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Recent Releases of cdk

cdk - CDK 2.11

Interim release fixing an issue in CDK 2.10.

- Java
Published by johnmay 9 months ago

cdk - CDK 2.10

DOI

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 all of ChEMBL 35 in only ~30 seconds (see Appendix A1).

```java 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]>>N+:1[O-] polar-nitro") .apply(mol); // exclusive apply mode String smiout = smigen.create(mol); // C1=CC(N+[O-])=CC=C1N+[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:

java 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,2H2,1H3<>C4H8O2/c1-3-6-4(2)5/h3H2,1-2H3!H2O/h1H2<>p+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 experimental data.

java 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.

```java // new way, no checked exception Cycles.markRingAtomsAndBonds(molecule); // 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(molecule)) { // } } catch (CDKException e) { // cycle computation was intractable } ```

Improved inorganic stereochemistry

It is now possible to represent degenerate inorganic stereochemistry where one 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[Co@OH3]Cl equatorial

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.

```java 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(mol);

// 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)); ```

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

```java 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/chembl35.smi")); BufferedWriter bwtr = new BufferedWriter(new FileWriter("/data/chembl35.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)

- Java
Published by johnmay 12 months ago

cdk - CDK 2.9

DOI

Summary

  • Improved abbreviation handling
  • More arrow types
  • Multi-step Reaction SMILES
  • Reaction Set and Multi-step depiction
  • More correct PubChemFingerprinter
  • Universal (InChI) SMILES for large molecules
  • Dependency updates and stability improvements, huge kudos to @uli-f for finding some longstanding issues

Improved abbreviation handling

991. The Abbreviation handling has been tweaked with more and cleaner options:

java Abbreviations abbreviations = new Abbreviations(); // abbreviations.setContractToSingleLabel(true); // old (still supported) abbreviations.with(Abbreviations.Option.ALLOW_SINGLETON); // new // abbreviations.setContractOnHetero(true); // old (still supported) abbreviations.with(Abbreviations.Option.AUTO_CONTRACT_HETERO); // new

The full options are described here: Abbreviations.Option.

More arrow types

Now includes NoGo/Equilibrium/RetroSynthetic - #927. See IReaction.Direction. Examples:

#1 (2)

#1 (3)

Multi-step Reaction SMILES

https://github.com/cdk/cdk/pull/986

An new entry point to the SMILES parser has been added to parse into a "multi-step" reaction where by the product of one step is the reactant the the next. The basic idea is to allow more than two '>'. Parts at even positions are reactants/products and odd positions are agents/catalysts/solvents.

Basic idea:

java SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance()); IReactionSet rset = sp.parseReactionSetSmiles("[Pb]>>[Ag]>>[Au] lead-to-silver-to-gold");

Real example (see next bullet for depiction):

ClC1=NC=2N(C(=C1)N(CC3=CC=CC=C3)CC4=CC=CC=C4)N=CC2C(OCC)=O>C1(=CC(=CC(=N1)C)N)N2C[C@H](CCC2)O.O1CCOCC1.CC1(C2=C(C(=CC=C2)P(C3=CC=CC=C3)C4=CC=CC=C4)OC5=C(C=CC=C15)P(C6=CC=CC=C6)C7=CC=CC=C7)C.C=1C=CC(=CC1)\C=C\C(=O)\C=C\C2=CC=CC=C2.C=1C=CC(=CC1)\C=C\C(=O)\C=C\C2=CC=CC=C2.C=1C=CC(=CC1)\C=C\C(=O)\C=C\C2=CC=CC=C2.[Pd].[Pd].[Cs]OC(=O)O[Cs]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(OCC)=O)N6C[C@H](CCC6)O>CO.C1CCOC1.O.O[Li]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(O)=O)N6C[C@H](CCC6)O>CN(C)C(=[N+](C)C)ON1C2=C(C=CC=N2)N=N1.F[P-](F)(F)(F)(F)F.[NH4+].[Cl-].CN(C)C=O.CCN(C(C)C)C(C)C>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(N)=O)N6C[C@H](CCC6)O>>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N)N=CC3C(N)=O)N4C[C@H](CCC4)O |f:4.5.6.7.8,16.17,18.19| US20190241576A1

Reaction Set and Multi-step depiction

https://github.com/cdk/cdk/pull/986

The DepictionGenerator has been extended to depict reaction sets. If the product of the previous reaction is the same as the reactant in the next (object identity) it is omitted for a terser depiction:

US20190241576A1 (3)

More correct PubChemFingerprinter

Explicit hydrogens are not longer required and there is an option to use a more correct ring set definition matching closer the original CACTVS substructure keys. This is now on by default:

IChemObject builder = SilentChemObjectBuilder.getInstance(); new PubchemFingerprinter(builder); // new - default is to use "ESSSR-like" ring set new PubchemFingerprinter(builder, false); // old - for backwards compatible with FP generated with older CDK versions

Universal (InChI) SMILES for large molecules

979.

The InChI now supports > 999 atoms, we have the option to generate a SMILES using the InChI canonical labelling, it makes sense to use the larger molecules flag and support more.

New Contributors

  • @Mailaender made their first contribution in https://github.com/cdk/cdk/pull/934
  • @parit made their first contribution in https://github.com/cdk/cdk/pull/980

All Contributors

75 John Mayfield 17 Egon Willighagen 6 Uli Fechner 4 Mark J. Williamson 3 Mark Williamson 1 Parit Bansal 1 Matthias Mailänder

Full Changelog: https://github.com/cdk/cdk/compare/cdk-2.8...cdk-2.9

- Java
Published by johnmay over 2 years ago

cdk - CDK 2.8

DOI

Key Changes

  • JDK Versions:
    • JDK 8 (minimum)
    • JDK 11 (minimum if not using cdk-iordf)
    • JDK 17 (recommended)
  • The project is now built with Java 11+ but compiled to target Java 8. If you have any issues please let us know.
  • The master branch has been renamed to main.
  • logj4-core is no longer a dependency of cdk-log4j, you should include these separately if you intend to use Log4j
  • A new cdk-slf4j module allows connecting logging to SLF4J
  • MayGen structure generator, provides the ability to generate millions and millions of structures that have a given formulae. java Maygen maygen = new Maygen(SilentChemObjectBuilder.getInstance()); maygen.setFormula("C3Cl2H4"); maygen.setConsumer(new SmiOutputConsumer(new OutputStreamWriter(System.out))); maygen.run(); Maygen is pure Java, if you need more speed consider Surge by the same author.
  • New Smallest Ring utilities for single atom/bond java if (Cycles.smallRingSize(atom, 7) != 0) { // atom is in a ring 7 or smaller } if (Cycles.smallRingSize(bond, 7) != 0) { // bond is in a ring 7 or smaller }
  • RAW/Count Path Fingerprints java IFingerprinter fpr = new Fingerprinter(); Map<String, Integer> feats = fpr.getRawFingerprint(mol);

  • Where possible "Re-inflate" convex rings on cyclcophanes: Before:Screenshot 2022-09-16 at 09 38 14 now: Screenshot 2022-09-16 at 09 38 10

  • New substructure/copy utility that allows a whole or part of a structure to be copied. Atoms are bonds are selected by providing a predicate: ```java IAtomContainer dst = builder.newAtomContainer(); AtomContainerManipulator.copy(dst, src, a -> a.isInRing(), b -> b.isInRing()); // select the cyclic part of a molecule

// select atoms in a set, the bonds will also be selected Set subset = ... AtomContainerManipulator.copy(dst, src, a -> subset.contains(a)); - New *exclusive* atoms filter that provides non-overlapping substructure matches, note the input order can determine which matches are selected. java for (int[] mapping : Pattern.findSubstructure(query).matchAll(mol).exclusiveAtoms()) { // ... } ``` - Stereo perception corner-cases. Reject: Screenshot 2022-09-16 at 09 45 22, Screenshot 2022-09-16 at 09 46 22, ok: Screenshot 2022-09-16 at 09 46 24

Summary

  • Merged all PRs and resolved all open issues related to bugs
  • InChINumbersTools: Use JNA InChI options by @johnmay in https://github.com/cdk/cdk/pull/799
  • Avoid integer overflow in MF by @johnmay in https://github.com/cdk/cdk/pull/808, https://github.com/cdk/cdk/pull/810
  • Ensure correct stereo consistency (Fix #812) by @johnmay in https://github.com/cdk/cdk/pull/813
  • SMILES: Fix an issue with stereochemistry being lost on generic atoms - @johnmay in https://github.com/cdk/cdk/pull/814, https://github.com/cdk/cdk/pull/866
  • Maygen structure generator by @MehmetAzizYirik in https://github.com/cdk/cdk/pull/811
  • Weighted path descriptor performance improvements by @johnmay in https://github.com/cdk/cdk/pull/817
  • Depiction: Fix missing bond annotations by @johnmay in https://github.com/cdk/cdk/pull/819
  • Utility functions for determining the smallest ring size of an atom/b… by @johnmay in https://github.com/cdk/cdk/pull/820
  • Better consistentcy in Stereochemistry and Sgroups when removing atoms by @johnmay in https://github.com/cdk/cdk/pull/821
  • Unify MOLfile V2000/V3000 options by @johnmay in https://github.com/cdk/cdk/pull/824, https://github.com/cdk/cdk/pull/852
  • Improved stereochemistry perception by @johnmay in https://github.com/cdk/cdk/pull/826, https://github.com/cdk/cdk/pull/839
  • Replace Atom symbol (String) comparison with atomic number (integer) by @johnmay in https://github.com/cdk/cdk/pull/827
  • Improved/fix bugs with XLogP, PiContact, and BCUT, HuLuIndex descriptors by @johnmay in https://github.com/cdk/cdk/pull/833, https://github.com/cdk/cdk/pull/656, https://github.com/cdk/cdk/pull/822, https://github.com/cdk/cdk/pull/832
  • Additional Raw and count path fingerprints by @johnmay in https://github.com/cdk/cdk/pull/834
  • "Re-inflate" convex rings in macrocycles. The macrocycle layout can en… by @johnmay in https://github.com/cdk/cdk/pull/836
  • Fix a corner case in repeat crossing bonds when we have variable atta… by @johnmay in https://github.com/cdk/cdk/pull/835
  • Restore space as delimiter for string-based definition of InChI options by @marco-foscato in https://github.com/cdk/cdk/pull/846
  • Update to Apache Jena 4.2 (requires JDK 11) by @egonw in https://github.com/cdk/cdk/pull/748
  • Fix localisation of alpha channel floats in SVG by @egonw in https://github.com/cdk/cdk/pull/868
  • Check string bounds on PDB COMPND line. Fixes #870 by @johnmay in https://github.com/cdk/cdk/pull/871
  • Methods to manipulate atom types in ReactionManipulator by @uli-f in https://github.com/cdk/cdk/pull/883, https://github.com/cdk/cdk/pull/879
  • Added ChemObjectBuilder.newReaction() by @uli-f in https://github.com/cdk/cdk/pull/888
  • Utilities for selecting a substructure of a molecule. by @johnmay in https://github.com/cdk/cdk/pull/889
  • Improved CDK Log4J/SLF4J interactions by @johnmay in https://github.com/cdk/cdk/pull/878, https://github.com/cdk/cdk/pull/876
  • Additional SMARTS/matching utilities by @johnmay in https://github.com/cdk/cdk/pull/896, https://github.com/cdk/cdk/pull/900
  • Use Junit5 by @johnmay in https://github.com/cdk/cdk/pull/901
  • Fix issue with hose code nesting by @johnmay in https://github.com/cdk/cdk/pull/828

Authors

278 John Mayfield 13 Egon Willighagen 11 Uli Fechner 5 Mark Williamson 3 Valentyn Kolesnikov 2 MehmetAzizYirik 2 Marco Foscato 1 dependabot[bot] 1 Tim Dudgeon 1 Otto Brinkhaus 1 Christoph Steinbeck 1 Alex

New Contributors

  • @marco-foscato made their first contribution in https://github.com/cdk/cdk/pull/846
  • @tdudgeon made their first contribution in https://github.com/cdk/cdk/pull/847
  • @OBrink made their first contribution in https://github.com/cdk/cdk/pull/851
  • @sashashura made their first contribution in https://github.com/cdk/cdk/pull/885

Full Changelog: https://github.com/cdk/cdk/compare/cdk-2.7.1...cdk-2.8

- Java
Published by johnmay over 3 years ago

cdk - CDK 2.7.1

DOI

This page documents the changes for CDK v2.7 and v2.7.1. The patch version was made after some minor issues with how the new InChI code was organised were discovered by downstream projects.

Features

Switch from JNI to JNA InChI.

There are two main technologies for calling native code JNI (Java Native Interface) and JNA (Java Native Access). JNI requires writing a custom native wrapper which is then bound to Java code, JNA allows you to call the native methods of an existing SO/DYLIB directly. Essentially what this means is to expose the native InChI library in Java one needs to first write (and maintain) a native wrapper, with JNA we can just drop the InChI SO directly in. JNI InChI exposed InChI v1.03 and worked well for many years - unfortunately this project was no longer maintained and as newer more stable versions of InChI were released (now v1.06) an alternative was needed. A few years ago Daniel Lowe started JNA InChI and recently made it feature complete and released v1.0.

ChemAxon have also independently used the JNA path to integrated newer InChI libraries into their tools: (slides). It is not clear if this was made available, it is not listed on GitHub/ChemAxon.

Build on Java 17

The Maven plugins were updated to allow building on Java 17

Verify declared dependencies

The maven modules were checked for unused declared dependencies and used undeclared dependencies (mvn dependency:analyze).

Organise and restructure test-jar and testdata

CDK was originally built with the ant build tool, under this scheme there was a jar for the main/ code and one the test/ code. Test modules could share an inherit dependencies. To replicate this in maven we install and deploy "test-jar" artefacts. The project test code was restructured to put all common test code in the "cdk-test" module.

All test data was stored in a cdk-testdata module, this data has now been relocated to the test/resources of each module where it is used. This meant some data was duplicated but means the ~18MB test-jar no longer needs to be uplodaded to maven central.

Remove Guava dependency

We have removed the use of Guava, the functionality could mostly be directly replaced with newer JDK idioms (Function/Predicate/Stream) which were not available in the past.

Use XorShift PRNG in ShortestPathFingerprinter (different fingerprint)

Commons Math3 was used in a single place to hash paths (Mersenne Twister) in the ShortestPathFingerprinter. Since this fingerprint method is not widely used and the hashes do not need to be cryptographically secure a simple https://en.wikipedia.org/wiki/Xorshift random generate is now used instead. This allows us to remove the dependency on Commons Math3. This does mean the fingerprint bits have changed, note the CDK version description is accessible via the Fingerprinter.getVersionDescription() method.

Authors

137 John Mayfield 6 Egon Willighagen 1 dependabot[bot]

Full Change Log

- Java
Published by johnmay almost 4 years ago

cdk - CDK 2.7

Please use v2.7.1

- Java
Published by johnmay almost 4 years ago

cdk - CDK 2.6

DOI Maven Central

Release Notes

- Java
Published by johnmay about 4 years ago

cdk - CDK 2.5

Release Notes

- Java
Published by johnmay over 4 years ago

cdk - CDK 2.3

DOI

Release Notes

- Java
Published by johnmay over 6 years ago

cdk - CDK 2.2

DOI

Please see 2.2 Release Notes for full details.

- Java
Published by johnmay about 7 years ago

cdk - CDK 2.1.1 (patch release)

DOI

This patch release removes the SNAPSHOT dependency. Release Notes

- Java
Published by johnmay about 8 years ago

cdk - CDK 2.1

DOI

Release Notes

- Java
Published by johnmay about 8 years ago

cdk - CDK 2.0

DOI

Release Notes

- Java
Published by johnmay over 8 years ago

cdk - CDK Release 1.5.15

DOI

- Java
Published by johnmay over 8 years ago

cdk - CDK Release 1.5.14

https://github.com/cdk/cdk/wiki/1.5.14-Release-Notes

DOI

- Java
Published by johnmay about 9 years ago

cdk - CDK Release 1.5.13

DOI

1.5.13 Release Notes

- Java
Published by johnmay over 9 years ago

cdk - CDK Release 1.5.12

DOI

1.5.12 Release Notes

- Java
Published by johnmay about 10 years ago

cdk - CDK Release 1.5.11

https://github.com/cdk/cdk/wiki/1.5.11-Release-Notes

- Java
Published by johnmay over 10 years ago

cdk - CDK Release 1.5.10

https://github.com/cdk/cdk/wiki/1.5.10-Release-Notes

- Java
Published by johnmay about 11 years ago

cdk - CDK Release 1.5.9

DOI

Full Release Notes

- Java
Published by johnmay about 11 years ago

cdk - CDK Release 1.5.8

1.5.8 Release Notes

- Java
Published by johnmay over 11 years ago

cdk - CDK Release 1.5.7

1.5.7 Release Notes

- Java
Published by johnmay over 11 years ago