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[Cdk-commits] [cdk/cdk] 44c9c8: Set foreground for reaction plus and arrow.
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From: GitHub <no...@gi...> - 2015-11-07 18:24:47
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Branch: refs/heads/patch/layout07Nov15 Home: https://github.com/cdk/cdk Commit: 44c9c8d80bc8b39c11db8c737fb75e190b1f2541 https://github.com/cdk/cdk/commit/44c9c8d80bc8b39c11db8c737fb75e190b1f2541 Author: John May <jo...@ne...> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java Log Message: ----------- Set foreground for reaction plus and arrow. Commit: b3919d8b45a2c62241f54da6be5b5ca9919e5e77 https://github.com/cdk/cdk/commit/b3919d8b45a2c62241f54da6be5b5ca9919e5e77 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/ReactionDepiction.java M tool/sdg/src/main/java/org/openscience/cdk/layout/LayoutRefiner.java Log Message: ----------- Parameter tweaks to layout refinement: - Require non-bonded atoms are further apart. - Accept a rotate if the congestion improvement is minimal but the overlap is resolved - Correct congestion update for distributed stretching Commit: 2780ed365cc405ff5fd0dda06b42ddcc34159c39 https://github.com/cdk/cdk/commit/2780ed365cc405ff5fd0dda06b42ddcc34159c39 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Remove old methods that no longer needed. Commit: e3fa8c60639655f029e1c6007935459b65f366a0 https://github.com/cdk/cdk/commit/e3fa8c60639655f029e1c6007935459b65f366a0 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Orientate final layout based on max width and bonds aligned to +/- 30 degrees. Commit: 1c0b0660fcbf04b555eee9c407ceff6662220f73 https://github.com/cdk/cdk/commit/1c0b0660fcbf04b555eee9c407ceff6662220f73 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M app/depict/src/main/java/org/openscience/cdk/depict/SvgDrawVisitor.java Log Message: ----------- Allow transparent colors for SVG output, mostly useful for background. Commit: 43a9c437c21ac8a83ef31c88bed03fa4dd4d1e36 https://github.com/cdk/cdk/commit/43a9c437c21ac8a83ef31c88bed03fa4dd4d1e36 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Store template coordinates as extended SMILES, easier to debug. Old format still read in. Commit: 6ff8d0a94f21926ebc157f61bb26910edb58e488 https://github.com/cdk/cdk/commit/6ff8d0a94f21926ebc157f61bb26910edb58e488 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java M tool/sdg/src/main/resources/org/openscience/cdk/layout/chebi-ring-templates.smi M tool/sdg/src/test/java/org/openscience/cdk/layout/IdentityTemplateLibraryTest.java Log Message: ----------- Current template library has 'ugly' SMILES because we simply cleared all hydrogen counts. We now set the default valence temporarily to produce nicer SMILES. This method is probably quite useful when we are chopping up molecules and may be moved to the SMILES generator in future. Commit: 2c4736822f14c22c4353e7da87cd836f0a521335 https://github.com/cdk/cdk/commit/2c4736822f14c22c4353e7da87cd836f0a521335 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- When two ring systems have the same number of rings (e.g. 1) prioritise those with more bonds. Commit: 564f92f6d790f8b06a4f9ce76283f3b0a54dec00 https://github.com/cdk/cdk/commit/564f92f6d790f8b06a4f9ce76283f3b0a54dec00 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSetManipulator.java M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Layout larger more complex rings first. Commit: 1ab86556b30ccb97b67cb5840a5946398dfffc68 https://github.com/cdk/cdk/commit/1ab86556b30ccb97b67cb5840a5946398dfffc68 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java A tool/sdg/src/main/resources/org/openscience/cdk/layout/macro.smi Log Message: ----------- Improved handling of macrocycles using enumerated templates based on hexagonal grids. Commit: 8995b63be73abb97cfe238251057700c1c96cc02 https://github.com/cdk/cdk/commit/8995b63be73abb97cfe238251057700c1c96cc02 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java M tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java Log Message: ----------- Remove use of substructure templates (to be replaced), they produced displeased results if the entire ring system wasn't mapped (https://github.com/cdk/cdk/pull/165) and since in that case we can use canonicalisation (Identity Templates) they are redundant. Commit: 007f95dd49b8f2164bcf3ca5f8efa2bba1b48671 https://github.com/cdk/cdk/commit/007f95dd49b8f2164bcf3ca5f8efa2bba1b48671 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Reformat code. Commit: 53c4e6a76327ace05f160f73713cf2191f4a9025 https://github.com/cdk/cdk/commit/53c4e6a76327ace05f160f73713cf2191f4a9025 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Realised the identity templates can be utilised for all ring systems, originally I skipped this for secondary ring systems used relative coordinates rather than absolute. On further inspection the SDG already rotates and shifts rings when attaching them so identity templates can be used here too. Commit: 0627c8e453d7244e429fc7758f71b84939269ae1 https://github.com/cdk/cdk/commit/0627c8e453d7244e429fc7758f71b84939269ae1 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Cleanup ring system layout method. Debug logging better as trace but we don't have that option. Commit: 68a1824b4e36597b0507d7f63ea6e8f29994fb58 https://github.com/cdk/cdk/commit/68a1824b4e36597b0507d7f63ea6e8f29994fb58 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java Log Message: ----------- Use local variables. Commit: ba2cdaaab4df57a8e100ba9fedf5606134a58d7a https://github.com/cdk/cdk/commit/ba2cdaaab4df57a8e100ba9fedf5606134a58d7a Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java Log Message: ----------- Improved ring vector for fused rings, we now use one perpendicular to the bond rather that the ring centre which in a crinkled macro cycle isn't ideal. Commit: 5e218bbc21d14db5282ed5da5769327c32fd753d https://github.com/cdk/cdk/commit/5e218bbc21d14db5282ed5da5769327c32fd753d Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Avoid anonymised general templates for macro cycles as we can probably do better. Commit: 9b09233c9cd94d2619c4728e2d1a9156348aa6e2 https://github.com/cdk/cdk/commit/9b09233c9cd94d2619c4728e2d1a9156348aa6e2 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java Log Message: ----------- Allow templates to have multiple alternatives (needed for selecting best macro cycles). Commit: b593612c2ee433298a39fe96d63725774d4db0b9 https://github.com/cdk/cdk/commit/b593612c2ee433298a39fe96d63725774d4db0b9 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java Log Message: ----------- Ring centre may be co-linear (e.g. when we have half a para substituted ring) so use the shared atom centre to work out direction. Commit: 78cde0cdfd291c9ae13b4d60a5aaa61fac74e0a7 https://github.com/cdk/cdk/commit/78cde0cdfd291c9ae13b4d60a5aaa61fac74e0a7 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java Log Message: ----------- Bridged ring snapping. Commit: 42f593699127f68446a2342f1b8fdfbd9edf9b05 https://github.com/cdk/cdk/commit/42f593699127f68446a2342f1b8fdfbd9edf9b05 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Use a snap hint for laying out macro cycles. Commit: 20cb6195ce3335f8e4a718b76c18d1f52b6c0770 https://github.com/cdk/cdk/commit/20cb6195ce3335f8e4a718b76c18d1f52b6c0770 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Don't select orientation when we have a single non-trivial ring systems, these are normally depicted in a de facto orientation (e.g. steroid). Commit: 4a73ee4a5eb20c7c6f15635316e01e86ca261a4d https://github.com/cdk/cdk/commit/4a73ee4a5eb20c7c6f15635316e01e86ca261a4d Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java Log Message: ----------- Better handling of extreme angles. Commit: 0b2ac86976863b8a07ae3bfd7cf5fcab733b5d15 https://github.com/cdk/cdk/commit/0b2ac86976863b8a07ae3bfd7cf5fcab733b5d15 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Mark cycle with other ring ops and also flag macrocycle we hit as primary. Commit: ad919ea2ebc8f2d2c3520a857a90ee404378fe19 https://github.com/cdk/cdk/commit/ad919ea2ebc8f2d2c3520a857a90ee404378fe19 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java Log Message: ----------- Adjust double-bond stereochemistry in rings, bad resolution but correct. Commit: f147358bcb85a02411aa6dd8ae97eb02d163843b https://github.com/cdk/cdk/commit/f147358bcb85a02411aa6dd8ae97eb02d163843b Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: A tool/sdg/src/main/java/org/openscience/cdk/layout/MacroCycleLayout.java M tool/sdg/src/main/resources/org/openscience/cdk/layout/macro.smi Log Message: ----------- Class for helping layout macrocycles. Commit: b0e7fcfc2c1809ff6e37f7a68ac61057f8b16074 https://github.com/cdk/cdk/commit/b0e7fcfc2c1809ff6e37f7a68ac61057f8b16074 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java Log Message: ----------- Allow terminal substituents to point into the centre of the ring. Commit: 5cc203d516696b9608ea8f37b145c98c40587d04 https://github.com/cdk/cdk/commit/5cc203d516696b9608ea8f37b145c98c40587d04 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/LayoutRefiner.java Log Message: ----------- Layout refinement of terminal macrocycle substituents. Commit: 5bec807eb4d02b8e4e3c03d33a978e218a546097 https://github.com/cdk/cdk/commit/5bec807eb4d02b8e4e3c03d33a978e218a546097 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/IdentityTemplateLibrary.java M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java A tool/sdg/src/main/resources/org/openscience/cdk/layout/custom-templates.smi Log Message: ----------- Manually specified templates in addition to those generated by ChEBI. Commit: 52129af9e333a950430f7eaedd0d9626612cbdd3 https://github.com/cdk/cdk/commit/52129af9e333a950430f7eaedd0d9626612cbdd3 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java M tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java M tool/sdg/src/test/java/org/openscience/cdk/layout/TemplateHandlerTest.java Log Message: ----------- Conversion of old templates to identity templates. Commit: 7315457d4ccf12ab671c11045031538860781533 https://github.com/cdk/cdk/commit/7315457d4ccf12ab671c11045031538860781533 Author: John May <jo...@ne...> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java Log Message: ----------- Fused ring peeling to increase template utility. Compare: https://github.com/cdk/cdk/compare/44c9c8d80bc8^...7315457d4ccf |