New Features/Key Changes AtomContainer new implementation (IMPORTANT) The new AtomContainer implementation is now the default after a gradual introduction. You can still use the old implementation but you must explicitly create an AtomContainerLegacy. This should be a seamless change for most but please notify if you have an unexpected error. SMIRKS JavaDoc SMIRKS support with the ability to approximate other implementations (inc. Daylight and RDKit Reaction Smarts). It includes convenience APIs for applying a transform to all places at once (i.e. dt_xapply) and efficient support for hydrogen handling (explicit hydrogen are not required on the input). Overall the speed it good and a transform can be run over the all of ChEMBL 35 in only ~30 seconds (see Appendix A1). IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default); String smminp = "c1cc(N(=O)=O)ccc1N(=O)=O"; IAtomContainer mol = smipar.parseSmiles(smminp); Smirks.compile("[N:1](=[OD1+0])=[OD1+0]>>[N+:1](=O)[O-] polar-nitro") .apply(mol); // exclusive apply mode String smiout = smigen.create(mol); // C1=CC([N+](=O)[O-])=CC=C1[N+](=O)[O-] More information can be found in the JavaDoc and functionality will be added to the CDK Depict Web Application. Reaction InChI (RInChI) generation JavaDoc A pure Java implementation of Reaction InChI has been added allowing generation of RInChI strings and keys: IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); IReaction reaction = smipar.parseReactionSmiles("CCO.[CH3:1][C:2](=[O:3])[OH:4]>[H+]>CC[O:4][C:2](=[O:3])[CH3:1].O Ethyl esterification [1.7.3]\n"); RInChIGenerator rinchigen = new RInChIGenerator(); rinchigen.generate(reaction); System.err.println(rinchigen.getRInChI()); // RInChI=1.00.1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)!C2H6O/c1-2-3/h3H,2H2,1H3C4H8O2/c1-3-6-4(2)5/h3H2,1-2H3!H2O/h1H2p+1/d+ System.err.println(rinchigen.getShortRInChIKey()); // Short-RInChIKey=SA-FUHFF-JJFIATRHOH-UDXZTNISGZ-GPRLSGONYQ-NUHFF-NUHFF-NUHFF-ZZZ RDfile reading support. JavaDoc RDfiles belong to the CT file family formats and allows records with associated data. The format is commonly used for reaction data from ELN or otherwise. RdfileReader rdReader = new RdfileReader(new FileReader("/tmp/pistachio-rxns-2501091627.rd"), SilentChemObjectBuilder.getInstance(), true); while (rdReader.hasNext()) { RdfileRecord record = rdReader.next(); if (record.isRxnFile()) { IReaction reaction = record.getReaction(); } else { IAtomContainer container = record.getAtomContainer(); } } Faster ring and aromaticity perception JavaDoc Faster ring membership and aromaticity assignment. The move to AtomContainer2 (see above) allows additional optimizations to these algorithms. The APIs will run faster however for aromaticity you must use Cycles.all() on it's own. There is also a new static method for convenience and improved aromatic model encoding. // new way, no checked exception Cycles.markRingAtomsAndBonds(mol); // prerequisite if (!Aromaticity.apply(Aromaticity.Model.Daylight, molecule)) { // return false = too many cycles to check } // old way (will still be faster) Aromaticity aromaticity = new Aromaticity(ElectronDonation.daylight(), Cycles.all()); IAtomContainer container = ...; try { if (aromaticity.apply(container)) { // } } catch (CDKException e) { // cycle computation was intractable } Improved inorganic stereochemistry It is now possible to represent degenerate inorganic stereochemistry where 1 or more neighbours are missing/implicit. For example we can describe a square pyramidal structure as an octahedral without a missing ligand. Support for implicit/explicit hydrogens around theses atoms has also been improved. [NH3][Co@OH25](Cl)(Cl)(Cl)(Cl) sqpyr [NH3][Co@OH4](Cl)(Cl)[NH3] seesaw You can also use this in SMARTS to match across atoms and equatorial using the following patterns: Cl[Co@OH1]Cl across (Cl)(Cl)(Cl)%20sqpyr&w=-1&h=-1&abbr=on&hdisp=S&sma=Cl%5BCo%40OH1%5DCl&zoom=1.3&annotate=none&r=0) (Cl)%5BNH3%5D%20seesaw&w=-1&h=-1&abbr=on&hdisp=S&sma=Cl%5BCo%40OH1%5DCl&zoom=1.3&annotate=none&r=0) Cl[Co@OH3]Cl equatorial (Cl)(Cl)(Cl)%20sqpyr&w=-1&h=-1&abbr=on&hdisp=S&sma=Cl%5BCo%40OH3%5DCl&zoom=1.3&annotate=none&r=0) (Cl)%5BNH3%5D%20seesaw&w=-1&h=-1&abbr=on&hdisp=S&sma=Cl%5BCo%40OH3%5DCl&zoom=1.3&annotate=none&r=0) Functional Group Finder JavaDoc A functional group finder has been added based on Peter Ertl's algorithm. Peter Ertl. 2017 Fritsch et al. 2019 The API allows you generate the functional groups as fragments or my favorite which is fill an array with identifier numbers - this is then very easy to depict. IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); String smiles = "C2C(NC)=NC3=C(C(C1=CC=CC=C1)=N2=O)C=C(Cl)C=C3"; IAtomContainer mol = smipar.parseSmiles(smiles); FunctionalGroupsFinder fgFinder = FunctionalGroupsFinder.withNoEnvironment(); Cycles.markRingAtomsAndBonds(mol); Aromaticity.apply(Aromaticity.Model.Daylight, mol); // extract the groups as new fragments List functionalGroupsList = fgFinder.extract(inputMol); // fill an array with numbers that indicate which functional group something belongs to int[] fgrps = new int[mol.getAtomCount()]; fgFinder.find(fgrps, mol); // Set the group as the atom map/class in SMILES for (IAtom atom : mol.atoms()) atom.setMapIdx(1+fgrps[atom.getIndex()]); System.out.println(new SmilesGenerator(SmiFlavor.AtomAtomMap).create(mol)); %3D%5BN%3A1%5DC2%3DC(%5BC%3A2%5D(C3%3DCC%3DCC%3DC3)%3D%5BN%3A2%5D1%3D%5BO%3A2%5D)C%3DC(%5BCl%3A3%5D)C%3DC2&w=-1&h=-1&abbr=off&hdisp=S&zoom=1.3&annotate=colmap&r=0) Sugar Moiety Removal JavaDoc. The Sugar Removal Utility (SRU) implements a generalized algorithm for automated detection of circular and linear sugars in molecular structures and their removal. Schaub et al 2020 Convenience APIs Iterate over molecules of a reaction and sets Creating atoms/bonds in the context of molecules with: mol.newAtom() and mol.newBond() and others. Better IO error handling Contributors 55 Egon Willighagen 8 Felix Bänsch 3 Jean Marois 245 John Mayfield 43 Jonas Schaub 2 Matthias Mailänder 5 Tyler Peryea 123 Uli Fechner 3 Valentyn Kolesnikov 3 Stefan Kuhn Overview of Pull Requests SonarCloud is not reporting test coverage correctly because it was no… by @johnmay in https://github.com/cdk/cdk/pull/1000 Improved the abbreviation handling over atom sets, this is useful for… by @johnmay in https://github.com/cdk/cdk/pull/996 Fix - avoid placing a wedge on the right-angled bond when a centre is… by @johnmay in https://github.com/cdk/cdk/pull/998 Quality of life API interfaces. The IAtomContainerSet and IReaction c… by @johnmay in https://github.com/cdk/cdk/pull/997 Sonar settings for aggregated test coverage. by @johnmay in https://github.com/cdk/cdk/pull/1001 CMLXOM 4.6 by @egonw in https://github.com/cdk/cdk/pull/1004 Redo @parit's changes for net/undirected reaction depiction on the ne… by @johnmay in https://github.com/cdk/cdk/pull/1009 Smiles 0 isotope by @johnmay in https://github.com/cdk/cdk/pull/1007 When atoms/bonds are aware of the container they are in - it is usefu… by @johnmay in https://github.com/cdk/cdk/pull/1010 Fix the CDK C.plus atom type, there was already comment in the test t… by @johnmay in https://github.com/cdk/cdk/pull/1011 Query bond funcs by @johnmay in https://github.com/cdk/cdk/pull/938 Read the atom-atom mapping info from a V3000 file. by @johnmay in https://github.com/cdk/cdk/pull/1012 Fixes https://github.com/cdk/depict/issues/76. We do not like -C=CO a… by @johnmay in https://github.com/cdk/cdk/pull/1015 Added an API for fatal IO errors by @egonw in https://github.com/cdk/cdk/pull/1019 Java21 by @johnmay in https://github.com/cdk/cdk/pull/1014 Fixes #1024 - we should perhaps rework the CDK radical representation… by @johnmay in https://github.com/cdk/cdk/pull/1025 Updated dependencies by @egonw in https://github.com/cdk/cdk/pull/1026 Fix for non-deterministic CIP designation bug by @tylerperyea in https://github.com/cdk/cdk/pull/1027 Fix and issue with contraction on terminal attachment points. by @johnmay in https://github.com/cdk/cdk/pull/1028 Fix a minor issue with an abbreviation like -NnButBu. Currently this … by @johnmay in https://github.com/cdk/cdk/pull/1030 Make sure Sgroups attached to reactions get passed through and emitte… by @johnmay in https://github.com/cdk/cdk/pull/1031 First pass at aligned depictions API. by @johnmay in https://github.com/cdk/cdk/pull/1032 Symmetry calculation may fail. by @johnmay in https://github.com/cdk/cdk/pull/1033 Code cleanup by @egonw in https://github.com/cdk/cdk/pull/1018 Fix a minor issue from sonarcloud, we check the counts elsewhere so t… by @johnmay in https://github.com/cdk/cdk/pull/1034 Additional tokens reagent label formatting. by @johnmay in https://github.com/cdk/cdk/pull/1036 Depict align tweaks by @johnmay in https://github.com/cdk/cdk/pull/1037 Added a missing test class for Elements by @egonw in https://github.com/cdk/cdk/pull/1042 Added isMetalloid utility method to Elements class by @JonasSchaub in https://github.com/cdk/cdk/pull/1041 Refine OSGi import rules by @Mailaender in https://github.com/cdk/cdk/pull/1043 AtomContainer2 Phase 2 by @johnmay in https://github.com/cdk/cdk/pull/1047 New convenience methods on the Atom API. by @johnmay in https://github.com/cdk/cdk/pull/1046 AtomContainer2 phase 3 by @johnmay in https://github.com/cdk/cdk/pull/1048 Binconnected - faster ring atom/bond marking by @johnmay in https://github.com/cdk/cdk/pull/1051 Add transform/SMIRKS support to CDK. by @johnmay in https://github.com/cdk/cdk/pull/916 The number of essential/relevant cycles can be exponential for some m… by @johnmay in https://github.com/cdk/cdk/pull/1052 Relavent cycles limit test by @johnmay in https://github.com/cdk/cdk/pull/1053 Updated JNA-InChI (JNA compatibility) by @egonw in https://github.com/cdk/cdk/pull/1054 Create CITATION.cff by @egonw in https://github.com/cdk/cdk/pull/1055 Fix a corner case when depicting cc(C)c by @johnmay in https://github.com/cdk/cdk/pull/1059 small doc fix for cdkAllowingExocyclic() by @JonasSchaub in https://github.com/cdk/cdk/pull/1060 Increase the max fragment count when generating abbreviations. by @johnmay in https://github.com/cdk/cdk/pull/1066 Ensure the ESSSR parameter is reported in the FP version info. by @johnmay in https://github.com/cdk/cdk/pull/1065 Updated ${version} in pom.xml by @javadev in https://github.com/cdk/cdk/pull/1070 CMLXOM 4.9 and log4j 2.23.1 by @egonw in https://github.com/cdk/cdk/pull/1072 Link to the ChemPyFormatics 'book' by @egonw in https://github.com/cdk/cdk/pull/1071 Maven build system updates by @egonw in https://github.com/cdk/cdk/pull/1074 Only run JaCoCo once by @egonw in https://github.com/cdk/cdk/pull/1076 Depiction issues by @johnmay in https://github.com/cdk/cdk/pull/1080 Moved a number of test classes to the same module as the tested classes by @egonw in https://github.com/cdk/cdk/pull/1081 Only copy mapped bonds when deciding how to align the structure. by @johnmay in https://github.com/cdk/cdk/pull/1082 Fix a bug in the MDLV2000Reader where the wrong "molecule" is used. by @johnmay in https://github.com/cdk/cdk/pull/1085 Removed a module that has been empty for a few years by @egonw in https://github.com/cdk/cdk/pull/1087 The path based fingerprint should be identical with/without explicit … by @johnmay in https://github.com/cdk/cdk/pull/1089 Stabilise the CDK atom type based aromaticity model. This causes a sm… by @johnmay in https://github.com/cdk/cdk/pull/1091 Use interfaces instead of instances and use silent by @egonw in https://github.com/cdk/cdk/pull/1094 Recovers the "simple" patches from testing2 by @egonw in https://github.com/cdk/cdk/pull/1093 Improving the testing coverage by @egonw in https://github.com/cdk/cdk/pull/1095 Overhaul and optimise the aromaticity procedures in CDK. by @johnmay in https://github.com/cdk/cdk/pull/1092 Invalid stereochemistry group causes infinite loop by @marois in https://github.com/cdk/cdk/pull/1098 add ability to read MDL RXN V3000 files with zero reactants but a REACTANT block by @uli-f in https://github.com/cdk/cdk/pull/1100 Fix CCD/WebMolKit Sgroups that are missing the SBL. by @johnmay in https://github.com/cdk/cdk/pull/1099 Fixes code examples by @egonw in https://github.com/cdk/cdk/pull/1104 support bond type gt4 in MDLV3000Reader by @uli-f in https://github.com/cdk/cdk/pull/1102 Make sure Atom/Bond's ged deref'd when going into a QueryAtomContainer. by @johnmay in https://github.com/cdk/cdk/pull/1105 Integration of functional groups identification functionality following the Ertl algorithm by @JonasSchaub in https://github.com/cdk/cdk/pull/1039 Generally cheminf formats use ASCII and we should not be checking the… by @johnmay in https://github.com/cdk/cdk/pull/1107 Rdfile reader by @uli-f in https://github.com/cdk/cdk/pull/942 add javadocs to RdfileReader and RdfileRecord, make RdfileReader final by @uli-f in https://github.com/cdk/cdk/pull/1109 Checked, updated, and formatted documentation of FunctionalGroupsFinder by @JonasSchaub in https://github.com/cdk/cdk/pull/1110 added test case in CDKAtomTypeMatcherFilesTest that gives rise to an NPE by @uli-f in https://github.com/cdk/cdk/pull/919 support bond type gt4 in MDLV3000Writer by @uli-f in https://github.com/cdk/cdk/pull/1106 Integration of sugar moiety removal functionality by @JonasSchaub in https://github.com/cdk/cdk/pull/1040 Resolved Sonar issue with addAll in unmodifiable set by @javadev in https://github.com/cdk/cdk/pull/1114 add test dependencies assertj and mockito-junit-jupiter by @uli-f in https://github.com/cdk/cdk/pull/1115 add DefaultChemObjectReaderErrorHandler by @uli-f in https://github.com/cdk/cdk/pull/1112 Fix a bug with the default SMILES output. AtomStereo was not emitted … by @johnmay in https://github.com/cdk/cdk/pull/1116 Update BEAM to v1.3.7 to fix a corner case with reading SMILES and ar… by @johnmay in https://github.com/cdk/cdk/pull/1117 Advanced Inorganic Handling by @johnmay in https://github.com/cdk/cdk/pull/1118 inorganic stereo 2 by @johnmay in https://github.com/cdk/cdk/pull/1120 Depiction Improvements (Nov 2024) by @johnmay in https://github.com/cdk/cdk/pull/1122 Fix a minor issue with a NPE on the AwtArea util and improve tests. by @johnmay in https://github.com/cdk/cdk/pull/1123 Fix (in)saturation expression behaviour by @johnmay in https://github.com/cdk/cdk/pull/1124 Update CMLCoreModule.java. So far, if there was no order defined for … by @stefhk3 in https://github.com/cdk/cdk/pull/1126 Patch/stefhk3 patch 2 fix by @johnmay in https://github.com/cdk/cdk/pull/1127 Create codeql.yml by @javadev in https://github.com/cdk/cdk/pull/1128 fix crash in SmilesGenerator when calling with reaction not having one or more reaction components by @uli-f in https://github.com/cdk/cdk/pull/1129 This fixes a problem with the ordering of &. by @stefhk3 in https://github.com/cdk/cdk/pull/1131 remove deprecated calls from InChIGeneratorTest by @uli-f in https://github.com/cdk/cdk/pull/1134 add getAgentCount method to IReaction interface by @uli-f in https://github.com/cdk/cdk/pull/1133 Updated dependencies by @egonw in https://github.com/cdk/cdk/pull/1136 improve and document agent handling in MDLRXNV2000Reader by @uli-f in https://github.com/cdk/cdk/pull/1138 update junit-jupiter dependencies to version 5.11.4 by @uli-f in https://github.com/cdk/cdk/pull/1139 RInChI implementation based on InChI native + Java logic by @uli-f in https://github.com/cdk/cdk/pull/1137 New Contributors @tylerperyea made their first contribution in https://github.com/cdk/cdk/pull/1027 @JonasSchaub made their first contribution in https://github.com/cdk/cdk/pull/1041 @stefhk3 made their first contribution in https://github.com/cdk/cdk/pull/1126 Full Changelog: https://github.com/cdk/cdk/compare/cdk-2.9...cdk-2.10 Appendix A1 IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance(); SmilesParser smipar = new SmilesParser(bldr); SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default); // -OH => -[O-] SmirksTransform deprotonate = Smirks.compile("[c:1][OX2v2+0:2][H]>>[c:1][O-:2] de-protonate\n"); long tBegin = System.nanoTime(); long tSmirks = 0; int count = 0; try (BufferedReader brdr = new BufferedReader(new FileReader("/data/chembl_35.smi")); BufferedWriter bwtr = new BufferedWriter(new FileWriter("/data/chembl_35.smi.norm"))) { String line; while ((line = brdr.readLine()) != null) { IAtomContainer mol = smipar.parseSmiles(line); long tSplit0 = System.nanoTime(); // SMIRKS pattern will do aromaticity automatically, if you // have multiple patterns being applied it may be better // to turn this of deprotonate.setPrepare(false); and do it // yourself boolean changed = deprotonate.apply(mol); long tSplit1 = System.nanoTime(); tSmirks += (tSplit1-tSplit0); if (changed) line = smigen.create(mol) + " " + mol.getTitle(); bwtr.write(line); bwtr.newLine(); ++count; if (count % 1000 == 0) System.err.printf("\r%d...", count); } } catch (IOException e) { throw new RuntimeException(e); } long tEnd = System.nanoTime(); long tElapsed = TimeUnit.NANOSECONDS.toMillis(tEnd-tBegin); System.err.printf("\rdone %d in %.3fs (%.0f mol/s)\n", count, tElapsed / 1e3, count / (tElapsed/1e3)); System.err.printf("SMIRKS in %.3fs (%.0f mol/s)\n", tSmirks / 1e9, count / (tSmirks/1e9)); M1 Pro 2021 results: done 2474590 in 29.449s (84030 mol/s) SMIRKS in 8.591s (288054 mol/s)

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