<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>
GitLab
</title>
<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>
<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">
<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andrius Merkys pushed to branch master at <a href="https://salsa.debian.org/java-team/openchemlib">Debian Java Maintainers / openchemlib</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/621792c71d75f73110db4862862aa7da9ec33797">621792c7</a></strong>
<div>
<span> by Andrius Merkys </span> <i> at 2026-02-23T04:07:44-05:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update the Files-Excluded list.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/d725b7539d23f001ca5c962c46bcab4cea32c2e2">d725b753</a></strong>
<div>
<span> by Andrius Merkys </span> <i> at 2026-02-23T04:10:40-05:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update debian/watch.
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/55e911439cfa90ea58615a22d3de0077626b0753">55e91143</a></strong>
<div>
<span> by Andrius Merkys </span> <i> at 2026-02-23T04:11:02-05:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 2026.2.2+ds</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/e2f5fe2c0e9d5258485f0f8cdba5106ddaf3cba6">e2f5fe2c</a></strong>
<div>
<span> by Andrius Merkys </span> <i> at 2026-02-23T04:11:13-05:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/2026.2.2+ds'
Update to upstream version '2026.2.2+ds'
with Debian dir 8e8644f203c7a4231ba1d1c2a3576e23cb4a3d3d</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/fda66702b536bfa46c7d42c958385e8b5db477fe">fda66702</a></strong>
<div>
<span> by Andrius Merkys </span> <i> at 2026-02-23T04:12:10-05:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update changelog for 2026.2.2+ds-1 release
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/java-team/openchemlib/-/commit/a3641461a1d8f19b065651381d72a184459ef30b">a3641461</a></strong>
<div>
<span> by Andrius Merkys </span> <i> at 2026-02-23T04:12:38-05:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove "non-free" stanza from debian/copyright: not needed anymore.
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
299 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#c709f6995f23dae0da365bff70068f8288fa89e0">
.github/workflows/maven.yml
</a>
</li>
<li class="file-stats">
<a href="#587d266bb27a4dc3022bbed44dfa19849df3044c">
<span class="new-file">
+
.gitlab-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">
pom.xml
</a>
</li>
<li class="file-stats">
<a href="#e757d44ff34c200663f615b28014ca9593c74edb">
src/main/java/com/actelion/research/calc/BinarySOM.java
</a>
</li>
<li class="file-stats">
<a href="#e7671dc46f3e70e56af6a03b98490361bbda252a">
src/main/java/com/actelion/research/calc/Matrix.java
</a>
</li>
<li class="file-stats">
<a href="#3fb31c91982f5b85df4399c611e26c13efebd796">
src/main/java/com/actelion/research/calc/MatrixFunctions.java
</a>
</li>
<li class="file-stats">
<a href="#fd525dcb384f9ccd980601d924a483aee2f43cb7">
src/main/java/com/actelion/research/calc/statistics/StatisticsOverview.java
</a>
</li>
<li class="file-stats">
<a href="#3f5337087ac5d25a71e6430314d07204f2471c0d">
src/main/java/com/actelion/research/chem/AbstractDepictor.java
</a>
</li>
<li class="file-stats">
<a href="#740d1b62554de0bb4911a3fc23e2387b26c0a2b4">
src/main/java/com/actelion/research/chem/AromaticityResolver.java
</a>
</li>
<li class="file-stats">
<a href="#7eaab837edf147069ffb0b63f5fc5a11c0cafe6a">
src/main/java/com/actelion/research/chem/AtomTypeList.java
</a>
</li>
<li class="file-stats">
<a href="#67800693fa8bb7e226e47f0411ca790ea518c656">
src/main/java/com/actelion/research/chem/Canonizer.java
</a>
</li>
<li class="file-stats">
<a href="#cc37dfa00dcad8df0f0b00276dee25504b95b4ea">
src/main/java/com/actelion/research/chem/Coordinates.java
</a>
</li>
<li class="file-stats">
<a href="#c08f7f154847a454b7fea9c415fdf25c8f8e7a7b">
src/main/java/com/actelion/research/chem/ExtendedDepictor.java
</a>
</li>
<li class="file-stats">
<a href="#a366ae93c6b2697647f789b85e058d12270016b2">
src/main/java/com/actelion/research/chem/ExtendedMolecule.java
</a>
</li>
<li class="file-stats">
<a href="#a4a9955a7a49064f89a1e83c8cc8c190f5678157">
src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java
</a>
</li>
<li class="file-stats">
<a href="#a1ec33c7804dfaa6cf903376c9e2af00e9a9a224">
src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java
</a>
</li>
<li class="file-stats">
<a href="#3357d4852d9e2d697d79a0b5c96ed0a78ce44afb">
src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java
</a>
</li>
<li class="file-stats">
<a href="#defba277761dfdcd51e6089fea736885eb756313">
src/main/java/com/actelion/research/chem/MarkushStructure.java
</a>
</li>
<li class="file-stats">
<a href="#7591869d39cf992c9eaa2bbe2598c5927a014b3b">
src/main/java/com/actelion/research/chem/Molecule.java
</a>
</li>
<li class="file-stats">
<a href="#85f02304086eced2dd2dc293f1d73a21c9243a40">
src/main/java/com/actelion/research/chem/Molecule3D.java
</a>
</li>
<li class="file-stats">
<a href="#c1af02d8c1a2ce77f8c1fb671601ae64d537a0bf">
src/main/java/com/actelion/research/chem/MolfileCreator.java
</a>
</li>
<li class="file-stats">
<a href="#129931cc7763032c22d6b8488a89331130ebe2dd">
src/main/java/com/actelion/research/chem/MolfileParser.java
</a>
</li>
<li class="file-stats">
<a href="#369ab0f266ef318c426ac1f34045b7b2701e8608">
src/main/java/com/actelion/research/chem/MolfileV3Creator.java
</a>
</li>
<li class="file-stats">
<a href="#4730c40c35b4fbc4d77963c12d761ea3f5ce9c7d">
src/main/java/com/actelion/research/chem/PeriodicTable.java
</a>
</li>
<li class="file-stats">
<a href="#30d84cf3c3cb1f3e258280f49da9e384acc79bf6">
src/main/java/com/actelion/research/chem/RingCollection.java
</a>
</li>
<li class="file-stats">
<a href="#10b4e82d1026383ff94d9ac253093b56ced2b275">
<span class="deleted-file">
−
src/main/java/com/actelion/research/chem/SDFileMolecule.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#c63e176da7c5c11f44a4e98c7fd4090e168b8470">
src/main/java/com/actelion/research/chem/SSSearcher.java
</a>
</li>
<li class="file-stats">
<a href="#b7a09c1bad58a2b1f3ad512afb001e9c3f04b6ea">
src/main/java/com/actelion/research/chem/SSSearcherWithIndex.java
</a>
</li>
<li class="file-stats">
<a href="#f634c84926d28712a0c6bce533057702e7141433">
src/main/java/com/actelion/research/chem/SVGDepictor.java
</a>
</li>
<li class="file-stats">
<a href="#0615f8faa39d511cb658a8ed2406bcb006827096">
<span class="deleted-file">
−
src/main/java/com/actelion/research/chem/SimpleCanonizer.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#72a076274f5e87729e15c6abd7704c024c592023">
src/main/java/com/actelion/research/chem/SmilesAtomParser.java
</a>
</li>
<li class="file-stats">
<a href="#eeae58405f88cc26b523e233b36d02d467d6d88a">
<span class="deleted-file">
−
src/main/java/com/actelion/research/chem/SmilesCreator.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#ba44c1f7e56c2598decf65ca012c856547ff2f0f">
src/main/java/com/actelion/research/chem/SmilesParser.java
</a>
</li>
<li class="file-stats">
<a href="#f9357fff8e8432aa7cdb58fafe5408824c211bc5">
src/main/java/com/actelion/research/chem/TextDrawingObject.java
</a>
</li>
<li class="file-stats">
<a href="#db187848225ffcb2c693ff202b3b3dec3b976b1b">
src/main/java/com/actelion/research/chem/UniqueStringList.java
</a>
</li>
<li class="file-stats">
<a href="#3c35249cb3564e8724370e8c6a85c4183fb991bd">
src/main/java/com/actelion/research/chem/alignment3d/KabschAlignment.java
</a>
</li>
<li class="file-stats">
<a href="#9f402fb8a8ea5e23e42a42f17e9c1a4b1c8f9ae3">
src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java
</a>
</li>
<li class="file-stats">
<a href="#9a2ed79430200e6b129705b238ce71301130f2de">
src/main/java/com/actelion/research/chem/alignment3d/transformation/Transformation.java
</a>
</li>
<li class="file-stats">
<a href="#4f0b88ca51864a00c73dca781f2d91e6664483be">
src/main/java/com/actelion/research/chem/chemicalspaces/ptree/PharmTreeSynthonReactionHelper.java
</a>
</li>
<li class="file-stats">
<a href="#43f55782352e60319b17e1aaaa11b983e8a6f6db">
src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonReactor.java
</a>
</li>
<li class="file-stats">
<a href="#83a27dcf36fe6fb86db4cf2ed6c93c74cba4d41d">
src/main/java/com/actelion/research/chem/conf/AtomAssembler.java
</a>
</li>
<li class="file-stats">
<a href="#d39389c480f1fb08e28599ca1ad01e2e1d34d345">
src/main/java/com/actelion/research/chem/conf/BondLengthSet.java
</a>
</li>
<li class="file-stats">
<a href="#c8262f3c7551f0e67f586b47594e320bf4d32db9">
src/main/java/com/actelion/research/chem/conf/BondRotationHelper.java
</a>
</li>
<li class="file-stats">
<a href="#05e26abbc02a57f3d862d4ce12ff4fc59d9c0380">
src/main/java/com/actelion/research/chem/conf/Conformer.java
</a>
</li>
<li class="file-stats">
<a href="#fde7966a4e81809618779347cb83887aa70f92b6">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/conf/HydrogenAssembler.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#b7b6e58b76c6ef4f8e67b950673fa55bb1ebabe7">
src/main/java/com/actelion/research/chem/conf/SymmetryCorrectedRMSDCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#49a98b6cc66b1891eecec280e05f3722b5bdfba2">
src/main/java/com/actelion/research/chem/conf/TorsionDB.java
</a>
</li>
<li class="file-stats">
<a href="#f03309c1d84b4020335a3734b0dfb9fb951582d9">
src/main/java/com/actelion/research/chem/conf/torsionstrain/StatisticalTorsionPotential.java
</a>
</li>
<li class="file-stats">
<a href="#256752e2abe4a8102450f0db5f0c2fd3b9cdf981">
src/main/java/com/actelion/research/chem/conf/torsionstrain/StatisticalTorsionTerm.java
</a>
</li>
<li class="file-stats">
<a href="#2324bbf7db1501a1bb2aaae4a1db707a20b5f9b1">
src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java
</a>
</li>
<li class="file-stats">
<a href="#5e82b1f04166bdd538caa94117c69554ccba3c83">
src/main/java/com/actelion/research/chem/coords/InventorDefaultTemplateList.java
</a>
</li>
<li class="file-stats">
<a href="#faf5d0d2614cfb508ac7801f8bd0450e36050d11">
src/main/java/com/actelion/research/chem/coords/InventorTemplate.java
</a>
</li>
<li class="file-stats">
<a href="#2442953af1fd8ff10d1212033c85dd623535992a">
src/main/java/com/actelion/research/chem/descriptor/DescriptorWeightsHelper.java
</a>
</li>
<li class="file-stats">
<a href="#23cd74e73aefa52cc477ec6fa8102ec50eb9d479">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/descriptor/flexophore/MDHFeature.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#347a7b6bb5978efa12b8bdfb1ceacdd7cb0e7d52">
src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHist.java
</a>
</li>
<li class="file-stats">
<a href="#f3fa75cc0abca683e2d41e3b1c3b666bdd900582">
src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistHelper.java
</a>
</li>
<li class="file-stats">
<a href="#d964edbae20e09cbce5c1233058a31fc47b9e866">
src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistViz.java
</a>
</li>
<li class="file-stats">
<a href="#d41c578395734ec30efa0f45c7fc477f6c74723d">
src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistVizHelper.java
</a>
</li>
<li class="file-stats">
<a href="#657809114bb3888849811a77765a7435efa98d07">
src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNode.java
</a>
</li>
<li class="file-stats">
<a href="#f2df548664f54da4e84e3a0a719eb77d74abb08b">
src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java
</a>
</li>
<li class="file-stats">
<a href="#2ff1e7b9f98b72b0760227c30486bd3fb75bb68a">
src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizMultCoord.java
</a>
</li>
<li class="file-stats">
<a href="#0eac2d9bc929910468266429cc340bca0accaba1">
src/main/java/com/actelion/research/chem/descriptor/flexophore/calculator/GeometryCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#e56c86c20bf6184ccfcc68710f754c84bbbca0ce">
src/main/java/com/actelion/research/chem/descriptor/flexophore/calculator/StructureCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#4196854a9684810a9e2daa15712fa52b4026cd7c">
src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/PPNodeSimilarity.java
</a>
</li>
<li class="file-stats">
<a href="#d01c05d4963c1ebd6035eb7a58249d54b1dc24b1">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/AtomTypeMap.java
</a>
</li>
<li class="file-stats">
<a href="#42976117f38fa37d60dd738b507feb19719d5616">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java
</a>
</li>
<li class="file-stats">
<a href="#0f667179656b060a6555beaecd8cb812d479689e">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ExceptionTimeOutConformerGeneration.java
</a>
</li>
<li class="file-stats">
<a href="#c7911b6d8a45ec2006f02d813e6a4095621145ed">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/InteractionTypeMap.java
</a>
</li>
<li class="file-stats">
<a href="#502aa51de245941e652faea5e38c5ce6403aa9e8">
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreExtractorHelper.java
</a>
</li>
<li class="file-stats">
<a href="#e3f1199429acfa46ca9d7214108cb11c1e887576">
src/main/java/com/actelion/research/chem/descriptor/flexophore/redgraph/SubGraphIndices.java
</a>
</li>
<li class="file-stats">
<a href="#ec05b3badbc5071521d94ee516cf51235293f843">
src/main/java/com/actelion/research/chem/docking/DockingEngine.java
</a>
</li>
<li class="file-stats">
<a href="#f678d35a688802dfd7e0cbfc6c14290a34944abc">
src/main/java/com/actelion/research/chem/docking/DockingUtils.java
</a>
</li>
<li class="file-stats">
<a href="#819430bd4feb0962132eaba56931cbec7c761fd8">
src/main/java/com/actelion/research/chem/docking/LigandPose.java
</a>
</li>
<li class="file-stats">
<a href="#5fbec471969d5b55acbbc8ca1426367584b3ee7c">
src/main/java/com/actelion/research/chem/docking/ScoringTask.java
</a>
</li>
<li class="file-stats">
<a href="#0cbf5360ca8983850a3e4193f41de61f08d5b7e0">
src/main/java/com/actelion/research/chem/docking/receptorpharmacophore/NegativeReceptorImage.java
</a>
</li>
<li class="file-stats">
<a href="#baf8de01d611855253f2edd965accfe572d7caf2">
src/main/java/com/actelion/research/chem/docking/receptorpharmacophore/NegativeReceptorImageCreator.java
</a>
</li>
<li class="file-stats">
<a href="#6bf6bc0e867dc60438664fa7e2197883ae9a4053">
src/main/java/com/actelion/research/chem/docking/scoring/AbstractScoringEngine.java
</a>
</li>
<li class="file-stats">
<a href="#35842adf3930ed08842a9c3177f4efd0161d8603">
src/main/java/com/actelion/research/chem/docking/scoring/ChemPLP.java
</a>
</li>
<li class="file-stats">
<a href="#1e236c5e43c30a02fbeea4e900a0c284f6fa34a8">
src/main/java/com/actelion/research/chem/docking/scoring/IdoScore.java
</a>
</li>
<li class="file-stats">
<a href="#121e9d137a32c1c323eccc6683d3b9f8e8c5ff62">
src/main/java/com/actelion/research/chem/docking/scoring/ProbeScanning.java
</a>
</li>
<li class="file-stats">
<a href="#da22f6e52ded95bb6cd35deae8268dff7a3b2839">
src/main/java/com/actelion/research/chem/docking/scoring/idoscore/InteractionTerm.java
</a>
</li>
<li class="file-stats">
<a href="#7c57ce545a8bf9a65f621537815a57c12f9a5d32">
src/main/java/com/actelion/research/chem/docking/scoring/plp/PLPTerm.java
</a>
</li>
<li class="file-stats">
<a href="#34dead2109902d5298d9a0c0f885676a1d1be789">
src/main/java/com/actelion/research/chem/docking/shape/ShapeDocking.java
</a>
</li>
<li class="file-stats">
<a href="#61b084daf0f2ad72fd97032fd20a3efc055af8b4">
src/main/java/com/actelion/research/chem/forcefield/AbstractForceField.java
</a>
</li>
<li class="file-stats">
<a href="#93fdf7b4aa9e25fabc019ce778f0743cce650bcd">
src/main/java/com/actelion/research/chem/forcefield/mmff/AngleBend.java
</a>
</li>
<li class="file-stats">
<a href="#09843bbc758130c7be1b76d20ca42ce6f28a974b">
src/main/java/com/actelion/research/chem/forcefield/mmff/BondStretch.java
</a>
</li>
<li class="file-stats">
<a href="#afb00c541f51f495f66c5646a07b1b6bc657e936">
src/main/java/com/actelion/research/chem/forcefield/mmff/Electrostatic.java
</a>
</li>
<li class="file-stats">
<a href="#1d3ecda08aa0a6c12b33c2b646d8063f2f71dd2f">
src/main/java/com/actelion/research/chem/forcefield/mmff/EnergyTerm.java
</a>
</li>
<li class="file-stats">
<a href="#dba67dc91de42bdf26165774158af90fda3299d9">
src/main/java/com/actelion/research/chem/forcefield/mmff/ForceFieldMMFF94.java
</a>
</li>
<li class="file-stats">
<a href="#126261fb067e1fa2597582203dc97d05348f1073">
src/main/java/com/actelion/research/chem/forcefield/mmff/MMFFExternalPositionConstraint.java
</a>
</li>
<li class="file-stats">
<a href="#6b1332ccfda9832da3e6db8ee7df440b4bbb2aca">
src/main/java/com/actelion/research/chem/forcefield/mmff/MMFFPositionConstraint.java
</a>
</li>
<li class="file-stats">
<a href="#e60852478c6a845b2af084bc1533f80d4e6e7d4b">
src/main/java/com/actelion/research/chem/forcefield/mmff/OutOfPlane.java
</a>
</li>
<li class="file-stats">
<a href="#7dbe1023be47f11db4774d02543f01f9596586b5">
src/main/java/com/actelion/research/chem/forcefield/mmff/SortedPair.java
</a>
</li>
<li class="file-stats">
<a href="#b46347a2ac2806050534d2bea9b99e5676ad66f1">
src/main/java/com/actelion/research/chem/forcefield/mmff/StretchBend.java
</a>
</li>
<li class="file-stats">
<a href="#3095b2e4593bc4e20b52b9d2bca38f721a15c2ea">
src/main/java/com/actelion/research/chem/forcefield/mmff/TorsionAngle.java
</a>
</li>
<li class="file-stats">
<a href="#d8acd65b55c3a27e66ffdb8623349f960a30de93">
src/main/java/com/actelion/research/chem/forcefield/mmff/VanDerWaals.java
</a>
</li>
<li class="file-stats">
<a href="#457379f11d7960850f4ae771a5c8a9bc284d5ade">
src/main/java/com/actelion/research/chem/forcefield/mmff/Vector3.java
</a>
</li>
<li class="file-stats">
<a href="#b994581ffe97b009eb0b92a7e96010340c1278bc">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/interactions/InteractionPoint.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#e5917c5b47aa612e52c1b00ddb925ede64889f4a">
src/main/java/com/actelion/research/chem/interactionstatistics/SplineFunction.java
→
src/main/java/com/actelion/research/chem/interactions/SplineFunction.java
</a>
</li>
<li class="file-stats">
<a href="#341948234f61f7217cff86d35a8fa7586b60685f">
src/main/java/com/actelion/research/chem/interactionstatistics/InteractionAtomTypeCalculator.java
→
src/main/java/com/actelion/research/chem/interactions/statistics/InteractionAtomTypeCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#886c9af3ee9ac09922dd5148b180165dcac65528">
src/main/java/com/actelion/research/chem/interactionstatistics/InteractionDistanceStatistics.java
→
src/main/java/com/actelion/research/chem/interactions/statistics/InteractionDistanceStatistics.java
</a>
</li>
<li class="file-stats">
<a href="#d08fb11108138cdbcb6583eecd87fa940a1fc793">
src/main/java/com/actelion/research/chem/interactionstatistics/InteractionSimilarityTable.java
→
src/main/java/com/actelion/research/chem/interactions/statistics/InteractionSimilarityTable.java
</a>
</li>
<li class="file-stats">
<a href="#eece13fbda698de3243f1e8b34ecefe3657a6670">
src/main/java/com/actelion/research/chem/io/CompoundFileHelper.java
</a>
</li>
<li class="file-stats">
<a href="#cf40108c840165d004c28f26bbfd06fa9b0a6a27">
src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java
</a>
</li>
<li class="file-stats">
<a href="#b913e9301eb349935afa9f9053995d0205bb3b8e">
src/main/java/com/actelion/research/chem/io/Mol2FileParser.java
</a>
</li>
<li class="file-stats">
<a href="#0c854cac98db0f3260370d71fcc5ffda68377d14">
src/main/java/com/actelion/research/chem/io/ODEFileParser.java
</a>
</li>
<li class="file-stats">
<a href="#0fb904da0a7a7bfb17ff0c93c8ad358efdc73945">
src/main/java/com/actelion/research/chem/io/RXNFileParser.java
</a>
</li>
<li class="file-stats">
<a href="#635d8e90b2252849290c6f61fe7e80a11a5b9360">
src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcids.java
→
src/main/java/com/actelion/research/chem/io/pdb/calc/AminoAcids.java
</a>
</li>
<li class="file-stats">
<a href="#857ed6f4bc4508a667efad1b5293891df6622f8f">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/io/pdb/calc/BondOrderCalculator.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#e0a04af8dfefbbc2988f0ebb4adffc7f1983d06f">
src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java
→
src/main/java/com/actelion/research/chem/io/pdb/calc/BondsCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#29b2167c9e082e3c3b62248760eb4cd8ee371b9e">
src/main/java/com/actelion/research/chem/io/pdb/converter/GeometryCalculator.java
→
src/main/java/com/actelion/research/chem/io/pdb/calc/GeometryCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#146dbff685694850adc1a2e02daacdb4d72f0f90">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/io/pdb/calc/GraphWalker.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#73b4d0346495125235bc22ecabf9f247140a98af">
src/main/java/com/actelion/research/chem/io/pdb/converter/MoleculeGrid.java
→
src/main/java/com/actelion/research/chem/io/pdb/calc/MoleculeGrid.java
</a>
</li>
<li class="file-stats">
<a href="#1258c7c5b6d11f4ee1ff3fca83ca05059e44d75d">
<span class="deleted-file">
−
src/main/java/com/actelion/research/chem/io/pdb/converter/BondCalculatorException.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#68ae7c97e72b1a3954b198534928f19b62a7ee1b">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFBlock.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#a39fe8bee2d4cd9fa04080d84d96ca59146c7d3c">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFElement.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#3822ed8aeb838895441b24b6605bff71fe1f8452">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFParser.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#18f1a2c8a56ef2ba7da449da37cf6f2983b8188b">
<span class="new-file">
+
src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFTable.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#5bfc4d7224530cc7d16abb351d23d34e79383809">
src/main/java/com/actelion/research/chem/io/pdb/parser/AtomRecord.java
</a>
</li>
<li class="file-stats">
<a href="#0916d58bee618f507ad83e11a52b1222049d112f">
src/main/java/com/actelion/research/chem/io/pdb/parser/ModelParser.java
</a>
</li>
<li class="file-stats">
<a href="#6ee818fe98e676b200f6f2a2abfce1f4bbbaf643">
src/main/java/com/actelion/research/chem/io/pdb/parser/PDBCoordEntryFile.java
→
src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileEntry.java
</a>
</li>
<li class="file-stats">
<a href="#7b32aee2bd2c1c0fe6cea4b3b6604cb7c21864dd">
src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileParser.java
</a>
</li>
<li class="file-stats">
<a href="#a71dfe0bdcceb53559528df972d3e8caa0738644">
src/main/java/com/actelion/research/chem/io/pdb/parser/ProteinSynthesizer.java
</a>
</li>
<li class="file-stats">
<a href="#e44318dc5e713fcc04825cb6ce1158d655b25241">
src/main/java/com/actelion/research/chem/io/pdb/parser/Residue.java
</a>
</li>
<li class="file-stats">
<a href="#3f819505489132c1437801426243964daee5f337">
src/main/java/com/actelion/research/chem/io/pdb/parser/StructureAssembler.java
</a>
</li>
<li class="file-stats">
<a href="#0e7eb5b37221d91a8aba94d639cd66dbcac7884d">
src/main/java/com/actelion/research/chem/mcs/MCS.java
</a>
</li>
<li class="file-stats">
<a href="#1b65660f92a3dd1e6c99b463a64bc45cc5549f9b">
src/main/java/com/actelion/research/chem/optimization/Lnsrch.java
</a>
</li>
<li class="file-stats">
<a href="#f735597cf3090c29e8246f16dbf2bd7d3d724694">
src/main/java/com/actelion/research/chem/phesa/DescriptorHandlerShape.java
</a>
</li>
<li class="file-stats">
<a href="#d0922db37ba2d4e1c4162276b7b27af29aeca835">
src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java
</a>
</li>
<li class="file-stats">
<a href="#96bb8ff532656da2a3edae141073b06105618292">
src/main/java/com/actelion/research/chem/phesa/Gaussian3D.java
</a>
</li>
<li class="file-stats">
<a href="#4fe15bd20be46a1e2a1edcace49127c62de42caf">
src/main/java/com/actelion/research/chem/phesa/MolecularVolume.java
</a>
</li>
<li class="file-stats">
<a href="#795ed11f6b2a3261df6328880a512cf25f96e7a1">
src/main/java/com/actelion/research/chem/phesa/PheSAAlignment.java
</a>
</li>
<li class="file-stats">
<a href="#9dde9ff7f42975297b687592133e71eaea9a0dd4">
src/main/java/com/actelion/research/chem/phesa/PheSAMolecule.java
</a>
</li>
<li class="file-stats">
<a href="#807d4e6aa78076432fcf4ee790de979f7c3cc936">
src/main/java/com/actelion/research/chem/phesa/ShapeVolume.java
</a>
</li>
<li class="file-stats">
<a href="#1567806cafadbce76aec2c8d19fc7d024b42cd02">
src/main/java/com/actelion/research/chem/phesa/VolumeGaussian.java
</a>
</li>
<li class="file-stats">
<a href="#1a2948d1808e5bf4b5ae448818a4c444d9b4870a">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#15bbd6c3e9c26a062ac15af6002962363a3be7b3">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/AcceptorPoint.java
</a>
</li>
<li class="file-stats">
<a href="#e8d34d0348c1a86f031ca4a4af7c69f881a68bdc">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/AliphaticPoint.java
</a>
</li>
<li class="file-stats">
<a href="#a34860c68f2f05e2c6f290bd79933dffb69315b3">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/AromRingPoint.java
</a>
</li>
<li class="file-stats">
<a href="#4c00a17a8bb83a185ea4215138416415dc631c49">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/ChargePoint.java
</a>
</li>
<li class="file-stats">
<a href="#2647ede6f21c94279d90a1d4542d5f700d7b8d80">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/DonorPoint.java
</a>
</li>
<li class="file-stats">
<a href="#aecb2c98ac5b41ba504619d88d56e212b8cd4360">
src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/ExitVectorPoint.java
</a>
</li>
<li class="file-stats">
<a href="#3dbbe7b950b7f9e3cf1fa45df59255c90fc56046">
src/main/java/com/actelion/research/chem/phesaflex/EvaluableFlexibleOverlap.java
</a>
</li>
<li class="file-stats">
<a href="#c3e32d0b449b2f28584d5ab5e936a05f30553c86">
src/main/java/com/actelion/research/chem/potentialenergy/EmpiricalLigandStrain.java
</a>
</li>
<li class="file-stats">
<a href="#9e950199e5df105be79e1390f0d650cb5c4369fe">
src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java
</a>
</li>
<li class="file-stats">
<a href="#12bd6edb800b70d5ab8685a1b5bf19e205892c59">
src/main/java/com/actelion/research/chem/prediction/MolecularPropertyHelper.java
</a>
</li>
<li class="file-stats">
<a href="#41fc5358a06f159c9c962fe9d1654ea476893f95">
src/main/java/com/actelion/research/chem/properties/complexity/MolecularComplexityCalculator.java
</a>
</li>
<li class="file-stats">
<a href="#0ba3fa1fc4125af48e14b1afbf1f1f9a6c8076f1">
src/main/java/com/actelion/research/chem/reaction/MoleculeAutoMapper.java
</a>
</li>
<li class="file-stats">
<a href="#1a1484eaa1fcf026ffe201ee065f2a3e1566d1d7">
src/main/java/com/actelion/research/chem/reaction/RSSSearcher.java
</a>
</li>
<li class="file-stats">
<a href="#954660ece8681dd84f3ab083aa03a51c3edb4235">
src/main/java/com/actelion/research/chem/reaction/Reaction.java
</a>
</li>
<li class="file-stats">
<a href="#cac745b26e6f9783326c3fe0b121bf937de646d0">
src/main/java/com/actelion/research/chem/reaction/ReactionArrow.java
</a>
</li>
<li class="file-stats">
<a href="#3b5fc443620dce432676ce62584e4b528b691957">
src/main/java/com/actelion/research/chem/reaction/ReactionEncoder.java
</a>
</li>
<li class="file-stats">
<a href="#1637bbc5b705a85f23e2eebc91e38d3551aca901">
src/main/java/com/actelion/research/chem/reaction/ReactionIndexer.java
</a>
</li>
<li class="file-stats">
<a href="#3d49305aace1a66f91cada555d01507fd7033881">
src/main/java/com/actelion/research/chem/reaction/ReactionSearch.java
</a>
</li>
<li class="file-stats">
<a href="#88f7248516cf1351766ec9d506223745b62982c0">
src/main/java/com/actelion/research/chem/reaction/Reactor.java
</a>
</li>
<li class="file-stats">
<a href="#b7949ccb5a22a6534e50cbb78f2559bb04a2100e">
src/main/java/com/actelion/research/chem/reaction/SRSearcher.java
</a>
</li>
<li class="file-stats">
<a href="#34d1c8aecff809d7ae03fb28886d34e5c936ffcc">
src/main/java/com/actelion/research/chem/reaction/TransformerRule.java
</a>
</li>
<li class="file-stats">
<a href="#a71b03327fe8906b5e42e21fedc57ffc72f61acb">
src/main/java/com/actelion/research/chem/reaction/mapping/ChemicalRule.java
</a>
</li>
<li class="file-stats">
<a href="#1f7870982526447f88a6c686cad3d92098962021">
src/main/java/com/actelion/research/chem/reaction/mapping/ChemicalRuleEnhancedReactionMapper.java
</a>
</li>
<li class="file-stats">
<a href="#cb31a3eb9ce056b7b6950e3c00e22e6ea9374b65">
src/main/java/com/actelion/research/chem/reaction/mapping/MappingScorer.java
</a>
</li>
<li class="file-stats">
<a href="#af3855197ece986f551ab2eddfdb198f86bcd630">
src/main/java/com/actelion/research/chem/reaction/mapping/ReactionCenterMapper.java
</a>
</li>
<li class="file-stats">
<a href="#60ccb435ab9538009a24ad8c50dfe7583b481728">
src/main/java/com/actelion/research/chem/reaction/mapping/RootAtomPairSource.java
</a>
</li>
<li class="file-stats">
<a href="#fd828ea16dfc40dd5d8d20957d2ed4a3e324497c">
src/main/java/com/actelion/research/chem/reaction/mapping/SimilarityGraphBasedReactionMapper.java
</a>
</li>
<li class="file-stats">
<a href="#a852212be3137beaba400fecf56da91179475697">
src/main/java/com/actelion/research/chem/sar/SARScaffoldGroup.java
</a>
</li>
<li class="file-stats">
<a href="#80f66e39fac601d3a07990a51d70b51e2ca2d88d">
src/main/java/com/actelion/research/chem/shredder/Fragment3D.java
</a>
</li>
<li class="file-stats">
<a href="#a09c3732b9c215369a65d3c56cefe7ae09d7e5bc">
src/main/java/com/actelion/research/chem/shredder/FragmentGeometry3D.java
</a>
</li>
<li class="file-stats">
<a href="#abc5e255277f3db6e51c6abd4978f541b7ced1d7">
src/main/java/com/actelion/research/chem/shredder/Fragmenter3D.java
</a>
</li>
<li class="file-stats">
<a href="#8eb423ad286c3fa6bd30a747c88932588abe93f4">
src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java
</a>
</li>
<li class="file-stats">
<a href="#0140704a097180253c595e52ebf3f3cdb19fc8f5">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JAtomLabelDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#15cc007707b7c1a31ad39e752baffae78496a92d">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JAtomQueryFeatureDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#e2e9f9863c877cdb0b57ac709ab1852940c20d5a">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JBondQueryFeatureDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#b79ed66de0dd694eb9d9001763bf57deb57a6bdf">
src/main/java/com/actelion/research/gui/JChemistryView.java
</a>
</li>
<li class="file-stats">
<a href="#483f2f042bcf1d99e1f987f6132e8fec07ea2cd6">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JDrawArea.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#e4a461ea6c1e83c20f9aecaffed9344cdcbe8a19">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JDrawDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2e7e9915bec0d7659ab0a711facaebb24da78259">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JDrawPanel.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#f1775592308a8afd1fc4ba389e5b9ce09e2d560e">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/JDrawToolbar.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#22a48b6441e4880a80fbbf8c21720f71585f7170">
src/main/java/com/actelion/research/gui/JStructureView.java
</a>
</li>
<li class="file-stats">
<a href="#b508f2cb28c9d6580c1768a82097731db9144bbd">
src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcidLabeled.java
→
src/main/java/com/actelion/research/gui/clipboard/ClipboardFormat.java
</a>
</li>
<li class="file-stats">
<a href="#0286e69308a5dc8f38cd96a6e642e56ef8ffa0e1">
src/main/java/com/actelion/research/gui/clipboard/ClipboardHandler.java
</a>
</li>
<li class="file-stats">
<a href="#45b158ec545ec3dd10cce98f035db1fb02eda5de">
src/main/java/com/actelion/research/gui/clipboard/NativeClipboardAccessor.java
</a>
</li>
<li class="file-stats">
<a href="#43b523c9c0438f258cdf7fab8c6a0a0eaf6d0a1a">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/dnd/SDFileMoleculeDropAdapter.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#4c9f31583b1eaddafa2f9b2a25b82af65486ec59">
<span class="deleted-file">
−
src/main/java/com/actelion/research/gui/dnd/SDFileMoleculeTransferable.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#b23ac1794ae5ae3ca39c5fd7604dd429cdcd2393">
src/main/java/com/actelion/research/gui/editor/AtomQueryFeatureDialogBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#2d894338a737d6a8c8a24ac0542b979549d1a70f">
src/main/java/com/actelion/research/gui/editor/BondQueryFeatureDialogBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#b341e4cdf17fffc6e1e991e2a06da8d8f601e80a">
src/main/java/com/actelion/research/gui/editor/CustomAtomDialogBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#6beaf552bffcc4a1cd00c38a9f5d484971610b54">
<span class="new-file">
+
src/main/java/com/actelion/research/gui/editor/DialogBuilderCallback.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#09d8b19e907c97711a718ea2b24b95c9d7fdb580">
src/main/java/com/actelion/research/gui/editor/FXEditorToolbar.java
</a>
</li>
<li class="file-stats">
<a href="#e88b3b664b23c3bbabb82fd6ea5abf663930ad9c">
src/main/java/com/actelion/research/gui/editor/GenericEditorArea.java
</a>
</li>
<li class="file-stats">
<a href="#1162dd54bb80411f0eafcd0e20c40acd0c0b69b5">
src/main/java/com/actelion/research/gui/editor/GenericEditorToolbar.java
</a>
</li>
<li class="file-stats">
<a href="#0fc3e3e69df5421574202604c83690a1a80e8986">
src/main/java/com/actelion/research/gui/editor/TextDrawingObjectDialogBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#3af2c344ee57d1cdbef20185cc7e02d33eac271c">
src/main/java/com/actelion/research/gui/fx/FXDialog.java
</a>
</li>
<li class="file-stats">
<a href="#62369142a7450f039882d0d8a8ff51eeda571a00">
src/main/java/com/actelion/research/gui/fx/FXKeyHandler.java
</a>
</li>
<li class="file-stats">
<a href="#0573e160f88f5b8288c0abdee0aa1b05847d4173">
src/main/java/com/actelion/research/gui/generic/GenericDialog.java
</a>
</li>
<li class="file-stats">
<a href="#897ade15200a5086fab9e7c208878e065da16b60">
<span class="new-file">
+
src/main/java/com/actelion/research/gui/generic/GenericDialogCallback.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#9f2b2658afe1ab438b356ec95f714fde01afe3cc">
src/main/java/com/actelion/research/gui/generic/GenericKeyEvent.java
</a>
</li>
<li class="file-stats">
<a href="#f45e440b0b4003178e3df9901be32382fce402af">
src/main/java/com/actelion/research/gui/swing/SwingDialog.java
</a>
</li>
<li class="file-stats">
<a href="#a6ceb37ff7a4a3accfc57f79b9ffa5865bfabd4f">
src/main/java/com/actelion/research/gui/swing/SwingKeyHandler.java
</a>
</li>
<li class="file-stats">
<a href="#36d67d65cd0379f7155fb83406c3ff973efdcd6e">
src/main/java/com/actelion/research/io/StringReadChannel.java
</a>
</li>
<li class="file-stats">
<a href="#688416058ba026adcb9364eebd979bb9ab46e9bb">
<span class="deleted-file">
−
src/main/java/com/actelion/research/jfx/gui/GraphicsContextImpl.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#5379e9ae0b7b292eb2103ced59f3d330345149f5">
<span class="deleted-file">
−
src/main/java/com/actelion/research/jfx/gui/chem/JFXCanvasDepictor.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#af3624296eb54b34a3e78d5bff876fcc1d5d2aa0">
src/main/java/com/actelion/research/jfx/gui/chem/MoleculeViewSkin.java
</a>
</li>
<li class="file-stats">
<a href="#0a2629912eb78b3747814d5bf09f83ab4fec7cd5">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/Arrow.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#64fcbf291e0801a013252019400d5b4a16532822">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/ChemistryGeometryHelper.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#b1d90f4d3d1ce5d49af735721846e5101d7757bf">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/Delegator.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#4bbabfe4427d823bb19151dd31741d2cfecb0e42">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/DialogResult.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#a0f6c23ae29ae691fa2b100f1d70439cbf938c3e">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/DrawConfig.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc980acd082b7bb97c79a11a6be19a4920835212">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/Polygon.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2daada072afc816d9d1ab2592475d01221d5da9d">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/ImageProvider.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#e9c6cee51bbd916bb8da22da0cf57a0ac7ff411c">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/Model.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#3ee9c1eaff49d479f3b2726b7c8a166c12256183">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/Action.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#6c872e27d5d0cc3e11c12648e47e90984624e13a">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/AddRingAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#10a4de311956d3a77c3100a43cfce63100099473">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ArrowAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#b38924c4c220b816c34d6d1e43cac874263c9497">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/AtomHighlightAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#731de6e678b8c1212b7016c55d5bd354f5d9a3c4">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/AtomMapAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#885825a0f849267f312a0614eed150995d947121">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/BondBaseAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#80fb87b2c9ccbf2014132026dac2a49350309ea7">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/BondHighlightAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#b6f4b756b45c9bb2cd839ab185252f8deeed8036">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ChangeAtomAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#4d014bd3063b558bb29939481215dbc27fb625e6">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ChangeAtomPropertiesAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#53d142cf33a0f9b4e2f95afe4b76ecfa041da006">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ChangeChargeAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#0e3abcd0c5622c387d490b1ef17a278f3766928d">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/CleanAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#c3cac5eb4889e2cf11d96cdc2088b32c24ab06a1">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ClearAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#58f10c972971c8ab70e4534402f072d405042c30">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/CommandAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#f3cd081c7c071bde71c9a3efa135169e4b581c3f">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/CopyAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#fa82251ed3a8f450fe3d9a12ce5df87900824f8d">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/CutAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#671ba7488221c81f4e4cbdc4d1576b9d2ab6a961">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/DeleteAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5352bc086a13c0e35f404c82b5ee75ab73ef088">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/DownBondAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#59ea8ad381a62c30a3df3fa176c501b31c4f0a36">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/DrawAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#f8aee3c519eab5cee38c42d3d6142837010e4d33">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/NewBondAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#aced345c2c24efd00dc02384cc8a00c26d158fb2">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/NewChainAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#6633940346354f6c71335edc18ed1b20dd649100">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/PasteAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#a05cce77529525e27687cb2d664605a378ca3c36">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/SelectionAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#496562f49cc00e21c3b5cda5f20d6e624cf14ffe">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ToolbarSelectionChange.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#91284b8552c1a6a17c90133b771e3a1b16468963">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/UndoAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#e37af45cdd55b175702eab150744e16fb3fec995">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/UnknownParityAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#60d2f1574876f214a0073b0894e9e8b76759752e">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/UpBondAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#550dffff89142250b4231e4e5c92d267363e89a2">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/actions/ZoomRotateAction.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#aed804a85ed76509bce7fbab4a51985f69821d91">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/chem/AbstractExtendedDepictor.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#741262034e5847f3f26e2a187aaf1749eaed62a5">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/chem/DrawingObject.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#cfb0ea7b2d16268e97aefb33ca66ef2afde6a665">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/chem/IArrow.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#7faf9c9a44425e0494585172918169a10a592cd0">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/chem/IDepictor.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#f661da971fcea41e468079ad501d270161e6595c">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/chem/IDrawingObject.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#fa4ed11c2f0359ab3165ce4b09427602a0a0716b">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/chem/IReactionArrow.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#9e3f9e820e252b36f78771652cc015321afa17f6">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/dialogs/IAtomPropertiesDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#9a9c92fbe42d627b04dd1614c807a176ca5d448b">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/dialogs/IAtomQueryFeaturesDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#cb571f2a03eee53e88a456bdee8755538c6d084b">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/dialogs/IBondQueryFeaturesDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#2d4e73c68854d9ebb570df40b15efbdc39c0254e">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/dialogs/IDialog.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#9fd3bca172a4b2caf43c15fb75b342eb7dd034c5">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/GeomFactory.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#d47903caa956618c947061890ba018363bd57b07">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/IColor.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#982b24d5d74b8a99864d72a83874f0b747b6b8a7">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/ICursor.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#6bbcaf47d3be2ef79b3491b2be248e6ba8eb2a44">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/IDrawContext.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#77497d86891d575ac4f8a8f726b94e1920d01deb">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/IPolygon.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#dffe78451107a5e911e17f663a9c6fc283864a69">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/IRectangle2D.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#dbb90e626ab7e5ed153399e4000bbb643f95db1d">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/StrokeLineCap.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#06a4993581665faf721e0e7731b51bcba8ee340e">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/geom/StrokeLineJoin.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#240bd33dfa54f6ba8abfd5c713f69967662db1c6">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/io/IKeyCode.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#9896dfd5b97b2a600782effd30777a52efdd102a">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/io/IKeyEvent.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#166a757fb25151b5f724a14d66b5f8b7b7e4a474">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/io/IMouseEvent.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#bd4cd18ce3a45968e1788f26e6b4c8e4ba52be8b">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/listeners/IChangeListener.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#8e939404956085a1852ef7b219b51357fa59c077">
<span class="deleted-file">
−
src/main/java/com/actelion/research/share/gui/editor/listeners/IValidationListener.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#389682891e8c9e6be345f3ee80bf003700295ca2">
src/main/java/com/actelion/research/util/ArrayUtils.java
</a>
</li>
<li class="file-stats">
<a href="#a40f75ba98c0e9ff68c124956ba8caa5c076e0a4">
src/main/java/com/actelion/research/util/BinaryEncoder.java
</a>
</li>
<li class="file-stats">
<a href="#fecfa57665196dcfd9c20f1a5042bfc06e6e9f0d">
src/main/java/com/actelion/research/util/BitUtils.java
</a>
</li>
<li class="file-stats">
<a href="#8aa33c9ba158596c73c9f4bda3ccc68d4d96d043">
src/main/java/com/actelion/research/util/CommandLineParser.java
</a>
</li>
<li class="file-stats">
<a href="#ec1e7f260c5e341b5b4551f820f746b392a3e2e8">
src/main/java/com/actelion/research/util/ConstantsDWAR.java
</a>
</li>
<li class="file-stats">
<a href="#7c225bfe364c1568b03e6fc666944a44f00da965">
src/main/java/com/actelion/research/util/DoubleFormat.java
</a>
</li>
<li class="file-stats">
<a href="#f1712ad5086a5e796cfe5dfc262757b209d75d7e">
src/main/java/com/actelion/research/util/FastSpline.java
</a>
</li>
<li class="file-stats">
<a href="#68508f06bf839645917906681c72e4ac00827031">
src/main/java/com/actelion/research/util/Formatter.java
</a>
</li>
<li class="file-stats">
<a href="#0ccd1774155b9cd87366a9e230233a3a512a44fc">
src/main/java/com/actelion/research/util/IO.java
</a>
</li>
<li class="file-stats">
<a href="#468ea7e76467b1dd6253a1ba2849cf65b0877871">
src/main/java/com/actelion/research/util/ListUtils.java
</a>
</li>
<li class="file-stats">
<a href="#823feab9b4de7bafa1b018dc6560652c6da74982">
src/main/java/com/actelion/research/util/Pipeline.java
</a>
</li>
<li class="file-stats">
<a href="#956cbd3df3b362b424fc4debbe766dd1b1bb8217">
src/main/java/com/actelion/research/util/SizeOf.java
</a>
</li>
<li class="file-stats">
<a href="#c6fb11ef8cf0fbb1e7c11d524354bb1ffad26757">
src/main/java/com/actelion/research/util/Sketch.java
</a>
</li>
<li class="file-stats">
<a href="#f09c8388a63d6f396185bb2279dc9aeab3a7107f">
src/main/java/com/actelion/research/util/SortedList.java
</a>
</li>
<li class="file-stats">
<a href="#92b36f06996dd90946fe60f3e47119ae8e863d89">
src/main/java/com/actelion/research/util/StringFunctions.java
</a>
</li>
<li class="file-stats">
<a href="#8ff1bccf8b6ef8d9aee806ee8235d291b440c33b">
src/main/java/com/actelion/research/util/TimeDelta.java
</a>
</li>
<li class="file-stats">
<a href="#02c06c0dc008822fa475b60ad34b49ad04c6564d">
src/main/java/com/actelion/research/util/datamodel/DoubleArray.java
</a>
</li>
<li class="file-stats">
<a href="#368b85ecf2c5c018c200fd994589c18a6b6dd641">
src/main/java/com/actelion/research/util/datamodel/IntArray.java
</a>
</li>
<li class="file-stats">
<a href="#fcebf4c2d294fb1c4c9179c29beb522a1e0df0cc">
src/main/java/com/actelion/research/util/datamodel/IntVec.java
</a>
</li>
<li class="file-stats">
<a href="#2c79cfeb292a5a3634fb551d2edb46d3b989db18">
src/main/java/org/openmolecules/chem/conf/gen/BaseConformer.java
</a>
</li>
<li class="file-stats">
<a href="#378504e08d8c679691dd18436e807f0ca2714b36">
src/main/java/org/openmolecules/chem/conf/gen/ConformerGenerator.java
</a>
</li>
<li class="file-stats">
<a href="#822194fbe99d88e2a4bd4d58f6e4a52ea49abf5a">
src/main/java/org/openmolecules/chem/conf/gen/RigidFragment.java
</a>
</li>
<li class="file-stats">
<a href="#8b4f7d2965813dfae68bdf1f60fca27f0e443b69">
src/main/java/org/openmolecules/chem/conf/gen/RigidFragmentProvider.java
</a>
</li>
<li class="file-stats">
<a href="#6552060eea8030b4ac6de30c68566d9c8e8a0a4f">
src/main/java/org/openmolecules/chem/conf/gen/RotatableBond.java
</a>
</li>
<li class="file-stats">
<a href="#767fe82027ac449d38dfa40b2774f48bbae6df6f">
src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategy.java
</a>
</li>
<li class="file-stats">
<a href="#6521bd95931c669be8f21367e722113323c133dd">
src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategyAdaptiveRandom.java
</a>
</li>
<li class="file-stats">
<a href="#d665e3c7beca893ee670fe7d80afc9d905b2eda3">
src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategyLikelySystematic.java
</a>
</li>
<li class="file-stats">
<a href="#53050ba42cb40bf4df58ff7ed1cd884a010dffd5">
src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategyRandom.java
</a>
</li>
<li class="file-stats">
<a href="#0a9eded2726e867dd8b0ba2376cb569b6203d24a">
src/main/java/org/openmolecules/chem/conf/so/ConformationSelfOrganizer.java
</a>
</li>
<li class="file-stats">
<a href="#ac25034272bbe826f0b81b4532e853a01604a64a">
src/main/java/smile/math/Math.java
</a>
</li>
<li class="file-stats">
<a href="#cf86b8d73149b2f766d8119ed77640e947a719a1">
src/main/resources/html/editor/editor.html
</a>
</li>
<li class="file-stats">
<a href="#b1b65b0e95695101e4057a8bfdb6d3039c0c7973">
src/main/resources/resources/cod/bondLengthData.txt
</a>
</li>
<li class="file-stats">
<a href="#d2ca8173fb14e298e5838db9163487a27baa4903">
src/main/resources/resources/cod/torsionAngle.txt
</a>
</li>
<li class="file-stats">
<a href="#160b2ff84acb05599f5c1777096041fdc437ad64">
src/main/resources/resources/cod/torsionBins.txt
</a>
</li>
<li class="file-stats">
<a href="#8e49d41bb99bb7af329523b1f269fc15b44264c2">
src/main/resources/resources/cod/torsionFrequency.txt
</a>
</li>
<li class="file-stats">
<a href="#0f8b9300e19e30b1f37d4f3e02333c8ca5330606">
src/main/resources/resources/cod/torsionID.txt
</a>
</li>
<li class="file-stats">
<a href="#6fc3e03cf1f4efe4dfe7ea24c56fe50dea013a9d">
src/main/resources/resources/cod/torsionRange.txt
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>
</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #626168;">
—
<br>
<a href="https://salsa.debian.org/java-team/openchemlib/-/compare/3b85e05ec719286fd90f2f44cdbcc72e6106ed94...a3641461a1d8f19b065651381d72a184459ef30b">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<span style="color: transparent; font-size: 0; display: none; overflow: hidden; opacity: 0; width: 0; height: 0; max-width: 0; max-height: 0;">
Notification message regarding https://salsa.debian.org/java-team/openchemlib/-/compare/3b85e05ec719286fd90f2f44cdbcc72e6106ed94...a3641461a1d8f19b065651381d72a184459ef30b at 1771837988
</span>
</p>
</div>
</body>
</html>