Activity for The Chemistry Development Kit

  • Felix Bänsch committed [c50ce6] on Code

    Introduce separate base counter for /F: layer parsing;

  • GitHub committed [5b0d72] on Code

    Merge pull request #1280 from uli-f/add-ctfile-reacting-center-status

  • Uli committed [e1e03f] on Code

    MDLV2000Reader: replace logger.warn with handleError; MDLReactingCenterStatus: implement switch-based value mapping in and add copyright notice

  • Uli committed [8c11d1] on Code

    add tests for handling reacting center status in MDL V3000 reader and writer; adjust V2000 test paths; fix order of actual and expected in assertions

  • Uli committed [782a6f] on Code

    add support for reacting center status in MDL V3000 reader and writer

  • Uli committed [09eb5b] on Code

    update reacting center status handling to use MDLReactingCenterStatus enum in MDLV2000Reader and adjust tests

  • Uli committed [c14f44] on Code

    add javadocs for MDLReactingCenterStatus enum and its methods

  • Uli committed [a75b4f] on Code

    migrate values for reacting center status from CDKConstants to MDLReactingCenterStatus;

  • GitHub committed [8198b8] on Code

    Merge branch 'main' into add-ctfile-reacting-center-status

  • Egon Willighagen Egon Willighagen committed [adf113] on Code

    Revert "replace artifact id slf4j-log4j12 with updated id slf4j-reload4j in storage/iordf/pom.xml"

  • Egon Willighagen Egon Willighagen committed [a937e0] on Code

    replace artifact id slf4j-log4j12 with updated id slf4j-reload4j in storage/iordf/pom.xml

  • Uli committed [74c22e] on Code

    support reacting center status in MDL V2000 reader and writer; introduce tests for reacting center status handling

  • GitHub committed [96732f] on Code

    Merge pull request #1277 from JonasSchaub/circular_fragmenter

  • GitHub committed [f548b7] on Code

    Merge branch 'main' into circular_fragmenter

  • Jonas Schaub committed [dfff5d] on Code

    resolve merge conflict by steering clear of the now removed cdk-test dependency

  • Jonas Schaub committed [39d782] on Code

    adds safeguards against null values

  • Jonas Schaub committed [db79a9] on Code

    move tag in front of code example

  • Jonas Schaub committed [d9d851] on Code

    adds note on aromaticity detection and test for previous HOSE code generator bug

  • Jonas Schaub committed [de48fa] on Code

    encapsulates the fragment atom container creation and stereo element mapping

  • Jonas Schaub committed [542f43] on Code

    avoid exceptions in stereo mapping

  • Jonas Schaub committed [7b1b6d] on Code

    queue only holds index instead of index and depth

  • Jonas Schaub committed [caed51] on Code

    replaces visitedIndeces set and originalAtomToDepthMap with one array

  • Jonas Schaub committed [f003fd] on Code

    enhances public API for retrieving only the fragment centered on a specific atom

  • Jonas Schaub committed [2ceab3] on Code

    replace pre-built atomIndexMap with atom.getIndex()

  • Jonas Schaub committed [322727] on Code

    make protected methods and public constants private

  • Jonas Schaub committed [6e7909] on Code

    adds a property to each fragment atom that contains its depth/sphere/level/height in the respective fragment

  • Jonas Schaub committed [31e5e3] on Code

    catch NoSuchBondException as well and correct malformatted doc

  • Jonas Schaub committed [45bd2c] on Code

    work on doc

  • Jonas Schaub committed [49c759] on Code

    mostly work on tests

  • Jonas Schaub committed [b02711] on Code

    adds settings for the preservation of stereochem and saturation by pseudo atoms; now uses the deep copy methods taken from the SDU; fixes saturation in general

  • Jonas Schaub committed [0db0cb] on Code

    adds a utility to calculate a suitable initial collection size for internal use

  • Jonas Schaub committed [f10faf] on Code

    WIP, removed the properties for the return ACs

  • Jonas Schaub committed [38be24] on Code

    initial implementation of CircularFragmenter

  • Egon Willighagen Egon Willighagen committed [d46080] on Code

    Update CDK version from 2.11 to 2.12 in README

  • Egon Willighagen Egon Willighagen committed [6d69b0] on Code

    Updated the GitHub Actions

  • Egon Willighagen Egon Willighagen committed [4089c0] on Code

    Bumped the year

  • Egon Willighagen Egon Willighagen committed [5cf1b8] on Code

    Reduce the occurrences of "extends CDKTestCase" many times this is not needed at all and allows us to remove "test-jar" dependency.

  • Egon Willighagen Egon Willighagen committed [00dabf] on Code

    Implement the option "EXPAND_HYDROGENS" we do this as a preprocessing step before the transform is run.

  • Egon Willighagen Egon Willighagen committed [f606b4] on Code

    Allow abbreviations with isotopes, for example CD3 for deuterated methyl.

  • Egon Willighagen Egon Willighagen committed [b87e30] on Code

    Remove commented code

  • Egon Willighagen Egon Willighagen committed [e11894] on Code

    Ensure small ring size check work correctly.

  • John Mayfield committed [2853e9] on Code

    Skip writing empty LOG (logic) definitions for RGroups.

  • John Mayfield committed [a5eaa2] on Code

    Treat R as R0 and allow partial enumeration of R groups. i.e. if one R group is not defined we can still enumerate the rest.

  • John Mayfield committed [b9e38f] on Code

    Make sure the hydrogen count is set to 0 when creating the attachment point.

  • John Mayfield committed [23f535] on Code

    Remove the checksum plugin - this is now done via a GH action.

  • John Mayfield committed [6106d6] on Code

    CDK dev version 2.13-SNAPSHOT

  • John Mayfield committed [90603f] on Code

    Missing <name> - needed for maven deployment

  • John Mayfield committed [ca4faa] on Code

    CDK 2.12

  • Egon Willighagen Egon Willighagen committed [fce871] on Code

    Improve ionic bond depictions - fixes https://github.com/cdk/depict/issues/26 and https://github.com/cdk/depict/issues/99.

  • Egon Willighagen Egon Willighagen committed [c21d5b] on Code

    Add in header

  • Egon Willighagen Egon Willighagen committed [b305d9] on Code

    Fixes #953 - Tweak the expression handling logic of the QueryAtomContainer.

  • Egon Willighagen Egon Willighagen committed [624b13] on Code

    Fix an issue with '>' appearing in the titles and messing up SMILES parsing.

  • Egon Willighagen Egon Willighagen committed [295e7e] on Code

    Fixes #1035 - rather than avoid using templates when we have DB stereo we try the template anyways. If the double bonds happen to be correct then all is find.

  • Egon Willighagen Egon Willighagen committed [50d1fd] on Code

    Fixes #1255 - Add in B3_Minus as a valid aromatic atom type.

  • Egon Willighagen Egon Willighagen committed [ed489a] on Code

    Fix test cases - we did want null here.

  • Egon Willighagen Egon Willighagen committed [1d729e] on Code

    Make sure formal charge is set to 0

  • Egon Willighagen Egon Willighagen committed [8ba589] on Code

    Move permissions to the job level

  • Egon Willighagen Egon Willighagen committed [bae8db] on Code

    Clean up some type casts

  • Egon Willighagen Egon Willighagen committed [9cc17c] on Code

    Use IElement instead of IAtom to access the static field

  • Egon Willighagen Egon Willighagen committed [d84713] on Code

    Fix warnings about illegal type cast from SonarCloud

  • GitHub committed [6c4481] on Code

    Merge pull request #1265 from cdk/isotopeFactory/noErrorButWarning

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

    Downgrade to warning: unnatural elements do not have major isotopes

  • Egon Willighagen Egon Willighagen committed [dcd453] on Code

    Simplify the atom placer logic to alway place atoms sprouting at correct angles. Fixes #1108

  • Egon Willighagen Egon Willighagen committed [bd0025] on Code

    Some speed improvements to the InChI tautomer generator (Fixes #1256).

  • Egon Willighagen Egon Willighagen committed [2675e0] on Code

    Fix corner case of wedge placement, focus is sometimes -1 here.

  • Egon Willighagen Egon Willighagen committed [a547a4] on Code

    Fixes #1038

  • Egon Willighagen Egon Willighagen committed [b33626] on Code

    Fixes #1195

  • Egon Willighagen Egon Willighagen committed [89d594] on Code

    Fix #1245 - the logic of skipping the bond i the neighbour is null is acceptable as the angle checking still works correctly. I have added a negative assertion to show this.

  • Egon Willighagen Egon Willighagen committed [76aad0] on Code

    Correct test case

  • Egon Willighagen Egon Willighagen committed [e0bf61] on Code

    Additional test cases and corner case fixes

  • Egon Willighagen Egon Willighagen committed [563fbb] on Code

    Refactor the hydrogen contraction/expansion to a separate (internal) class (Hydrogens.java) keeping all the logic together. We also improve the logic such that the user can have a single entry point and they specify how they want their hydrogens.

  • Egon Willighagen Egon Willighagen committed [046a9c] on Code

    Process ligand ordering in CXSMARTS

  • Egon Willighagen Egon Willighagen committed [9d7dde] on Code

    Layout and depiction of RGroup/Markush definitions.

  • Egon Willighagen Egon Willighagen committed [67ccce] on Code

    Handling of RGroups to/from CXSMILES - this includes implying attachment points where needed and disambiguating nested definitions.

  • Egon Willighagen Egon Willighagen committed [3d604a] on Code

    Allow RGroupQueries to be flattened to/from molecules - this makes certain operations easier and will greatly simplify JChemPaint since we work in flattened mode and then turn it into a real RgroupQuery as needed.

  • Egon Willighagen Egon Willighagen committed [958ca3] on Code

    Two of the CDK's test cases (rgfile.5.mol and rgfile.7.mol) are not accepted by BIOVIA's tools - both of these have inconsistencies between the parent/root structure and defined attachments. I agree these are wrong. Here I have added a verify check to strict reading mode which checks and reports on these errors.

  • GitHub committed [e46a51] on Code

    Merge pull request #1259 from cdk/updates/twoMoreForJava8

  • Egon Willighagen Egon Willighagen committed [fac8b5] on Code

    Updated JavaCC to 3.2.0

  • Egon Willighagen Egon Willighagen committed [8deb8d] on Code

    Updated JUnit to 5.14.3

  • Egon Willighagen Egon Willighagen committed [320c78] on Code

    Update the connectivity checker to either respect/ignore (default) var/multi attach bonds and explicit component grouping.

  • Egon Willighagen Egon Willighagen committed [1a2c35] on Code

    A previous change means data Sgroups were not being applied to reactions.

  • Egon Willighagen Egon Willighagen committed [513a78] on Code

    Minor tweaks/additions to some rendering APIs.

  • Egon Willighagen Egon Willighagen committed [cc4d51] on Code

    * can be both aliphatic and aromatic in SMILES and so it is not a hard error if the bond is aromatic when connected to these and the atom it's self is not marked as aromatic.

  • Egon Willighagen Egon Willighagen committed [75175e] on Code

    Fixup

  • Egon Willighagen Egon Willighagen committed [a123f8] on Code

    Bug fix in the SDG layout of multiple molecules in a grid, because the y-axis is flipped (0 at bottom) we need to accumulate in reverse going up the page.

  • 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

1 >
MongoDB Logo MongoDB