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Activity for The Chemistry Development Kit

  • 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.

  • Egon Willighagen Egon Willighagen committed [284335] on Code

    Handle Link Nodes in CXSMILES

  • Egon Willighagen Egon Willighagen committed [777291] on Code

    Simplify the SybylAtomTypeMatcherTest.

  • Egon Willighagen Egon Willighagen committed [76b65e] on Code

    Move around some XML config files.

  • Egon Willighagen Egon Willighagen committed [e93b8c] on Code

    Remove XYZ reader from this test, we don't need to the full mol to isolate what is actually being asserted on.

  • Egon Willighagen Egon Willighagen committed [9ac05e] on Code

    Move the atom type aware saturation check to cdk-legacy, this is replaced by Kekulisation which is (a) the

  • Egon Willighagen Egon Willighagen committed [87f099] on Code

    Move the CDK AtomType Repos File test and fix the PDB one and the PubChem ASN reader.

  • Egon Willighagen Egon Willighagen committed [413224] on Code

    Replace import of CMLReader with direct molecule creation. Bug 1014344 (https://sourceforge.net/p/cdk/bugs/231/) is testing CML round tripping so I've moved it there and switch it so CML depends on SMILES (test) rather than the other way around.

  • Egon Willighagen Egon Willighagen committed [f27dcb] on Code

    Avoid depending on the HinReader and create the molecule directly.

  • GitHub committed [2a7c3c] on Code

    Merge pull request #1225 from JonasSchaub/sugar-detection-utility

  • Jonas Schaub committed [6e5f83] on Code

    adds the Sugar Detection Utility and fixes a few things in the Sugar Removal Utility

  • Egon Willighagen Egon Willighagen committed [acd73c] on Code

    Do not sett rootAttachmentPoints if null.

  • Egon Willighagen Egon Willighagen committed [b195d7] on Code

    Do not explicitly store the attachment atoms, instead we infer this from the explicit attachment points (wiggly crossed line).

  • Egon Willighagen Egon Willighagen committed [babea2] on Code

    When reading/writing RGroup queries we add on/trim explicit attachment points (wavy line across bond).

  • Egon Willighagen Egon Willighagen committed [36c623] on Code

    Add a utility method to AtomPlace which allows us to place a single atom which is sprouted off the structure.

  • Egon Willighagen Egon Willighagen committed [42facc] on Code

    Add a new utility to get the median bond length and fallback to a provided default if needed.

  • Egon Willighagen Egon Willighagen committed [9c6270] on Code

    Move the AtomPlace to cdk-standard, we are going to need this. This does split the "layout" package but in future (CDK v3) they will all be collapsed together.

  • Egon Willighagen Egon Willighagen committed [c55dd9] on Code

    In CXSMILES we use an SGroup to store the attachment order. Rather than store a map in the 'RGroup' we can reuse this SGroup and get nicer rendering.

  • Egon Willighagen Egon Willighagen committed [650217] on Code

    Improved stereochemistry invalidation when modifying molecules (Fixes #1221).

  • Egon Willighagen Egon Willighagen committed [a71800] on Code

    Grr DebugBong issues.

  • Egon Willighagen Egon Willighagen committed [141859] on Code

    A constructor argument is also useful for refactoring code.

  • Egon Willighagen Egon Willighagen committed [c46e16] on Code

    More replacements of IBond.Stereo with IBond.Display

  • Egon Willighagen Egon Willighagen committed [1402a3] on Code

    A new addBond which accepts a display property as well so we can cleanup more usages of IBond.Stereo

  • Egon Willighagen Egon Willighagen committed [8c09b3] on Code

    Don't store crossed bonds as wavy.

  • Egon Willighagen Egon Willighagen committed [5d0142] on Code

    Replace calls to IBond.getStereo() with IBond.getDisplay().

  • Egon Willighagen Egon Willighagen committed [f25453] on Code

    Replace usages of setStereo with setDisplay. We also add some alias names Up/Down for convenience.

  • Egon Willighagen Egon Willighagen committed [93e3ae] on Code

    Step 1 in cleaning up IBond.Stereo vs IBond.Display conflation. We deprecate IBond.Stereo get/set and implement them in terms of Display.

  • Egon Willighagen Egon Willighagen committed [24d811] on Code

    Allow hollowwedge display style.

  • Egon Willighagen Egon Willighagen committed [1bab11] on Code

    Fix a corner case with titles for reactions not being set if no CXSMILES layers were present.

  • GitHub committed [2b80f9] on Code

    Merge pull request #1218 from JonasSchaub/LargestPiSystemDescriptor-visited-fix

  • Jonas Schaub committed [aafeeb] on Code

    makes LargestPiSystemDescriptor use an internal visited array instead of IChemObject flag VISITED for safe parallelisation

  • Egon Willighagen Egon Willighagen committed [5e9145] on Code

    Improver generated SVG when we have an alpha colour or NULL background.

  • Egon Willighagen Egon Willighagen committed [d3c100] on Code

    Some additional documentation.

  • Egon Willighagen Egon Willighagen committed [73a102] on Code

    Correct reaction background box dimensions. I had used the wrong Dimensions here, we want to paint the box to be the size of the whole canvas.

  • John Mayfield committed [c4870f] on Code

    Remove stray print to stderr.

  • Egon Willighagen Egon Willighagen committed [a337ee] on Code

    Now the DepictionGenerator is the normal way of rendering, align the default values of these parameters.

  • Egon Willighagen Egon Willighagen committed [edcc31] on Code

    Provide a function to bulk apply parameters.

  • Egon Willighagen Egon Willighagen committed [7438d9] on Code

    Allow parameters to be explicitly set null, currently if you set it to null it reverts to default. Now it starts as default but can be set to null (or back to default if desired).

  • GitHub committed [7f9525] on Code

    Merge pull request #1214 from uli-f/depiction-empty-annotation

  • Uli committed [f30020] on Code

    replace System.getProperty("line.separator") with System.lineSeparator in DepictionTest; simplify stream operations in DepictionTest; remove unused imports and redundant whitespace in StandardGenerator; minor code cleanup in StandardGenerator

  • Uli committed [3246d8] on Code

    add test for handling empty atom property annotation labels in DepictionTest; update StandardGenerator to skip empty annotation labels

  • Egon Willighagen Egon Willighagen committed [bbda1c] on Code

    InchIToStructure and AuxInfoToStructure now both in same class;

  • Egon Willighagen Egon Willighagen committed [935541] on Code

    Add missing copyrights, javadocs;

  • Egon Willighagen Egon Willighagen committed [090eb5] on Code

    Remove doNotAddH option; implicit hydrogens set to null if information is missing;

  • Egon Willighagen Egon Willighagen committed [ce444f] on Code

    Add InChI AuxInfo to structure functionality;

  • Egon Willighagen Egon Willighagen committed [1fdd7c] on Code

    Allow annotation of bond numbers, this was useful for debugging the atropisomer logic.

  • Egon Willighagen Egon Willighagen committed [6304d8] on Code

    For these tests we really want to assert these are not tetrahedral.

  • Egon Willighagen Egon Willighagen committed [f9e5d4] on Code

    Additional check needed

  • Egon Willighagen Egon Willighagen committed [837f30] on Code

    Some tweaks to 2D atropisomer perception to ensure the Wikipedia tautomer of Sotorasib is accepted.

  • Egon Willighagen Egon Willighagen committed [6ad0a0] on Code

    Test cases for atropisomers

  • Egon Willighagen Egon Willighagen committed [516864] on Code

    Parse wedges up/down from CXSMILES.

  • GitHub committed [441d18] on Code

    Merge pull request #1211 from JonasSchaub/ConjugatedPiSystemsDetector-fix

  • Jonas Schaub committed [c5f1ef] on Code

    fixes issue with path-dependent conjugated system detection if allenes are involved

  • GitHub committed [73b28b] on Code

    Merge pull request #1207 from cdk/nwocdk/moreTesting6

  • Egon Willighagen Egon Willighagen committed [7206c0] on Code

    Fixes two more warnings

  • Egon Willighagen Egon Willighagen committed [db670e] on Code

    Silence a warning

  • Egon Willighagen Egon Willighagen committed [b1d927] on Code

    Moved two more classes: BsptTest and PointTest

  • Egon Willighagen Egon Willighagen committed [c841d4] on Code

    Moved ProblemMarkerTest from test-standard to standard

  • Egon Willighagen Egon Willighagen committed [c2fff0] on Code

    downgrade mockito dependencies to version 4.11.0 in pom.xml to stay compatible with Java 8

  • Egon Willighagen Egon Willighagen committed [a62a98] on Code

    update maven-compiler-plugin configuration to use <release> instead of <source> and <target>; bump junit, assertj, and mockito dependencies versions

  • GitHub committed [cbfa6b] on Code

    Merge pull request #1204 from cdk/deps/updates-20250725

  • Egon Willighagen Egon Willighagen committed [75cdd5] on Code

    Various Maven plugin updates

  • Egon Willighagen Egon Willighagen committed [b44e2f] on Code

    Updated dependencies: CMLXOM 4.13, Log4j 2.25.1, and JUnit 5.13.3

  • Egon Willighagen Egon Willighagen committed [2a17de] on Code

    update maven-compiler-plugin configuration to use <release> instead of <source> and <target>

  • GitHub committed [fe44b8] on Code

    Merge pull request #1203 from uli-f/depict-gen-atom-property-cleanup-fix

  • Uli committed [28ab27] on Code

    update DepictionGenerator to remove atom value annotations; add test for atom property annotation label cleanup

  • Egon Willighagen Egon Willighagen committed [6cd856] on Code

    This doesn't need to be central-snapshots, it was the <repositories> which was wrong and not <distributionManagement>.

  • Egon Willighagen Egon Willighagen committed [260c16] on Code

    Update to BEAM 1.3.10. This adds support for lone-pairs on extended tetrahedral atoms (e.g. CN=[C@AL1]=NC).

  • Egon Willighagen Egon Willighagen committed [9953ac] on Code

    Stabilise the comparator ordering of transformation op-codes. DeleteAtom MUST appear after DeleteBond of the bond it's involved in. This might defeat some optimisations (where we try to move ops and replace them with larger concepts - i.e. ReplaceAtom) but testing shows it to be acceptable.

  • Egon Willighagen Egon Willighagen committed [770b0f] on Code

    Fix some issues highlighted by SonarCloud

  • John Mayfield committed [22d6a0] on Code

    Fix the build, the snapshots repo needs a distinct name.

  • Egon Willighagen Egon Willighagen committed [f03d72] on Code

    Build plugin updates: PMD, compiler, and some harmonization

  • Egon Willighagen Egon Willighagen committed [87a653] on Code

    New deploy plugin and config for Sonatype

  • Egon Willighagen Egon Willighagen committed [2b466b] on Code

    README updated for the latest stable release

  • Egon Willighagen Egon Willighagen committed [a640d4] on Code

    Allow the ExtendedFingerprinter to setHashExplicitHydrogens

  • Egon Willighagen Egon Willighagen committed [c3ff08] on Code

    Remove some redundant exceptions.

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