From: GitHub <no...@gi...> - 2012-07-01 08:43:27
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Branch: refs/heads/master Home: https://github.com/cdk/cdk Commit: 2116ef4fe3dd03a807ffabdffc49d45518a08f3c https://github.com/cdk/cdk/commit/2116ef4fe3dd03a807ffabdffc49d45518a08f3c Author: John May <joh...@gm...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M src/main/org/openscience/cdk/libio/cml/Convertor.java Log Message: ----------- Improved conversion of AtomContainer to CMLMolecule Tools in the CML library tend to use the XMLContent value (see. [1]) Also ChemAxon MarvinSketch will not import with the bondStereo invalid (probably a bug) but adding the XML value fixes this. [1] http://www.jarvana.com/jarvana/view/org/xml-cml/jumbo/6.0/jumbo-6.0-sour ces.jar!/org/xmlcml/cml/tools/StereochemistryTool.java?format=ok Change-Id: I141a43ca9e028b1da7cbf79cd13bf72934638012 Signed-off-by: Egon Willighagen <eg...@us...> Commit: 70a354aed01b9774a63adde2a7d2dc447d8f6954 https://github.com/cdk/cdk/commit/70a354aed01b9774a63adde2a7d2dc447d8f6954 Author: John May <joh...@gm...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M src/test/org/openscience/cdk/libio/cml/ConvertorTest.java M src/test/org/openscience/cdk/modulesuites/MlibiocmlTests.java Log Message: ----------- CML Bond Conversion Test [patch:3530233] - Added tests for correct wedge/hatch bond conversion - Added ConvertorTest to libiocml test suite Change-Id: Ia77be2d00267159ebb24ca3e43d3340914258e15 Signed-off-by: Egon Willighagen <eg...@us...> Commit: 3f4c145aacbe8826739c589fd2560d3d50ea625d https://github.com/cdk/cdk/commit/3f4c145aacbe8826739c589fd2560d3d50ea625d Author: Tomas Pluskal <pl...@gm...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java M src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java Log Message: ----------- Change the getHTML method to return the elements in the Hill System order (bug #3432131). Change-Id: I0ca3c26a87f9af88de29e2c1a6b339a16b23ddf4 Signed-off-by: Egon Willighagen <eg...@us...> Commit: b6eb250902dfd8a9d0c0861cea2589ddc6abc22e https://github.com/cdk/cdk/commit/b6eb250902dfd8a9d0c0861cea2589ddc6abc22e Author: Rajarshi Guha <raj...@gm...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java Log Message: ----------- Updated a method based on Ninas suggestion to avoid modifiying a atom container when looping over it. This avoids a concurrent modification exception. Also updated some Javadocs Change-Id: If01762c6cff615d7a25de8b8f9bcee49c41eba16 Signed-off-by: Egon Willighagen <eg...@us...> Commit: 52a7f1dd87a3c38a7e5c25353b161c2047e36416 https://github.com/cdk/cdk/commit/52a7f1dd87a3c38a7e5c25353b161c2047e36416 Author: Rajarshi Guha <raj...@gm...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java M src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java Log Message: ----------- Added Ninas modifcations to ensure that getting a molecular formula includes implicit hydrogens. Addressed bug 2983334. Also updated a unit test to take into account that H's are being considered Change-Id: I9881e31c05d0f1bfb965393bd806e562a6158a0e Signed-off-by: Egon Willighagen <eg...@us...> Conflicts: src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java Commit: d0f38b034d5a1a6419a5319528e51c7280fcffe0 https://github.com/cdk/cdk/commit/d0f38b034d5a1a6419a5319528e51c7280fcffe0 Author: Egon Willighagen <eg...@us...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M README Log Message: ----------- Updated the README (fixes #3538451) - updated outdated links and added the CDK G+ page - updated the copyright line - added an example on how to compile an individual module Change-Id: I8b7232ffb5e2ee0e8804aa1f5bfb1c75aa238358 Commit: 3179394ce2a515c20d74ef2e453a79f06cb08abc https://github.com/cdk/cdk/commit/3179394ce2a515c20d74ef2e453a79f06cb08abc Author: Egon Willighagen <eg...@us...> Date: 2012-07-01 (Sun, 01 Jul 2012) Changed paths: M src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java Log Message: ----------- Update for a patch from cdk-1.4.x: s/NoNotification/Silent/ Change-Id: I0f9758b2abaed48647a314b3775c780ebebbdcce Compare: https://github.com/cdk/cdk/compare/6626a2d2120d...3179394ce2a5 |