https://sourceforge.net/p/cdk/activity/Recent activity for The Chemistry Development KitenFri, 03 Apr 2026 18:34:46 -0000https://sourceforge.net/p/cdk/code/ci/c50ce68df4ccbf18e31829ed91f9ef51a265122e/Introduce separate base counter for /F: layer parsing;Felix BänschFri, 03 Apr 2026 18:34:46 -0000https://sourceforge.net/p/cdk/code/ci/c50ce68df4ccbf18e31829ed91f9ef51a265122e/https://sourceforge.net/p/cdk/code/ci/5b0d72fa6753ccbd5479c652909601c4fc3fd817/Merge pull request #1280 from uli-f/add-ctfile-reacting-center-statusGitHubFri, 03 Apr 2026 18:34:46 -0000https://sourceforge.net/p/cdk/code/ci/5b0d72fa6753ccbd5479c652909601c4fc3fd817/https://sourceforge.net/p/cdk/code/ci/e1e03f4a70ee946ee193d157e3df99e33f41524a/MDLV2000Reader: replace logger.warn with handleError; MDLReactingCenterStatus: implement switch-based value mapping in and add copyright noticeUliFri, 03 Apr 2026 18:34:46 -0000https://sourceforge.net/p/cdk/code/ci/e1e03f4a70ee946ee193d157e3df99e33f41524a/https://sourceforge.net/p/cdk/code/ci/8c11d14b2a2ac16e676c31c99dc627737db278bb/add tests for handling reacting center status in MDL V3000 reader and writer; adjust V2000 test paths; fix order of actual and expected in assertionsUliFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/8c11d14b2a2ac16e676c31c99dc627737db278bb/https://sourceforge.net/p/cdk/code/ci/782a6fd7a202962484acd97c1bb64462da0515ef/add support for reacting center status in MDL V3000 reader and writerUliFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/782a6fd7a202962484acd97c1bb64462da0515ef/https://sourceforge.net/p/cdk/code/ci/09eb5bbf008a12cd7350e0e2079b8723c22a53d9/update reacting center status handling to use MDLReactingCenterStatus enum in MDLV2000Reader and adjust testsUliFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/09eb5bbf008a12cd7350e0e2079b8723c22a53d9/https://sourceforge.net/p/cdk/code/ci/c14f44c8d65e6289369f67b83111c5bc6dabe2d5/add javadocs for MDLReactingCenterStatus enum and its methodsUliFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/c14f44c8d65e6289369f67b83111c5bc6dabe2d5/https://sourceforge.net/p/cdk/code/ci/a75b4faadf438391c2eaab1c9016d2ca03762e93/migrate values for reacting center status from CDKConstants to MDLReactingCenterStatus;UliFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/a75b4faadf438391c2eaab1c9016d2ca03762e93/https://sourceforge.net/p/cdk/code/ci/8198b825dca6f2ec3b9d6d0a6f09a0ca6746c8d5/Merge branch 'main' into add-ctfile-reacting-center-statusGitHubFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/8198b825dca6f2ec3b9d6d0a6f09a0ca6746c8d5/https://sourceforge.net/p/cdk/code/ci/adf113c73a5c0e74903cc336eb1e2fa9b72d637f/Revert "replace artifact id slf4j-log4j12 with updated id slf4j-reload4j in storage/iordf/pom.xml"Egon WillighagenFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/adf113c73a5c0e74903cc336eb1e2fa9b72d637f/https://sourceforge.net/p/cdk/code/ci/a937e057617cc43abab82aa6800d425d9a5c620f/replace artifact id slf4j-log4j12 with updated id slf4j-reload4j in storage/iordf/pom.xmlEgon WillighagenFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/a937e057617cc43abab82aa6800d425d9a5c620f/https://sourceforge.net/p/cdk/code/ci/74c22e6cdefca464284fab153140c7a08c0c4906/support reacting center status in MDL V2000 reader and writer; introduce tests for reacting center status handlingUliFri, 03 Apr 2026 18:34:45 -0000https://sourceforge.net/p/cdk/code/ci/74c22e6cdefca464284fab153140c7a08c0c4906/https://sourceforge.net/p/cdk/code/ci/96732f64153126127f57096d690a4b93d06fe223/Merge pull request #1277 from JonasSchaub/circular_fragmenterGitHubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/96732f64153126127f57096d690a4b93d06fe223/https://sourceforge.net/p/cdk/code/ci/f548b7db4bb93a26f1fa5bc364621cda562c378a/Merge branch 'main' into circular_fragmenterGitHubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/f548b7db4bb93a26f1fa5bc364621cda562c378a/https://sourceforge.net/p/cdk/code/ci/dfff5dcff768a1b984561863b412f27a4e84ca7a/resolve merge conflict by steering clear of the now removed cdk-test dependencyJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/dfff5dcff768a1b984561863b412f27a4e84ca7a/https://sourceforge.net/p/cdk/code/ci/39d7825fdd3f21f069db72025e21dd4606b7e7a8/adds safeguards against null valuesJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/39d7825fdd3f21f069db72025e21dd4606b7e7a8/https://sourceforge.net/p/cdk/code/ci/db79a97f86bc015e58878fe4c7ee58c8e205c7c7/move tag in front of code exampleJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/db79a97f86bc015e58878fe4c7ee58c8e205c7c7/https://sourceforge.net/p/cdk/code/ci/d9d8516f1ad2f07b8c767dd1aa4cbdb6befa74a3/adds note on aromaticity detection and test for previous HOSE code generator bugJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/d9d8516f1ad2f07b8c767dd1aa4cbdb6befa74a3/https://sourceforge.net/p/cdk/code/ci/de48fa3efa8f09852390c747b382d8f0db513969/encapsulates the fragment atom container creation and stereo element mappingJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/de48fa3efa8f09852390c747b382d8f0db513969/https://sourceforge.net/p/cdk/code/ci/542f43f285699e9336ca8a4b220e7d89e2b92f7d/avoid exceptions in stereo mappingJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/542f43f285699e9336ca8a4b220e7d89e2b92f7d/https://sourceforge.net/p/cdk/code/ci/7b1b6da12cbb912cfcef51e0309c7b52e0d14462/queue only holds index instead of index and depthJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/7b1b6da12cbb912cfcef51e0309c7b52e0d14462/https://sourceforge.net/p/cdk/code/ci/caed519df5bf0bb84c6f5c2d4fb01164a66a5b0b/replaces visitedIndeces set and originalAtomToDepthMap with one arrayJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/caed519df5bf0bb84c6f5c2d4fb01164a66a5b0b/https://sourceforge.net/p/cdk/code/ci/f003fd5052a3ad2c6b6ff2530aabd9a6b011bcc9/enhances public API for retrieving only the fragment centered on a specific atomJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/f003fd5052a3ad2c6b6ff2530aabd9a6b011bcc9/https://sourceforge.net/p/cdk/code/ci/2ceab3cb79339b795f98f9571b1536ef3f11e118/replace pre-built atomIndexMap with atom.getIndex()Jonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/2ceab3cb79339b795f98f9571b1536ef3f11e118/https://sourceforge.net/p/cdk/code/ci/32272718d305d882547341106a8aa1af87c88129/make protected methods and public constants privateJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/32272718d305d882547341106a8aa1af87c88129/https://sourceforge.net/p/cdk/code/ci/6e7909e36290b6333e9a384cde404141511e279c/adds a property to each fragment atom that contains its depth/sphere/level/height in the respective fragmentJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/6e7909e36290b6333e9a384cde404141511e279c/https://sourceforge.net/p/cdk/code/ci/31e5e32a3cf491c2750d6c3d16a8fc58ad67d87f/catch NoSuchBondException as well and correct malformatted docJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/31e5e32a3cf491c2750d6c3d16a8fc58ad67d87f/https://sourceforge.net/p/cdk/code/ci/45bd2c86eeba0beec5da095f6b8f40351aa198f5/work on docJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/45bd2c86eeba0beec5da095f6b8f40351aa198f5/https://sourceforge.net/p/cdk/code/ci/49c75931527a27a8c523e15d3eb4fa07cd0db1e9/mostly work on testsJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/49c75931527a27a8c523e15d3eb4fa07cd0db1e9/https://sourceforge.net/p/cdk/code/ci/b02711f61108259bc2f89b515b8bda9bfcb65ec1/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 generalJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/b02711f61108259bc2f89b515b8bda9bfcb65ec1/https://sourceforge.net/p/cdk/code/ci/0db0cbe9176bc0d7527ec61cf6e4f63d2f94a3db/adds a utility to calculate a suitable initial collection size for internal useJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/0db0cbe9176bc0d7527ec61cf6e4f63d2f94a3db/https://sourceforge.net/p/cdk/code/ci/f10fafba86bcb6fea792b44da8f5f9cba3457bfe/WIP, removed the properties for the return ACsJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/f10fafba86bcb6fea792b44da8f5f9cba3457bfe/https://sourceforge.net/p/cdk/code/ci/38be24ab72145a0f892b5ae1af898ffd4257996b/initial implementation of CircularFragmenterJonas SchaubTue, 24 Mar 2026 09:59:18 -0000https://sourceforge.net/p/cdk/code/ci/38be24ab72145a0f892b5ae1af898ffd4257996b/https://sourceforge.net/p/cdk/code/ci/d460802f116a11c52eb12310bf7464f3b9086be5/Update CDK version from 2.11 to 2.12 in READMEEgon WillighagenSat, 21 Mar 2026 07:49:39 -0000https://sourceforge.net/p/cdk/code/ci/d460802f116a11c52eb12310bf7464f3b9086be5/https://sourceforge.net/p/cdk/code/ci/6d69b0c96ad6b149667d8fe6832e797d7c081af6/Updated the GitHub ActionsEgon WillighagenSun, 15 Mar 2026 16:20:53 -0000https://sourceforge.net/p/cdk/code/ci/6d69b0c96ad6b149667d8fe6832e797d7c081af6/https://sourceforge.net/p/cdk/code/ci/4089c06f94f3967bfafab4fe30ecd009c6ae5f1d/Bumped the yearEgon WillighagenSat, 14 Mar 2026 15:44:55 -0000https://sourceforge.net/p/cdk/code/ci/4089c06f94f3967bfafab4fe30ecd009c6ae5f1d/https://sourceforge.net/p/cdk/code/ci/5cf1b88f538f23d8b4e35d2523b0cfc4b5b70e89/Reduce the occurrences of "extends CDKTestCase" many times this is not needed at all and allows us to remove "test-jar" dependency.Egon WillighagenSat, 14 Mar 2026 15:44:55 -0000https://sourceforge.net/p/cdk/code/ci/5cf1b88f538f23d8b4e35d2523b0cfc4b5b70e89/https://sourceforge.net/p/cdk/code/ci/00dabf099091f28de426c0b4f2a56271127a610f/Implement the option "EXPAND_HYDROGENS" we do this as a preprocessing step before the transform is run.Egon WillighagenSat, 14 Mar 2026 15:44:55 -0000https://sourceforge.net/p/cdk/code/ci/00dabf099091f28de426c0b4f2a56271127a610f/https://sourceforge.net/p/cdk/code/ci/f606b45ee011b7c43d904be49c6d3ce069e0ff58/Allow abbreviations with isotopes, for example CD3 for deuterated methyl.Egon WillighagenSat, 14 Mar 2026 15:44:55 -0000https://sourceforge.net/p/cdk/code/ci/f606b45ee011b7c43d904be49c6d3ce069e0ff58/https://sourceforge.net/p/cdk/code/ci/b87e30164a6f45a30a5a833f913a7e13b6be84ce/Remove commented codeEgon WillighagenFri, 06 Mar 2026 17:53:34 -0000https://sourceforge.net/p/cdk/code/ci/b87e30164a6f45a30a5a833f913a7e13b6be84ce/https://sourceforge.net/p/cdk/code/ci/e11894593011c723b6360be79fedff33d15ba93f/Ensure small ring size check work correctly.Egon WillighagenFri, 06 Mar 2026 17:53:34 -0000https://sourceforge.net/p/cdk/code/ci/e11894593011c723b6360be79fedff33d15ba93f/https://sourceforge.net/p/cdk/code/ci/2853e9de77def8c7d402a18e3953a9649d4a6efc/Skip writing empty LOG (logic) definitions for RGroups.John MayfieldFri, 06 Mar 2026 17:53:34 -0000https://sourceforge.net/p/cdk/code/ci/2853e9de77def8c7d402a18e3953a9649d4a6efc/https://sourceforge.net/p/cdk/code/ci/a5eaa242312b9daa603760abb5f282231b2df923/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 MayfieldFri, 06 Mar 2026 17:53:34 -0000https://sourceforge.net/p/cdk/code/ci/a5eaa242312b9daa603760abb5f282231b2df923/https://sourceforge.net/p/cdk/code/ci/b9e38f9e10ac8aa38cd8be6500739c894e8521bc/Make sure the hydrogen count is set to 0 when creating the attachment point.John MayfieldFri, 06 Mar 2026 17:53:34 -0000https://sourceforge.net/p/cdk/code/ci/b9e38f9e10ac8aa38cd8be6500739c894e8521bc/https://sourceforge.net/p/cdk/code/ci/23f535cb37234e057fed57b6569659ad422bb82e/Remove the checksum plugin - this is now done via a GH action.John MayfieldFri, 06 Mar 2026 17:53:34 -0000https://sourceforge.net/p/cdk/code/ci/23f535cb37234e057fed57b6569659ad422bb82e/https://sourceforge.net/p/cdk/code/ci/6106d65f840e0cfacb033b2109d360b683841f7b/CDK dev version 2.13-SNAPSHOTJohn MayfieldTue, 03 Mar 2026 18:20:11 -0000https://sourceforge.net/p/cdk/code/ci/6106d65f840e0cfacb033b2109d360b683841f7b/https://sourceforge.net/p/cdk/code/ci/90603f65cf7c19d094830e402a95ca02c4c30fb2/Missing <name> - needed for maven deploymentJohn MayfieldTue, 03 Mar 2026 18:20:11 -0000https://sourceforge.net/p/cdk/code/ci/90603f65cf7c19d094830e402a95ca02c4c30fb2/https://sourceforge.net/p/cdk/code/ci/ca4faabbc37a42fed16cfc2ee683636b519b91cd/CDK 2.12John MayfieldTue, 03 Mar 2026 18:20:11 -0000https://sourceforge.net/p/cdk/code/ci/ca4faabbc37a42fed16cfc2ee683636b519b91cd/https://sourceforge.net/p/cdk/code/ci/fce871ebac3c7c867c6e8366147ca010b527c1c3/Improve ionic bond depictions - fixes https://github.com/cdk/depict/issues/26 and https://github.com/cdk/depict/issues/99.Egon WillighagenTue, 03 Mar 2026 18:20:11 -0000https://sourceforge.net/p/cdk/code/ci/fce871ebac3c7c867c6e8366147ca010b527c1c3/https://sourceforge.net/p/cdk/code/ci/c21d5b211f4b911bdb382bddcd28da01649c6376/Add in headerEgon WillighagenTue, 03 Mar 2026 13:08:20 -0000https://sourceforge.net/p/cdk/code/ci/c21d5b211f4b911bdb382bddcd28da01649c6376/https://sourceforge.net/p/cdk/code/ci/b305d9d5426dee5a412a2e9889a837a0139ca47b/Fixes #953 - Tweak the expression handling logic of the QueryAtomContainer.Egon WillighagenTue, 03 Mar 2026 13:08:20 -0000https://sourceforge.net/p/cdk/code/ci/b305d9d5426dee5a412a2e9889a837a0139ca47b/https://sourceforge.net/p/cdk/code/ci/624b13386e544223d32d8d3af17cc10046a5d2db/Fix an issue with '>' appearing in the titles and messing up SMILES parsing.Egon WillighagenTue, 03 Mar 2026 13:08:20 -0000https://sourceforge.net/p/cdk/code/ci/624b13386e544223d32d8d3af17cc10046a5d2db/https://sourceforge.net/p/cdk/code/ci/295e7ec53c6b57b5846c88b34b8fc1d8477d4e7b/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 WillighagenTue, 03 Mar 2026 13:08:20 -0000https://sourceforge.net/p/cdk/code/ci/295e7ec53c6b57b5846c88b34b8fc1d8477d4e7b/https://sourceforge.net/p/cdk/code/ci/50d1fdd8f15cd367a590d135a255fdc5e47eb5b5/Fixes #1255 - Add in B3_Minus as a valid aromatic atom type.Egon WillighagenTue, 03 Mar 2026 13:08:20 -0000https://sourceforge.net/p/cdk/code/ci/50d1fdd8f15cd367a590d135a255fdc5e47eb5b5/https://sourceforge.net/p/cdk/code/ci/ed489a426050ba3a8b984fc51ce88513466b87f0/Fix test cases - we did want null here.Egon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/ed489a426050ba3a8b984fc51ce88513466b87f0/https://sourceforge.net/p/cdk/code/ci/1d729e7b960750631b632645ee1f158c02809290/Make sure formal charge is set to 0Egon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/1d729e7b960750631b632645ee1f158c02809290/https://sourceforge.net/p/cdk/code/ci/8ba589346413bdb60dcf15618bd77b72ffb2b0f5/Move permissions to the job levelEgon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/8ba589346413bdb60dcf15618bd77b72ffb2b0f5/https://sourceforge.net/p/cdk/code/ci/bae8db4e3da68a78f1fef72f7ae163caf8da9023/Clean up some type castsEgon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/bae8db4e3da68a78f1fef72f7ae163caf8da9023/https://sourceforge.net/p/cdk/code/ci/9cc17c16ee39a262758ea8198502fd75d22f2552/Use IElement instead of IAtom to access the static fieldEgon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/9cc17c16ee39a262758ea8198502fd75d22f2552/https://sourceforge.net/p/cdk/code/ci/d847135d6f9c081ccffce8d24b1e88a6c0006d98/Fix warnings about illegal type cast from SonarCloudEgon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/d847135d6f9c081ccffce8d24b1e88a6c0006d98/https://sourceforge.net/p/cdk/code/ci/6c44813a724d9ff5fe9aff4178ba7967caa74d7c/Merge pull request #1265 from cdk/isotopeFactory/noErrorButWarningGitHubTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/6c44813a724d9ff5fe9aff4178ba7967caa74d7c/https://sourceforge.net/p/cdk/code/ci/5bdbfc0a721ed8888ad01798854530fb25c358e4/Downgrade to warning: unnatural elements do not have major isotopesEgon WillighagenTue, 03 Mar 2026 11:18:13 -0000https://sourceforge.net/p/cdk/code/ci/5bdbfc0a721ed8888ad01798854530fb25c358e4/https://sourceforge.net/p/cdk/code/ci/dcd453efbda6288285d62fef9f43c915a5ac5b2f/Simplify the atom placer logic to alway place atoms sprouting at correct angles. Fixes #1108Egon WillighagenTue, 03 Mar 2026 10:18:28 -0000https://sourceforge.net/p/cdk/code/ci/dcd453efbda6288285d62fef9f43c915a5ac5b2f/https://sourceforge.net/p/cdk/code/ci/bd002554719b74ce4b49f61b1a41c56b0c8fe933/Some speed improvements to the InChI tautomer generator (Fixes #1256).Egon WillighagenTue, 03 Mar 2026 10:18:28 -0000https://sourceforge.net/p/cdk/code/ci/bd002554719b74ce4b49f61b1a41c56b0c8fe933/https://sourceforge.net/p/cdk/code/ci/2675e0953ff726d1e89100a043849ee8e2393c75/Fix corner case of wedge placement, focus is sometimes -1 here.Egon WillighagenTue, 03 Mar 2026 10:18:28 -0000https://sourceforge.net/p/cdk/code/ci/2675e0953ff726d1e89100a043849ee8e2393c75/https://sourceforge.net/p/cdk/code/ci/a547a4430def15c4a7551a0344d0e32b426a5b2c/Fixes #1038Egon WillighagenTue, 03 Mar 2026 10:18:28 -0000https://sourceforge.net/p/cdk/code/ci/a547a4430def15c4a7551a0344d0e32b426a5b2c/https://sourceforge.net/p/cdk/code/ci/b33626a19d211e566e2104cfc502181d065ed92c/Fixes #1195Egon WillighagenTue, 03 Mar 2026 10:18:28 -0000https://sourceforge.net/p/cdk/code/ci/b33626a19d211e566e2104cfc502181d065ed92c/https://sourceforge.net/p/cdk/code/ci/89d594a2ae971ead2e23ca661c3e242bbe8524f5/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 WillighagenTue, 03 Mar 2026 10:18:28 -0000https://sourceforge.net/p/cdk/code/ci/89d594a2ae971ead2e23ca661c3e242bbe8524f5/https://sourceforge.net/p/cdk/code/ci/76aad0eaee430ebfd9603ca2b9713d9876e81c5c/Correct test caseEgon WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/76aad0eaee430ebfd9603ca2b9713d9876e81c5c/https://sourceforge.net/p/cdk/code/ci/e0bf61877e34e6fd20cfeeccbf3f29dd08586eaf/Additional test cases and corner case fixesEgon WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/e0bf61877e34e6fd20cfeeccbf3f29dd08586eaf/https://sourceforge.net/p/cdk/code/ci/563fbb965b1ab3aa6f874a7d865d18c44f8070ce/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 WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/563fbb965b1ab3aa6f874a7d865d18c44f8070ce/https://sourceforge.net/p/cdk/code/ci/046a9c343f72bed14e3d9c9fff66bc7e92bb8117/Process ligand ordering in CXSMARTSEgon WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/046a9c343f72bed14e3d9c9fff66bc7e92bb8117/https://sourceforge.net/p/cdk/code/ci/9d7dde70c97faf4ceaa8c20bb93dae10b5179b55/Layout and depiction of RGroup/Markush definitions.Egon WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/9d7dde70c97faf4ceaa8c20bb93dae10b5179b55/https://sourceforge.net/p/cdk/code/ci/67ccce9d8045698924181c5eb5cbaee1e0b83403/Handling of RGroups to/from CXSMILES - this includes implying attachment points where needed and disambiguating nested definitions.Egon WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/67ccce9d8045698924181c5eb5cbaee1e0b83403/https://sourceforge.net/p/cdk/code/ci/3d604aa995a957d6166d4eddefa57d9b32f8df8e/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 WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/3d604aa995a957d6166d4eddefa57d9b32f8df8e/https://sourceforge.net/p/cdk/code/ci/958ca30f9f6fd6677adf641008f11c0aa82753ee/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.Egon WillighagenMon, 02 Mar 2026 15:26:09 -0000https://sourceforge.net/p/cdk/code/ci/958ca30f9f6fd6677adf641008f11c0aa82753ee/https://sourceforge.net/p/cdk/code/ci/e46a515d8cec9abeb1b956781402c54bc81c372d/Merge pull request #1259 from cdk/updates/twoMoreForJava8GitHubSun, 01 Mar 2026 09:14:30 -0000https://sourceforge.net/p/cdk/code/ci/e46a515d8cec9abeb1b956781402c54bc81c372d/https://sourceforge.net/p/cdk/code/ci/fac8b55d1b21db62e8eff9b5663973c9987c133d/Updated JavaCC to 3.2.0Egon WillighagenSun, 01 Mar 2026 09:14:30 -0000https://sourceforge.net/p/cdk/code/ci/fac8b55d1b21db62e8eff9b5663973c9987c133d/https://sourceforge.net/p/cdk/code/ci/8deb8d26cdd11cd51c3933861de23349078a158f/Updated JUnit to 5.14.3Egon WillighagenSun, 01 Mar 2026 09:14:30 -0000https://sourceforge.net/p/cdk/code/ci/8deb8d26cdd11cd51c3933861de23349078a158f/https://sourceforge.net/p/cdk/code/ci/320c780a817e084baebc70c2e2043beaa0295982/Update the connectivity checker to either respect/ignore (default) var/multi attach bonds and explicit component grouping.Egon WillighagenSat, 28 Feb 2026 13:48:31 -0000https://sourceforge.net/p/cdk/code/ci/320c780a817e084baebc70c2e2043beaa0295982/https://sourceforge.net/p/cdk/code/ci/1a2c35ac55e4cd59a7d999afa64a6db233bb312f/A previous change means data Sgroups were not being applied to reactions.Egon WillighagenFri, 27 Feb 2026 17:46:38 -0000https://sourceforge.net/p/cdk/code/ci/1a2c35ac55e4cd59a7d999afa64a6db233bb312f/https://sourceforge.net/p/cdk/code/ci/513a7836b4580fc9b8957f238c1928f8a65364c2/Minor tweaks/additions to some rendering APIs.Egon WillighagenFri, 27 Feb 2026 17:46:38 -0000https://sourceforge.net/p/cdk/code/ci/513a7836b4580fc9b8957f238c1928f8a65364c2/https://sourceforge.net/p/cdk/code/ci/cc4d5121d04d579dd3b6cc597a73e95917a9d99a/* 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 WillighagenFri, 27 Feb 2026 17:46:38 -0000https://sourceforge.net/p/cdk/code/ci/cc4d5121d04d579dd3b6cc597a73e95917a9d99a/https://sourceforge.net/p/cdk/code/ci/75175e4caeee36415eb1d87d60abbad15552d493/FixupEgon WillighagenFri, 27 Feb 2026 17:46:38 -0000https://sourceforge.net/p/cdk/code/ci/75175e4caeee36415eb1d87d60abbad15552d493/https://sourceforge.net/p/cdk/code/ci/a123f87f25d5a2c3538deb02296849a0a4633dff/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 WillighagenFri, 27 Feb 2026 17:46:38 -0000https://sourceforge.net/p/cdk/code/ci/a123f87f25d5a2c3538deb02296849a0a4633dff/https://sourceforge.net/p/cdk/code/ci/abad6b8cf1d497475def3b2d59cff477458fe70e/Updated versionEgon WillighagenTue, 27 Jan 2026 07:39:43 -0000https://sourceforge.net/p/cdk/code/ci/abad6b8cf1d497475def3b2d59cff477458fe70e/https://sourceforge.net/p/cdk/code/ci/ea71f8152a42445866ee052b7910011a169df142/Updated Maven Central version badgeGitHubTue, 13 Jan 2026 14:26:06 -0000https://sourceforge.net/p/cdk/code/ci/ea71f8152a42445866ee052b7910011a169df142/https://sourceforge.net/p/cdk/code/ci/edc65f285f9a3129812046b5e81ee35fc5917ce4/Spelling.Egon WillighagenTue, 13 Jan 2026 13:46:16 -0000https://sourceforge.net/p/cdk/code/ci/edc65f285f9a3129812046b5e81ee35fc5917ce4/https://sourceforge.net/p/cdk/code/ci/3e7550ce37d3b8489966a4cb4e6b86460ddefb6a/Simplify.Egon WillighagenTue, 13 Jan 2026 13:46:16 -0000https://sourceforge.net/p/cdk/code/ci/3e7550ce37d3b8489966a4cb4e6b86460ddefb6a/https://sourceforge.net/p/cdk/code/ci/db3ab785a151a02bd01442f7336bf511ccf4d287/Performance: use is empty.Egon WillighagenTue, 13 Jan 2026 13:46:16 -0000https://sourceforge.net/p/cdk/code/ci/db3ab785a151a02bd01442f7336bf511ccf4d287/https://sourceforge.net/p/cdk/code/ci/a9e889ef7bc644cfcba571bd029fac507dbc987a/Fix null pointer exceptions.Egon WillighagenTue, 13 Jan 2026 13:46:16 -0000https://sourceforge.net/p/cdk/code/ci/a9e889ef7bc644cfcba571bd029fac507dbc987a/https://sourceforge.net/p/cdk/code/ci/c7ee679cd91f464d6235a00c7ced5a32ecb3b56f/Merge pull request #1252 from cdk/update/cmlxom4.15GitHubTue, 13 Jan 2026 13:46:16 -0000https://sourceforge.net/p/cdk/code/ci/c7ee679cd91f464d6235a00c7ced5a32ecb3b56f/https://sourceforge.net/p/cdk/code/ci/43d206fa40965d2f0966fa360e7cd00122c75ea7/CMLXOM 4.15 and Log4j 2.25.3Egon WillighagenTue, 13 Jan 2026 13:46:16 -0000https://sourceforge.net/p/cdk/code/ci/43d206fa40965d2f0966fa360e7cd00122c75ea7/https://sourceforge.net/p/cdk/code/ci/260d72d555480c2a15ce313903c88d209b3552a4/Merge pull request #1250 from cdk/feature/depsManagementGitHubSat, 20 Dec 2025 10:38:51 -0000https://sourceforge.net/p/cdk/code/ci/260d72d555480c2a15ce313903c88d209b3552a4/https://sourceforge.net/p/cdk/code/ci/91a94784307d052cb060e46f6b04fd08e5610725/Use <pluginManagement>Egon WillighagenSat, 20 Dec 2025 10:38:51 -0000https://sourceforge.net/p/cdk/code/ci/91a94784307d052cb060e46f6b04fd08e5610725/https://sourceforge.net/p/cdk/code/ci/dbfacc2f9fd5ce79f171cfcbd8ba323a6b74606a/Add a method to the SDG which allows wedges to be assigned to a structure.Egon WillighagenSun, 30 Nov 2025 14:40:29 -0000https://sourceforge.net/p/cdk/code/ci/dbfacc2f9fd5ce79f171cfcbd8ba323a6b74606a/https://sourceforge.net/p/cdk/code/ci/602c9110e4680b45dc062e72e432d99a6173acf3/Add support for loading selection/highlight from CXSMILES and MDL Molfiles.Egon WillighagenSun, 30 Nov 2025 14:40:29 -0000https://sourceforge.net/p/cdk/code/ci/602c9110e4680b45dc062e72e432d99a6173acf3/https://sourceforge.net/p/cdk/code/ci/9c3f48f4b36cd7cde507428ea80d07362c759c25/Some tweaks to abbreviations - based on feedback from https://github.com/cdk/depict/issues/97Egon WillighagenTue, 11 Nov 2025 05:33:41 -0000https://sourceforge.net/p/cdk/code/ci/9c3f48f4b36cd7cde507428ea80d07362c759c25/https://sourceforge.net/p/cdk/code/ci/ae0d100382d6494b09f5c332142f8cf3d4ac2dcd/Merge pull request #1242 from cdk/deps/updates/202511GitHubTue, 11 Nov 2025 05:33:41 -0000https://sourceforge.net/p/cdk/code/ci/ae0d100382d6494b09f5c332142f8cf3d4ac2dcd/https://sourceforge.net/p/cdk/code/ci/a752b3525ae821771a9e84e24e5b7feba64c8cd0/Central (and updated) CMLXOM versionEgon WillighagenTue, 11 Nov 2025 05:33:41 -0000https://sourceforge.net/p/cdk/code/ci/a752b3525ae821771a9e84e24e5b7feba64c8cd0/