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[Cdk-commits] [cdk/cdk] 751488: Set up a CIP module.
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From: <no...@gi...> - 2010-12-04 17:17:09
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Branch: refs/heads/cdk-1.4.x Home: https://github.com/cdk/cdk Commit: 751488bdcd334959e51953c279845507d2854011 https://github.com/cdk/cdk/commit/751488bdcd334959e51953c279845507d2854011 Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M build.xml M doc/refs/cheminf.bibx M javadoc.xml M pmd-migrating.xml M pmd-unused.xml M pmd.xml A src/META-INF/cip.cdkdepends A src/META-INF/cip.libdepends A src/META-INF/test-cip.cdkdepends A src/META-INF/test-cip.devellibdepends A src/META-INF/test-cip.libdepends A src/main/org/openscience/cdk/geometry/cip/CIPTool.java A src/main/org/openscience/cdk/geometry/cip/ILigand.java A src/main/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java A src/main/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigand.java A src/main/org/openscience/cdk/geometry/cip/LigancyFourChirality.java A src/main/org/openscience/cdk/geometry/cip/Ligand.java A src/main/org/openscience/cdk/geometry/cip/TerminalLigand.java A src/main/org/openscience/cdk/geometry/cip/rules/AtomicNumberRule.java A src/main/org/openscience/cdk/geometry/cip/rules/CIPLigandRule.java A src/main/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRule.java A src/main/org/openscience/cdk/geometry/cip/rules/ISequenceSubRule.java A src/main/org/openscience/cdk/geometry/cip/rules/MassNumberRule.java M src/main/org/openscience/cdk/stereo/TetrahedralChirality.java A src/test/org/openscience/cdk/coverage/CipCoverageTest.java A src/test/org/openscience/cdk/geometry/cip/CIPSMILESTest.java A src/test/org/openscience/cdk/geometry/cip/CIPToolTest.java A src/test/org/openscience/cdk/geometry/cip/ImmutableHydrogenTest.java A src/test/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigandTest.java A src/test/org/openscience/cdk/geometry/cip/LigancyFourChiralityTest.java A src/test/org/openscience/cdk/geometry/cip/LigandTest.java A src/test/org/openscience/cdk/geometry/cip/TerminalLigandTest.java A src/test/org/openscience/cdk/geometry/cip/rules/AtomicNumberRuleTest.java A src/test/org/openscience/cdk/geometry/cip/rules/CIPLigandRuleTest.java A src/test/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRuleTest.java A src/test/org/openscience/cdk/geometry/cip/rules/MassNumberRuleTest.java A src/test/org/openscience/cdk/modulesuites/McipTests.java Log Message: ----------- Set up a CIP module. * implements a *subset* of the CIP rules, those which we can reasonably do with the current CDK data model. Therefore, no axial stereochemistry, etc, but the rule that differentiate ligands based on chirality of atoms in the ligands is not implemented either. * CIPTool to calculate R,S based on the implemented rules. Commit: 8eedef0fae7ef4811bef31bf2c0d248f9d43063b https://github.com/cdk/cdk/commit/8eedef0fae7ef4811bef31bf2c0d248f9d43063b Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/test/org/openscience/cdk/geometry/cip/CIPSMILESTest.java Log Message: ----------- Test case provided by Gilleain around termination, using the SMILES as input Commit: 25936d5fe7a431ddc77508715bbcb8aae11e96b0 https://github.com/cdk/cdk/commit/25936d5fe7a431ddc77508715bbcb8aae11e96b0 Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/rules/CIPLigandRule.java M src/test/org/openscience/cdk/geometry/cip/CIPToolTest.java Log Message: ----------- Test case for another termination problem: the previous 'fix' broke the proper ordering of ligands when there is more than one, IAOI one ligand count was only 1 (thanx to Gilleain for spotting this) Commit: 118e52d1688a4f70119b9c832cf910debe25b648 https://github.com/cdk/cdk/commit/118e52d1688a4f70119b9c832cf910debe25b648 Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/test/org/openscience/cdk/geometry/cip/CIPToolTest.java Log Message: ----------- Added unit test to make sure no chirality is detected for the FC(Me)(Me)R carbon Commit: df28f00c4f531b2f45be05bc4d436cbd9d7f677f https://github.com/cdk/cdk/commit/df28f00c4f531b2f45be05bc4d436cbd9d7f677f Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/META-INF/test-cip.cdkdepends A src/test/data/cml/mol28.cml M src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherFilesTest.java M src/test/org/openscience/cdk/geometry/cip/CIPToolTest.java Log Message: ----------- Added unit tests to uncover a non-termination issue in the CIP algorithm reported by Ola Commit: 8a81aa2ad0fbdc89141a674bdcb91df827f55d82 https://github.com/cdk/cdk/commit/8a81aa2ad0fbdc89141a674bdcb91df827f55d82 Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/CIPTool.java M src/main/org/openscience/cdk/geometry/cip/ILigand.java M src/main/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigand.java M src/main/org/openscience/cdk/geometry/cip/LigancyFourChirality.java M src/main/org/openscience/cdk/geometry/cip/Ligand.java M src/main/org/openscience/cdk/geometry/cip/TerminalLigand.java A src/main/org/openscience/cdk/geometry/cip/VisitedAtoms.java M src/test/org/openscience/cdk/geometry/cip/CIPToolTest.java M src/test/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigandTest.java M src/test/org/openscience/cdk/geometry/cip/LigancyFourChiralityTest.java M src/test/org/openscience/cdk/geometry/cip/LigandTest.java M src/test/org/openscience/cdk/geometry/cip/TerminalLigandTest.java M src/test/org/openscience/cdk/geometry/cip/rules/AtomicNumberRuleTest.java M src/test/org/openscience/cdk/geometry/cip/rules/CIPLigandRuleTest.java M src/test/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRuleTest.java M src/test/org/openscience/cdk/geometry/cip/rules/MassNumberRuleTest.java Log Message: ----------- Keep track of which atoms have already been visited, to properly terminate when we give up Commit: 274cddc381fea9940c1d62f592df8af79a4b7388 https://github.com/cdk/cdk/commit/274cddc381fea9940c1d62f592df8af79a4b7388 Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/rules/CIPLigandRule.java M src/test/org/openscience/cdk/geometry/cip/CIPSMILESTest.java Log Message: ----------- Only consider recursion if all ligand atoms are identical and equal in number (fixes R detection in PubChem CID 42475007) Commit: 408d458b1edccd23ebb806522484e5c65193bafb https://github.com/cdk/cdk/commit/408d458b1edccd23ebb806522484e5c65193bafb Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/test/org/openscience/cdk/geometry/cip/CIPSMILESTest.java M src/test/org/openscience/cdk/geometry/cip/rules/CIPLigandRuleTest.java Log Message: ----------- Added testing of bromochlorofluoroiodomethane Commit: e80d620121f81fc5c5bbce6799835a2d4051a9f6 https://github.com/cdk/cdk/commit/e80d620121f81fc5c5bbce6799835a2d4051a9f6 Author: Egon Willighagen <eg...@us...> Date: 2010-12-03 (Fri, 03 Dec 2010) Changed paths: M src/test/org/openscience/cdk/signature/MoleculeSignatureTest.java Log Message: ----------- Added unit test for aromatic molecular signatures Commit: 291a39fa53b1dbcde4fa0ffb73af1afcdf8d0527 https://github.com/cdk/cdk/commit/291a39fa53b1dbcde4fa0ffb73af1afcdf8d0527 Author: Egon Willighagen <eg...@us...> Date: 2010-12-04 (Sat, 04 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/CIPTool.java Log Message: ----------- Added comment in JavaDoc about the sorted nature of the method input Commit: bf4fa91a02d1bd328d746dbda5b0b943eb61d25b https://github.com/cdk/cdk/commit/bf4fa91a02d1bd328d746dbda5b0b943eb61d25b Author: Egon Willighagen <eg...@us...> Date: 2010-12-04 (Sat, 04 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java M src/main/org/openscience/cdk/geometry/cip/LigancyFourChirality.java M src/main/org/openscience/cdk/geometry/cip/TerminalLigand.java M src/main/org/openscience/cdk/geometry/cip/rules/AtomicNumberRule.java M src/main/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRule.java M src/main/org/openscience/cdk/geometry/cip/rules/MassNumberRule.java Log Message: ----------- Made a few classes private to the package Commit: f1349ef09f8df93b49cac80a63c32fdece02f9bf https://github.com/cdk/cdk/commit/f1349ef09f8df93b49cac80a63c32fdece02f9bf Author: Egon Willighagen <eg...@us...> Date: 2010-12-04 (Sat, 04 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/CIPTool.java Log Message: ----------- Added a simple code example for how to use the CIPTool Commit: 60552657c45ea5d51359f32fb1f3769a04e7518c https://github.com/cdk/cdk/commit/60552657c45ea5d51359f32fb1f3769a04e7518c Author: Egon Willighagen <eg...@us...> Date: 2010-12-04 (Sat, 04 Dec 2010) Changed paths: M src/main/org/openscience/cdk/geometry/cip/VisitedAtoms.java A src/test/org/openscience/cdk/geometry/cip/VisitedAtomsTest.java M src/test/org/openscience/cdk/modulesuites/McipTests.java Log Message: ----------- Added missing JavaDoc and unit tests for VisitedAtoms Commit: 76e79919e32fa5fc42b439dff8a59069c213cd3a https://github.com/cdk/cdk/commit/76e79919e32fa5fc42b439dff8a59069c213cd3a Author: Egon Willighagen <eg...@us...> Date: 2010-12-04 (Sat, 04 Dec 2010) Changed paths: M src/test/org/openscience/cdk/geometry/cip/VisitedAtomsTest.java Log Message: ----------- Added missing copyright/license and cdk.module statements |