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Activity for The Chemistry Development Kit

  • 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.

  • 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.

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