Activity for The Chemistry Development Kit

  • Egon Willighagen Egon Willighagen committed [abad6b] on Code

    Updated version

  • GitHub committed [ea71f8] on Code

    Updated Maven Central version badge

  • Egon Willighagen Egon Willighagen committed [edc65f] on Code

    Spelling.

  • Egon Willighagen Egon Willighagen committed [3e7550] on Code

    Simplify.

  • Egon Willighagen Egon Willighagen committed [db3ab7] on Code

    Performance: use is empty.

  • Egon Willighagen Egon Willighagen committed [a9e889] on Code

    Fix null pointer exceptions.

  • GitHub committed [c7ee67] on Code

    Merge pull request #1252 from cdk/update/cmlxom4.15

  • Egon Willighagen Egon Willighagen committed [43d206] on Code

    CMLXOM 4.15 and Log4j 2.25.3

  • GitHub committed [260d72] on Code

    Merge pull request #1250 from cdk/feature/depsManagement

  • Egon Willighagen Egon Willighagen committed [91a947] on Code

    Use <pluginManagement>

  • Egon Willighagen Egon Willighagen committed [dbfacc] on Code

    Add a method to the SDG which allows wedges to be assigned to a structure.

  • Egon Willighagen Egon Willighagen committed [602c91] on Code

    Add support for loading selection/highlight from CXSMILES and MDL Molfiles.

  • Egon Willighagen Egon Willighagen committed [9c3f48] on Code

    Some tweaks to abbreviations - based on feedback from https://github.com/cdk/depict/issues/97

  • GitHub committed [ae0d10] on Code

    Merge pull request #1242 from cdk/deps/updates/202511

  • Egon Willighagen Egon Willighagen committed [a752b3] on Code

    Central (and updated) CMLXOM version

  • Egon Willighagen Egon Willighagen committed [de621d] on Code

    Updated JUnit to 5.14.1

  • Egon Willighagen Egon Willighagen committed [098aeb] on Code

    Two more central version: mockito and junit

  • Egon Willighagen Egon Willighagen committed [5fe6ec] on Code

    Central log4j version

  • Egon Willighagen Egon Willighagen committed [34a403] on Code

    Added this config, to silence ChecksumFailureException's in recent Maven versions

  • Egon Willighagen Egon Willighagen committed [1fc4b3] on Code

    Updated sonatype publishing plugin version

  • Egon Willighagen Egon Willighagen committed [8754d7] on Code

    Updated deps for maven-dependency and maven-enforcer, and more central versions: jacoco, maven-jar, maven-javadoc

  • Egon Willighagen Egon Willighagen committed [f78533] on Code

    Update javacc version and one more central versions: maven-pmd

  • Egon Willighagen Egon Willighagen committed [060e4e] on Code

    Two more central versions: maven-compiler and maven-shade

  • Egon Willighagen Egon Willighagen committed [585424] on Code

    Central maven-surefire-plugin version

  • Egon Willighagen Egon Willighagen committed [0d72a4] on Code

    Fix wording.

  • Egon Willighagen Egon Willighagen committed [016407] on Code

    Allow variable attachments in SMARTS/substructure queries using a post-processing filter of the mapped atoms.

  • GitHub committed [13b77a] on Code

    Merge pull request #1238 from ToLeWeiss/exhaustive_fragmenter

  • ToLeWeiss committed [59e232] on Code

    fixed missing value

  • ToLeWeiss committed [9ca394] on Code

    added exception to mitigate the indexing of the fragmentation result map to overflow

  • ToLeWeiss committed [7abb1f] on Code

    adjusted maximum tree depth in the comments to 27

  • ToLeWeiss committed [7734d8] on Code

    Merge remote-tracking branch 'upstream/main' into exhaustive_fragmenter

  • ToLeWeiss committed [6a0330] on Code

    I finally read the documentation of git cherry-pick and therefore applied the changes from BigInt back to int manually

  • ToLeWeiss committed [b186c0] on Code

    cherry picked hopefully the right commit commit:d6f52e8 to revert to integers instead of BigInt

  • ToLeWeiss committed [e7c548] on Code

    cherry picked commit: 71da5e6e4d to revert to integers instead of BigInt

  • ToLeWeiss committed [521afe] on Code

    switching to big integers to lift the upper limit of 31 splittable Bonds per fragmentation

  • ToLeWeiss committed [71da5e] on Code

    made param comments more consistent and beginning with lowercase

  • ToLeWeiss committed [d6f52e] on Code

    added documentation for custom assertion

  • ToLeWeiss committed [29781a] on Code

    Merge branch 'main' into exhaustive_fragmenter

  • ToLeWeiss committed [6302f6] on Code

    fixed typo

  • ToLeWeiss committed [d66993] on Code

    improved comments and code aesthetic for stereo information copying

  • ToLeWeiss committed [40a655] on Code

    fixed documentation links, added constructor for just saturation and added a setting for copying setereo information + tests

  • ToLeWeiss committed [3eeb88] on Code

    fixed regression in test and fixed wrong maximum tree depth

  • ToLeWeiss committed [c7084a] on Code

    implemented stereo chemistry copying, a respective test and added missing documentation

  • ToLeWeiss committed [0890b0] on Code

    implemented test for double bonds, cleaned up code and tests

  • ToLeWeiss committed [829fb4] on Code

    improved comments and removed dependencies in the test class

  • ToLeWeiss committed [1acf2b] on Code

    removed useless comments and imports and added documentation if it is not possible to generate any fragments

  • ToLeWeiss committed [a46401] on Code

    Merge branch 'main' into exhaustive_fragmenter

  • ToLeWeiss committed [33ce57] on Code

    added null check for input molecule and elaborated on comments

  • ToLeWeiss committed [2e50f4] on Code

    implemented comments and improved ring detection and aromaticity copying

  • ToLeWeiss committed [0fce4a] on Code

    WIP fixing issues in documentation and conformities in the code

  • ToLeWeiss committed [53633e] on Code

    fixed docs and corrected calculation for HashSet capacity

  • ToLeWeiss committed [65fef6] on Code

    small test documentation fix

  • ToLeWeiss committed [2ba2fc] on Code

    improved tests and documentation

  • ToLeWeiss committed [59425d] on Code

    refactored splitting function to improve saturation and improved documentation

  • ToLeWeiss committed [194d44] on Code

    Merge remote-tracking branch 'origin/main' into exhaustive_fragmenter

  • ToLeWeiss committed [f9faed] on Code

    work in progress: added tests for pseudo-R-atom saturation and first tries to implement the pseudo-R-atom saturation

  • ToLeWeiss committed [c1596f] on Code

    work in progress: first tries to add an saturation option with R-Atoms

  • ToLeWeiss committed [eaa69e] on Code

    Merge branch 'main' into exhaustive_fragmenter

  • ToLeWeiss committed [c2fd01] on Code

    work in progress: further improvements to comments and more private fields

  • ToLeWeiss committed [49536e] on Code

    work in progress: refining comments

  • ToLeWeiss committed [6ed08b] on Code

    work in progress: adding a setter for the maximum tree depth

  • ToLeWeiss committed [259eb8] on Code

    work in progress: cleaning up imports

  • ToLeWeiss committed [225a56] on Code

    work in progress: cleaning up and adding documentation

  • ToLeWeiss committed [c01722] on Code

    work in progress: working reimplementation of the exhaustive fragmenter

  • ToLeWeiss committed [40dfd8] on Code

    work in progress: fixing for end atoms not in container

  • ToLeWeiss committed [167762] on Code

    work in progress: figuring out why the end atoms are in a different container

  • ToLeWeiss committed [dc328c] on Code

    work in progress: fix size limitation of the subset generation

  • ToLeWeiss committed [49cfd6] on Code

    work in progress: switch to primitive int matrices for subset generation and added more comprehensive comments for subset generation

  • ToLeWeiss committed [a3f1d3] on Code

    work in progress: fixed indexing and fix of check for size constraint

  • ToLeWeiss committed [1831ce] on Code

    switching to primitive integers because java Lists are indexed by these and therefore cant have more elements than 2^31 - 1

  • ToLeWeiss committed [158452] on Code

    fix subset generation for case where initial capacity might be negative or too small because of truncation of BigInt to int

  • ToLeWeiss committed [db70ad] on Code

    work in progress: first copy approaches to fix saturation problem and algorithm changes to use a power set to reduce computations

  • ToLeWeiss committed [9ad00c] on Code

    added tests for unsaturated setting and fixed unsaturated run

  • ToLeWeiss committed [66bdb9] on Code

    work in progress: implemented the option for the fragmenter to return saturated or unsaturated fragments, added a test and renamed some tests to prepare for the tests for unsaturated fragments

  • Egon Willighagen Egon Willighagen committed [03cb25] on Code

    use thread safe collection in RoundRobinFormulaGenerator

  • GitHub committed [834d1e] on Code

    Merge pull request #1226 from uli-f/doublebondstereochemistry-create-alignment-fix

  • GitHub committed [a5e758] on Code

    Merge branch 'main' into doublebondstereochemistry-create-alignment-fix

  • Egon Willighagen Egon Willighagen committed [f14d48] on Code

    Add JDK-25 to CI

  • John Mayfield committed [d1135d] on Code

    Show how to use the SmirksTransform.

  • John Mayfield committed [d4b52d] on Code

    Update the documentation to make it clearer how to use the API

  • GitHub committed [ee35b7] on Code

    Merge pull request #3 from cdk/doublebondstereochemistry-create-alignment-fix

  • John Mayfield committed [a005c5] on Code

    Some additional null checks and fix the test assertion now the order is corrected.

  • Uli committed [835568] on Code

    introduce processCarriers hook in AbstractStereo to allow subclasses to process carriers; move carrier swap logic from DoubleBondStereochemistry::create to overridden DoubleBondStereochemistry::processCarriers method

  • Uli committed [763422] on Code

    fix carrier consistency in DoubleBondStereochemistry::create; add tests for strict carrier swap behavior in DoubleBondStereochemistry::create; change DoubleBondStereochemistry::testMap_Map_Map to reflect changes in DoubleBondStereochemistry::create

  • Egon Willighagen Egon Willighagen committed [285da9] on Code

    Avoid regex DoS.

  • Egon Willighagen Egon Willighagen committed [99213a] on Code

    Move the InChI Readers to cdk-inchi module.

  • GitHub committed [50ecd9] on Code

    Merge pull request #1234 from JonasSchaub/descriptor-parallelisation

  • Jonas Schaub committed [4907fd] on Code

    a bit of refactoring and linting in the ALogPDescriptor class

  • Jonas Schaub committed [07a89d] on Code

    a bit of refactoring in the ALogPDescriptor class

  • Jonas Schaub committed [ebeec0] on Code

    a bit of code formatting and refactoring

  • Jonas Schaub committed [5f0516] on Code

    makes SmallRingDescriptor threadsafe

  • Jonas Schaub committed [e8ef0f] on Code

    makes ALogPDescriptor threadsafe

  • Jonas Schaub committed [225361] on Code

    makes Wiener numbers descriptor threadsafe

  • Egon Willighagen Egon Willighagen committed [a48fb6] on Code

    Fix the terse SGroup test

  • Egon Willighagen Egon Willighagen committed [dfe6f9] on Code

    Fix tests and cleanup CXSMILES output.

  • Egon Willighagen Egon Willighagen committed [36bc9c] on Code

    Allow terse SRU sgroups

  • Egon Willighagen Egon Willighagen committed [d7ac66] on Code

    Some extra test cases

  • Egon Willighagen Egon Willighagen committed [41bf5d] on Code

    Make sure when xbonds are specified they get added to the Sgroup

  • Egon Willighagen Egon Willighagen committed [562122] on Code

    Fix an issue in SvgDrawVisitor which caused brackets not be drawn.

  • Egon Willighagen Egon Willighagen committed [83c42b] on Code

    Fix a failing test, the force field configurator needs ring flags clearing.

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