</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;">rootAtom</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;">getAllAtoms</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">rootAtom</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" 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;">rootAtom</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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93
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<pre style="margin: 0;">-<span id="LC93" 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;">fill</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atomMask</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"></span>
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95
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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;">min</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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96
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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;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<pre style="margin: 0;">-<span id="LC97" 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;">sphere</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;">sphere</span><span class="o" style="font-weight: 600;"><</span><span class="no" style="color: #008080;">SPHERE_COUNT</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="n" style="color: #333;">mol</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="n" style="color: #333;">sphere</span><span class="o" style="font-weight: 600;">++)</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="k" style="font-weight: 600;">if</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="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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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">atomList</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;">rootAtom</span><span class="o" style="font-weight: 600;">;</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">atomMask</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rootAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">max</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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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <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="k" style="font-weight: 600;">else</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newMax</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>
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105
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<pre style="margin: 0;">-<span id="LC105" 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="n" style="color: #333;">min</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;">max</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" 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;">atomList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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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="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;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">atom</span><span class="o" style="font-weight: 600;">)+</span><span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getMetalBondedConnAtoms</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;">j</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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;">atom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" 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;">atomMask</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">atomMask</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="n" style="color: #333;">atomList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">newMax</span><span class="o" style="font-weight: 600;">++]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connAtom</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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="LC114" class="line" lang="java"> <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;">min</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>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newMax</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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118
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<pre style="margin: 0;">-<span id="LC118" 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="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyMoleculeByAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fragment</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">atomMask</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// take fragment as it is</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <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="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Canonizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fragment</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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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;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">BurtleHasher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hashlittle</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="no" style="color: #008080;">HASH_INIT</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="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">&</span> <span class="nc" style="color: #458; font-weight: 600;">BurtleHasher</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hashmask</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">HASH_BITS</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="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setBit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"></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;">//System.out.println("atom:"+rootAtom+"\tsphere:"+sphere+"\thash:"+h+"\t"+idcode);</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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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<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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">iv</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>
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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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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">getSimilarity</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;">o1</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;">o2</span><span class="o" style="font-weight: 600;">)</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;">return</span> <span class="n" style="color: #333;">o1</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">o2</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">o1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">o2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">0.0f</span></span>
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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">normalizeValue</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="na" style="color: #008080;">getSimilarityTanimoto</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">o1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">o2</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="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>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">normalizeValue</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.0f</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">0.0f</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">1.0f</span></span>
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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> <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;">float</span><span class="o" style="font-weight: 600;">)(</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">-</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</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="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">CORRECTION_FACTOR</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="no" style="color: #008080;">CORRECTION_FACTOR</span><span class="o" style="font-weight: 600;">));</span></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>
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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="nc" style="color: #458; font-weight: 600;">DescriptorHandler</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="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getThreadSafeCopy</span><span class="o" style="font-weight: 600;">()</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;">return</span> <span class="k" style="font-weight: 600;">this</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="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>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#4e2d9b56ee5e6cfbdc91257503f8c30f1071d7ad"><strong>src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerPharmPath.java</strong>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 1997 - 2016</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Actelion Pharmaceuticals Ltd.</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Gewerbestrasse 16</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* CH-4123 Allschwil, Switzerland</span></span>
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<pre style="margin: 0;">-<span id="LC6" 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="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* All rights reserved.</span></span>
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<pre style="margin: 0;">-<span id="LC8" 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="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Redistribution and use in source and binary forms, with or without</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* modification, are permitted provided that the following conditions are met:</span></span>
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<pre style="margin: 0;">-<span id="LC11" 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="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 1. Redistributions of source code must retain the above copyright notice, this</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* list of conditions and the following disclaimer.</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 2. Redistributions in binary form must reproduce the above copyright notice,</span></span>
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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 list of conditions and the following disclaimer in the documentation</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;">* and/or other materials provided with the distribution.</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;">* 3. Neither the name of the the copyright holder nor the</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;">* names of its contributors may be used to endorse or promote products</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;">* derived from this software without specific prior written permission.</span></span>
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<pre style="margin: 0;">-<span id="LC20" 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="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR</span></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;">* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES</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;">* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;</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;">* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND</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;">* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</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;">* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</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;">* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></span>
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<pre style="margin: 0;">-<span id="LC31" 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="LC32" 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="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor</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>
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<pre style="margin: 0;">-<span id="LC36" 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="LC37" class="line" lang="java"></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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerPharmPath</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractDescriptorHandlerFP</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="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorConstants</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 class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="no" style="color: #008080;">CORRECTION_FACTOR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.85</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerPharmPath</span> <span class="n" style="color: #333;">sDefaultInstance</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="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;">DescriptorHandlerPharmPath</span> <span class="nf" style="color: #900; font-weight: 600;">getDefaultInstance</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="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DescriptorHandlerPharmPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">class</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sDefaultInstance</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="LC46" class="line" lang="java"> <span class="n" style="color: #333;">sDefaultInstance</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;">DescriptorHandlerPharmPath</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="o" style="font-weight: 600;">}</span></span>
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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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sDefaultInstance</span><span class="o" style="font-weight: 600;">;</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorInfo</span> <span class="nf" style="color: #900; font-weight: 600;">getInfo</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;">return</span> <span class="no" style="color: #008080;">DESCRIPTOR_PFP512</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getVersion</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="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorConstants</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">DESCRIPTOR_PFP512</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">version</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="o" style="font-weight: 600;">}</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="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">createDescriptor</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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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;">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>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC63" class="line" lang="java"></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="n" style="color: #333;">java</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">BitSet</span> <span class="n" style="color: #333;">bitset</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;">FingerPrintGeneratorPharmGraph</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getFingerprint</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>
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65
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<pre style="margin: 0;">-<span id="LC65" 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;">bitset</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="LC67" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="no" style="color: #008080;">FAILED_OBJECT</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>
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<pre style="margin: 0;">-<span id="LC69" 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;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">16</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;">mask</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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71
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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;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">32</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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72
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<pre style="margin: 0;">-<span id="LC72" 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="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++)</span></span>
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73
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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;">bitset</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;">16</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;">j</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="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mask</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="n" style="color: #333;">mask</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="LC76" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fp</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">DescriptorHandler</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="nc" style="color: #458; font-weight: 600;">StereoMolecule</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">getThreadSafeCopy</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="LC82" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> <span class="nd">@Override</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" 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;">getSimilarity</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;">o1</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;">o2</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="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">normalizeValue</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSimilarity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">o1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">o2</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">normalizeValue</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">value</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="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.0f</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">0.0f</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">1.0f</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 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="mf" style="color: #099;">1.0</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;">pow</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="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pow</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">CORRECTION_FACTOR</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="no" style="color: #008080;">CORRECTION_FACTOR</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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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#ed22655495db08a2aca5f09f76905385ae99687a"><strong>src/main/java/com/actelion/research/chem/descriptor/FingerPrintGenerator.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(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">@@ -151,7 +151,7 @@ public class FingerPrintGenerator</td>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="java"> <span class="n" style="color: #333;">paths</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;">Hashtable</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">debugCounter</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="LC154" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atoms</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;">getA<span class="idiff left right">llA</span>toms</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atoms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAtoms</span><span class="o" style="font-weight: 600;">();</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</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="LC156" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atoms</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;">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;">atoms</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,7 +178,7 @@ public class FingerPrintGenerator</td>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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179
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<pre style="margin: 0;"> <span id="LC179" 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;">traverseDFS</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastAtom</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;">rootAtom</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;">path</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;">depth</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">flags</span><span class="o" style="font-weight: 600;">[])</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java"> <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 class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connAtoms</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;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rootAtom</span><span class="o" style="font-weight: 600;">);</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">connAtoms</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;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rootAtom</span><span class="o" style="font-weight: 600;">)</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">mol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">getMetalBondedConnAtoms</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rootAtom</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>;</span></span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nextAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">newPath</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;">StringBuilder</span><span class="o" style="font-weight: 600;">();</span></span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -206,6 +206,8 @@ public class FingerPrintGenerator</td>
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206
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"="</span><span class="o" style="font-weight: 600;">);</span></span>
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207
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#"</span><span class="o" style="font-weight: 600;">);</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">bond</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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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">);</span></span>
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209
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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210
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212
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<pre style="margin: 0;"> <span id="LC212" 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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211
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java"> <span class="s" style="color: #d14;">"FingerPrintGenerator.depthFirstSearch() "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#799dbb15966654dfe6c09e7675f2260997c84d43"><strong>src/main/java/com/actelion/research/chem/descriptor/FingerPrintGeneratorPharmGraph.java</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 1997 - 2016</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Actelion Pharmaceuticals Ltd.</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Gewerbestrasse 16</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* CH-4123 Allschwil, Switzerland</span></span>
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<pre style="margin: 0;">-<span id="LC6" 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="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* All rights reserved.</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* Redistribution and use in source and binary forms, with or without</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* modification, are permitted provided that the following conditions are met:</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 1. Redistributions of source code must retain the above copyright notice, this</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* list of conditions and the following disclaimer.</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 2. Redistributions in binary form must reproduce the above copyright notice,</span></span>
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15
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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 list of conditions and the following disclaimer in the documentation</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* and/or other materials provided with the distribution.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* 3. Neither the name of the the copyright holder nor the</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* names of its contributors may be used to endorse or promote products</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* derived from this software without specific prior written permission.</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR</span></span>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC25" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES</span></span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="cm" style="color: #998; font-style: italic;">* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND</span></span>
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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</span></span>
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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS</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;">* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></span>
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<pre style="margin: 0;">-<span id="LC31" 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="LC32" 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="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.chem.descriptor</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>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.IDCodeParser</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" 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="LC38" 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="LC39" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.BufferedReader</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.InputStreamReader</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.BitSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Enumeration</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Hashtable</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="LC46" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC47" 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="LC48" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Generator of a path-based Fingerprint</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Not thread safe!</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" 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;">FingerPrintGeneratorPharmGraph</span> </span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"><span class="o" style="font-weight: 600;">{</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_BITS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_DEPTH</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">;</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">DEBUG</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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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">debugCounter</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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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Hashtable</span> <span class="n" style="color: #333;">paths</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>
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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="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Generates a fingerprint of the default size for the given ExtendedMolecule</span></span>
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<pre style="margin: 0;">-<span id="LC62" 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="LC63" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param mol The ExtendedMolecule for which a Fingerprint is generated</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return The Fingerprint (A one-dimensional bit array)</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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="LC66" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">BitSet</span> <span class="nf" style="color: #900; font-weight: 600;">getFingerprint</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">)</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <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="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">getFingerprint</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="no" style="color: #008080;">MAX_BITS</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="o" style="font-weight: 600;">}</span></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>
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<pre style="margin: 0;">-<span id="LC72" 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="LC73" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Generates the fingerprint of a molecule</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;"> * @param mol The ExtendedMolecule for which a Fingerprint is generated</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;"> * @param size The desired size of the fingerprint</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return The Fingerprint (A one-dimensional bit array)</span></span>
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<pre style="margin: 0;">-<span id="LC78" 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="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">BitSet</span> <span class="nf" style="color: #900; font-weight: 600;">getFingerprint</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</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="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;">String</span> <span class="n" style="color: #333;">path</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="LC82" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</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="n" style="color: #333;">mol</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;">cHelperRings</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="n" style="color: #333;">findAllPaths</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>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BitSet</span> <span class="n" style="color: #333;">bs</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;">BitSet</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="LC87" 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;">Enumeration</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">elements</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;">hasMoreElements</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="LC88" class="line" lang="java"> <span class="n" style="color: #333;">path</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;">String</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;">nextElement</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;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">java</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Random</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hashCode</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;">size</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DEBUG</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="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;">print</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;">toString</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">40</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="LC92" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.out.println("Setting bit " + position + " for " + path);</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">bs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</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>
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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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bs</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"></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="LC100" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC102" 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="LC103" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Find all paths up to MAX_DEPTH length.</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The paths are acquired by a number of depth first searches, one for each atom.</span></span>
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<pre style="margin: 0;">-<span id="LC105" 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="LC106" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param mol The Molecule which is to be searched.</span></span>
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<pre style="margin: 0;">-<span id="LC107" 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="LC108" 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;">findAllPaths</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">paths</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;">Hashtable</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="n" style="color: #333;">debugCounter</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="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">atoms</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;">getAllAtoms</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="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">s</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="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">atoms</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="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;">atoms</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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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">s</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;">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>
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117
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<pre style="margin: 0;">-<span id="LC117" 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;">atoms</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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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="n" style="color: #333;">flags</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;">false</span><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="n" style="color: #333;">addPath</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="LC120" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DEBUG</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC121" 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;">"\t***Starting at atom "</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="s" style="color: #d14;">" with symbol "</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;">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>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">traverseDFS</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="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;">atom</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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">flags</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC127" 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="LC128" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Performs a recursive depth first search</span></span>
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<pre style="margin: 0;">-<span id="LC129" 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="LC130" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param mol The Molecule to be searched</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param lastAtom The Atom we came from</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param rootAtom The Atom to start the search at</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param path The Path that has been generated so far</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param depth The current depth in this recursive search</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param flags Helper flags</span></span>
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<pre style="margin: 0;">-<span id="LC136" 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="LC137" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC138" 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;">traverseDFS</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">StereoMolecule</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastAtom</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;">rootAtom</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;">path</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;">depth</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">flags</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="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;">connAtoms</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;">getConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rootAtom</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;">getMetalBondedConnAtoms</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rootAtom</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nextAtom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="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="LC142" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuilder</span> <span class="n" style="color: #333;">newPath</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;">StringBuilder</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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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="n" style="color: #333;">depth</span><span class="o" style="font-weight: 600;">++;</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Check all connected atoms</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" 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;">connAtoms</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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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Flag starting point</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="n" style="color: #333;">flags</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rootAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="n" style="color: #333;">nextAtom</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;">rootAtom</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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150
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<pre style="margin: 0;">-<span id="LC150" 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;">nextAtom</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">lastAtom</span><span class="o" style="font-weight: 600;">)</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="k" style="font-weight: 600;">continue</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="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>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Not yet seen</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;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">flags</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nextAtom</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="n" style="color: #333;">bond</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getConnBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rootAtom</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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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setLength</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Construct a string with Daylight kind of bond encoding</span></span>
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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
160
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<pre style="margin: 0;">-<span id="LC160" 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;">isDelocalizedBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mol</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAromaticBond</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bond</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">);</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">bond</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>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"="</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">bond</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">bond</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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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">);</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" 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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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="s" style="color: #d14;">"FingerPrintGenerator.depthFirstSearch() "</span> <span class="o" style="font-weight: 600;">+</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="s" style="color: #d14;">"Error: Invalid Bond order! "</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;">bond</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mol</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;">nextAtom</span><span class="o" style="font-weight: 600;">));</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Mark nextAtom as visited</span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="n" style="color: #333;">flags</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nextAtom</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> <span class="n" style="color: #333;">addPath</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newPath</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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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" 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;">depth</span> <span class="o" style="font-weight: 600;">==</span> <span class="no" style="color: #008080;">MAX_DEPTH</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 old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Unmark nextAtoms so we might visit it again during another run</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">flags</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nextAtom</span><span class="o" style="font-weight: 600;">]</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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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// System.out.println("Reached end of depth!!! " + newPath);</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;"><</span> <span class="no" style="color: #008080;">MAX_DEPTH</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// System.out.println("Visiting " + rootAtom + " + " + nextAtom + " " + newPath);</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="n" style="color: #333;">traverseDFS</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;">rootAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nextAtom</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newPath</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 class="n" style="color: #333;">depth</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">flags</span><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="c1" style="color: #998; font-style: italic;">// Unmark nextAtoms so we might visit it again during another run</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="n" style="color: #333;">flags</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nextAtom</span><span class="o" style="font-weight: 600;">]</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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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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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">addPath</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;">newPath</span><span class="o" style="font-weight: 600;">)</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">storePath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newPath</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">reversePath</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;">StringBuilder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">storePath</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">reverse</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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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ok</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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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Find the "smaller" version</span></span>
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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
200
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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;">reversePath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compareTo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">newPath</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="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/* reversePath is smaller than newPath so we keep reversePath */</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"> <span class="n" style="color: #333;">storePath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reversePath</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="o" style="font-weight: 600;">}</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DEBUG</span><span class="o" style="font-weight: 600;">)</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" 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;">"Checking for existence of Path "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">storePath</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">paths</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;">storePath</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="LC207" class="line" lang="java"> <span class="n" style="color: #333;">paths</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;">storePath</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">storePath</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;">ok</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="LC209" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">DEBUG</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="LC210" class="line" lang="java"> <span class="n" style="color: #333;">debugCounter</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="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;">"Storing path no. "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">debugCounter</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;">storePath</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", Hash: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">storePath</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hashCode</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="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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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ok</span><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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"></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></pre>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#eb906fd58f60b7b86b0fb0d40ae47f3639d5a510"><strong>src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java</strong></a>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#7b32aee2bd2c1c0fe6cea4b3b6604cb7c21864dd"><strong>src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileParser.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">@@ -519,7 +519,7 @@ public class PDBFileParser {</td>
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<pre style="margin: 0;"> <span id="LC519" 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="LC520" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="java"> <span class="n" style="color: #333;">indexLine</span><span class="o" style="font-weight: 600;">--;</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>indexLine--;</span></span>
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523
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523
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<pre style="margin: 0;"> <span id="LC523" 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;">AtomRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hetAtomRecords</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;">AtomRecord</span><span class="o" style="font-weight: 600;">>();</span></span>
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524
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524
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<pre style="margin: 0;"> <span id="LC524" 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;">AtomRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">protAtomRecords</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;">AtomRecord</span><span class="o" style="font-weight: 600;">>();</span></span>
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525
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="java"> <span class="n" style="color: #333;">modelParser</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;">liRaw</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indexLine</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">protAtomRecords</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">hetAtomRecords</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#e44318dc5e713fcc04825cb6ce1158d655b25241"><strong>src/main/java/com/actelion/research/chem/io/pdb/parser/Residue.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,13 +89,16 @@ public class Residue {</td>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">fragment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomY</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;">record</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getY</span><span class="o" style="font-weight: 600;">());</span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">fragment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setAtomZ</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;">record</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getZ</span><span class="o" style="font-weight: 600;">());</span></span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">fragment</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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92
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94
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<pre style="margin: 0;"> <span id="LC94" 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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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BondsCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">createBonds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fragment</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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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BondsCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">calculateBondOrders</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fragment</span><span class="o" style="font-weight: 600;">);</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BondsCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">createBonds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fragment</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 class="idiff left">,</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BondsCalculator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">calculateBondOrders</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fragment</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></span><span class="o" style="font-weight: 600;">);</span></span>
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95
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">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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96
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<td class="diff-line-num new_line old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Cannot process structure"</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="c1" style="color: #998; font-style: italic;">// TODO Auto-generated catch block</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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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="LC98" class="line" lang="java"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fragment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">ensureHelperArrays</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Molecule</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">cHelperCIP</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">);</span></span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fragment</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="o" style="font-weight: 600;">}</span></span>
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101
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"> </span>
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<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/6f58c52f5edb935c5b289541aaf4be3d906693f5...6479ea7ed19dedf17fe8ee9bf03268d76dd07738#b79ed66de0dd694eb9d9001763bf57deb57a6bdf"><strong>src/main/java/com/actelion/research/gui/JChemistryView.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">@@ -34,6 +34,8 @@</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">com.actelion.research.gui</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>
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<pre style="margin: 0;"> <span id="LC36" 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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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.CompoundFileHelper</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.RDFileParser</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.io.RXNFileParser</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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.chem.reaction.Reaction</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">com.actelion.research.gui.clipboard.ClipboardHandler</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">@@ -373,11 +375,23 @@ public class JChemistryView extends JComponent</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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376
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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 class="k" style="font-weight: 600;">if</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;">getActionCommand</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">ITEM_OPEN_RXN</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mIsEditable</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">rxnFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">FileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFile</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="s" style="color: #d14;">"Please select a reaction file"</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">FileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cFileTypeRXN</span><span class="o" style="font-weight: 600;">);</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">rxnFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">FileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFile</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="s" style="color: #d14;">"Please select a reaction file"</span><span class="o" style="font-weight: 600;">,</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">FileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cFileTypeRXN</span> <span class="o" style="font-weight: 600;">|</span> <span class="nc" style="color: #458; font-weight: 600;">CompoundFileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cFileTypeRD</span><span class="o" style="font-weight: 600;">);</span></span>
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377
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380
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<pre style="margin: 0;"> <span id="LC380" 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;">rxnFile</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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378
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381
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<pre style="margin: 0;"> <span id="LC381" 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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379
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<pre style="margin: 0;">-<span id="LC379" 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;">RXNFileParser</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxnFile</span><span class="o" style="font-weight: 600;">);</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="java"> <span class="n" style="color: #333;">pasteOrDropReaction</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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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" 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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFileType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxnFile</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="nc" style="color: #458; font-weight: 600;">FileHelper</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">cFileTypeRXN</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 new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="java"> <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;">RXNFileParser</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getReaction</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxnFile</span><span class="o" style="font-weight: 600;">);</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" 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="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RDFileParser</span> <span class="n" style="color: #333;">rdfParser</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;">RDFileParser</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rxnFile</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rdfParser</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isReactionNext</span><span class="o" style="font-weight: 600;">())</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="java"> <span class="n" style="color: #333;">reaction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rdfParser</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNextReaction</span><span class="o" style="font-weight: 600;">();</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="java"></span>
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393
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<pre style="margin: 0;">+<span id="LC393" 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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="java"> <span class="n" style="color: #333;">pasteOrDropReaction</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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381
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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382
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396
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<pre style="margin: 0;"> <span id="LC396" 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;">ex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{}</span></span>
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383
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397
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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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