cdk/cdk: CDK 2.9

New Features and APIs

Hydrogen normalisation

A new API has been added to simplify hydrogen representation normalisation. In the past we had the ability to suppress all hydrogens, make them all explicit or remove all non-chiral hydrogens. We now have a single function which does all of this, the caller specifies what you want and it will add/remove hydrogens as needed keeping all internal state correct and in sync.

IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
SmilesParser smipar = new SmilesParser(bldr);
SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default);

IAtomContainer mol = smipar.parseSmiles("C1[C@@H]2CCC(C[C@H](O)C)C[C@@H]2C(C1)[2H]");
AtomContainerManipulator.normalizeHydrogens(mol, HydrogenState.Depiction);
System.err.println(smigen.create(mol) + " Depiction");
AtomContainerManipulator.normalizeHydrogens(mol, HydrogenState.Stereo);
System.err.println(smigen.create(mol) + " Stereo");
AtomContainerManipulator.normalizeHydrogens(mol, HydrogenState.Minimal);
System.err.println(smigen.create(mol) + " Minimal");
AtomContainerManipulator.normalizeHydrogens(mol, HydrogenState.Unsafe);
System.err.println(smigen.create(mol) + " Minimal (unsafe)");

Result:

C1[C@@]2(CCC(C[C@H](O)C)C[C@@]2(C(C1)[2H])[H])[H] Depiction
C1[C@@]2(CCC(C[C@](O)(C)[H])C[C@@]2(C(C1)[2H])[H])[H] Stereo
C1[C@@H]2CCC(C[C@H](O)C)C[C@@H]2C(C1)[2H] Minimal
C1[C@@H]2CCC(C[C@H](O)C)C[C@@H]2CC1 Minimal (unsafe)

<img src="https://private-user-images.githubusercontent.com/983232/440539732-6d5c451c-3aec-4e47-b06b-400ccc5edb18.svg?jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3NzI1NDk4MTQsIm5iZiI6MTc3MjU0OTUxNCwicGF0aCI6Ii85ODMyMzIvNDQwNTM5NzMyLTZkNWM0NTFjLTNhZWMtNGU0Ny1iMDZiLTQwMGNjYzVlZGIxOC5zdmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjYwMzAzJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI2MDMwM1QxNDUxNTRaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1mNmViMmUyMTA3OGZlOGYxNGNlZTk3ODBiYTYwYjFiNmIxOWZmMDkwNTBjM2IxZGU3ZThmNTIyZmVkNzBlZjgzJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCJ9.KCSQLfnhCC2lREtj-SQClND8dESA66qBKVw10XBo2Sw" width="300px">

Markush / RGroup support

We already had some basic support for R Group Query files but this was not tied in nicely to the main toolkit. This release adds the ability to work with these files easier as well as support in CXSMILES. It is now possible to load a CXSMILES with R groups and depict it correctly.

IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
SmilesParser smipar = new SmilesParser(bldr);
IAtomContainer mol = smipar.parseSmiles("C1CNCC(*)C1 |$;;;;;R1$,LN:0:1.3,RG:_R1={OC},{Cl},{C#N}|");
new DepictionGenerator().depict(mol).writeTo("/tmp/tmp.svg");

<img width="617" height="407" alt="Screenshot 2026-03-03 at 15 04 39" src="https://github.com/user-attachments/assets/21dabbda-c373-4350-a723-0e8dec14c5f2" />

Note: the link node is now also parsed and stored.

Atropisomers (via RDKit extension)

We have supported atropisomers for some time but only via 2D coordinates with layouts and CIP naming etc working as expected. RDKit has an extension to allow loading from CXSMILES - although it is not perfect I was at a loss to think of something better and so it makes sense to support it. Currently this is read-only and mainly intended for depiction.

C=CC(=O)N1CCN(c2nc(=O)n(-c3c(C)ccnc3C(C)C)c3nc(-c4c(O)cccc4F)c(F)cc23)[C@@H](C)C1 |wU:12.23| (m)-sotorasib

<img width="193" height="252" alt="image" src="https://github.com/user-attachments/assets/032b630b-8af8-468f-8455-7deeb7ae48bf" /> (via CDK depict)

API to set wedge bonds

A new API has been added to allow setting of wedge bonds to a structure where the coordinates are already known. Note: This function is called automatically when a layout is generated.

StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.generateWedges(mol);

Sugar Detection Utility

See https://github.com/cdk/cdk/pull/1225

<img width="3626" height="1462" alt="image" src="https://github.com/user-attachments/assets/90952096-607a-4e31-85e8-66de8439601f" />

If you want to see the SugarDetectionUtility in action, check out our MOlecule fRagmenTAtion fRamework (MORTAR) application, the SDU will be part of the next release.

What's Changed

• Merged test-extra into extra and more by @egonw in https://github.com/cdk/cdk/pull/1180
• Ported cdk.core test classes to the module being tested by @egonw in https://github.com/cdk/cdk/pull/1179
• If any bond is hidden in the ring, it should not be filled. by @johnmay in https://github.com/cdk/cdk/pull/1181
• Fix #1174. We need better logic when the ring closures are near exten… by @johnmay in https://github.com/cdk/cdk/pull/1182
• FIx #1183 InChITautomerGenerator on AtomContainer2 by @johnmay in https://github.com/cdk/cdk/pull/1184
• Ensure MDLV3000 stereo 0d works correctly. by @johnmay in https://github.com/cdk/cdk/pull/1187
• We need a static variable to be able to use it from a static context. by @johnmay in https://github.com/cdk/cdk/pull/1186
• Fix some corner cases in reading of stereochemistry from chair projec… by @johnmay in https://github.com/cdk/cdk/pull/1192
• Remove some redundant exceptions. by @johnmay in https://github.com/cdk/cdk/pull/1194
• Allow the ExtendedFingerprinter to setHashExplicitHydrogens by @johnmay in https://github.com/cdk/cdk/pull/1196
• Fix some issues highlighted by SonarCloud by @johnmay in https://github.com/cdk/cdk/pull/1200
• Fixes/smirks 9jul by @johnmay in https://github.com/cdk/cdk/pull/1201
• Patch/beam central by @johnmay in https://github.com/cdk/cdk/pull/1202
• fix atom property cleanup in DepictionGenerator by @uli-f in https://github.com/cdk/cdk/pull/1203
• update maven-compiler-plugin configuration to use <release> instead of <source> and <target> by @uli-f in https://github.com/cdk/cdk/pull/1205
• Depedency updated 2025-07-25 by @egonw in https://github.com/cdk/cdk/pull/1204
• dependency updates 08-Aug-2025, use <release> instead of <source> and <target> by @uli-f in https://github.com/cdk/cdk/pull/1209
• Moved more tests from test-standard to standard by @egonw in https://github.com/cdk/cdk/pull/1207
• ConjugatedPiSystemsDetector allene handling fix by @JonasSchaub in https://github.com/cdk/cdk/pull/1211
• RDKit atropisomers by @johnmay in https://github.com/cdk/cdk/pull/1212
• Allow annotation of bond numbers, this was useful for debugging the a… by @johnmay in https://github.com/cdk/cdk/pull/1213
• Add InChI AuxInfo to structure functionality; by @fbaensch-beilstein in https://github.com/cdk/cdk/pull/1208
• fix issue with empty annotation in depiction by @uli-f in https://github.com/cdk/cdk/pull/1214
• Tweaks for jchempaint by @johnmay in https://github.com/cdk/cdk/pull/1215
• Depict background size by @johnmay in https://github.com/cdk/cdk/pull/1216
• Depict background by @johnmay in https://github.com/cdk/cdk/pull/1217
• LargestPiSystemDescriptor visited flags and minor code improvements by @JonasSchaub in https://github.com/cdk/cdk/pull/1218
• Fix a corner case with titles for reactions not being set if no CXSMI… by @johnmay in https://github.com/cdk/cdk/pull/1219
• Clean up IBond.Stereo and IBond.Display by @johnmay in https://github.com/cdk/cdk/pull/1220
• Improved stereochemistry invalidation when modifying molecules (Fixes… by @johnmay in https://github.com/cdk/cdk/pull/1222
• Rgroup Improvements by @johnmay in https://github.com/cdk/cdk/pull/1223
• Sugar Detection Utility by @JonasSchaub in https://github.com/cdk/cdk/pull/1225
• Test cleanup by @johnmay in https://github.com/cdk/cdk/pull/1228
• Additional test simplification/dreprecation by @johnmay in https://github.com/cdk/cdk/pull/1229
• Move around some XML config files. by @johnmay in https://github.com/cdk/cdk/pull/1230
• Simplify the SybylAtomTypeMatcherTest. by @johnmay in https://github.com/cdk/cdk/pull/1231
• Handle Link Nodes in CXSMILES (Ring flags now set when reading from SMILES) by @johnmay in https://github.com/cdk/cdk/pull/1232
• Make SmallRingDescriptor, WienerNumbersDescriptor, and ALogPDescriptor parallelisable by @JonasSchaub in https://github.com/cdk/cdk/pull/1234
• Move the InChI Readers to cdk-inchi module. by @johnmay in https://github.com/cdk/cdk/pull/1235
• Add JDK-25 to CI by @mjw99 in https://github.com/cdk/cdk/pull/1237
• swap carrier order in DoubleBondStereochemistry::create to satisfy bond alignment constraint by @uli-f in https://github.com/cdk/cdk/pull/1226
• use thread safe collection in RoundRobinFormulaGenerator by @SteffenHeu in https://github.com/cdk/cdk/pull/1239
• Exhaustive fragmenter fix and improvements by @ToLeWeiss in https://github.com/cdk/cdk/pull/1238
• Varattach matching by @johnmay in https://github.com/cdk/cdk/pull/1243
• Updated dependencies: maven plugins and library deps by @egonw in https://github.com/cdk/cdk/pull/1242
• Some tweaks to abbreviations - based on feedback from https://github.… by @johnmay in https://github.com/cdk/cdk/pull/1247
• Add support for loading selection/highlight from CXSMILES and MDL Mol… by @johnmay in https://github.com/cdk/cdk/pull/1246
• Add a method to the SDG which allows wedges to be assigned to a struc… by @johnmay in https://github.com/cdk/cdk/pull/1249
• adopt <dependencyManagment> and <pluginManagement> by @egonw in https://github.com/cdk/cdk/pull/1250
• CMLXOM 4.15 and Log4j 2.25.3 by @egonw in https://github.com/cdk/cdk/pull/1252
• Fix a null pointer exception in MDLV2000Reader by @Mailaender in https://github.com/cdk/cdk/pull/1254
• Misc tweaks for Markush rendering. by @johnmay in https://github.com/cdk/cdk/pull/1257
• Update the connectivity checker to either respect/ignore (default) va… by @johnmay in https://github.com/cdk/cdk/pull/1258
• two more dependency updates (compatible with java 8) by @egonw in https://github.com/cdk/cdk/pull/1259
• CDK RGroups by @johnmay in https://github.com/cdk/cdk/pull/1260
• Hydrogen Normalization by @johnmay in https://github.com/cdk/cdk/pull/1188
• Mar 2026 fixes by @johnmay in https://github.com/cdk/cdk/pull/1261
• Downgrade to warning: unnatural elements do not have major isotopes by @egonw in https://github.com/cdk/cdk/pull/1265
• Sonarcloud fixes by @johnmay in https://github.com/cdk/cdk/pull/1264
• Fixes #1255 - Add in B3_Minus as a valid aromatic atom type. by @johnmay in https://github.com/cdk/cdk/pull/1267
• Fixes #1035 - rather than avoid using templates when we have DB stere… by @johnmay in https://github.com/cdk/cdk/pull/1266
• Fix an issue with '>' appearing in the titles and messing up SMILES p… by @johnmay in https://github.com/cdk/cdk/pull/1269
• Fixes #953 - Tweak the expression handling logic of the QueryAtomCont… by @johnmay in https://github.com/cdk/cdk/pull/1268
• Improve ionic bond depictions - fixes https://github.com/cdk/depict/i… by @johnmay in https://github.com/cdk/cdk/pull/1270

New Contributors

• @fbaensch-beilstein made their first contribution in https://github.com/cdk/cdk/pull/1208
• @SteffenHeu made their first contribution in https://github.com/cdk/cdk/pull/1239
• @ToLeWeiss made their first contribution in https://github.com/cdk/cdk/pull/1238

Full Changelog: https://github.com/cdk/cdk/compare/cdk-2.11...cdk-2.12