bump the version of opsin we are using to 2.5.0 #86
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manuelschwarze
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Feb 23, 2021
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I reviewed and tested on Window 10 for KNIME 4.3, and it is working fine.
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commit 575ca0b Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Feb 25 16:03:43 2021 +0100 simplify reaction copy in ChemicalTransformation node (#87) commit fa68610 Author: Greg Landrum <greg.landrum@gmail.com> Date: Tue Feb 23 13:50:42 2021 +0100 bump the version of opsin we are using to 2.5.0 (#86) commit 14696f5 Author: greg landrum <greg.landrum@gmail.com> Date: Mon Feb 22 05:52:06 2021 +0100 forgot one marvin dependency commit 3a14e54 Author: Greg Landrum <greg.landrum@gmail.com> Date: Fri Feb 12 05:54:21 2021 +0100 Add RDKit renderers for SMILES/SMARTS/MOL/SDF (#85) * version bump * initial pass at adding an RDKit renderer for mol, SDF, SMILES, and SMARTS commit f1a8105 Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Dec 17 15:20:14 2020 +0100 Remove dependency on ChemAxon nodes (#84) * remove MarvinSketch dependency in the tests * add TP defn for 4.3 commit aa80970 Author: Greg Landrum <greg.landrum@gmail.com> Date: Wed Dec 9 16:44:59 2020 +0100 remove freetype dependency from the mac binary commit 6972801 Author: Greg Landrum <greg.landrum@gmail.com> Date: Mon Nov 23 20:23:38 2020 +0100 A couple optimizations of the diversity picker (#82) * some optimization of the diversity picker * Performance tuning for fingerprint calculation or conversion Implemented multi-threading for time-consuming code * Central bugfix to unleash performance power of RDKit nodes in general The cleanup tracker for RDKit objects got a performance boost by using now a set instead of a list to track RDKit objects marked for future cleanup - this saves us from checking if an object was already contained in the list, and apparently the set implementation is much better and faster, internally using hashes (for RDKit objects probably direct pointers) to compare objects. This resulted in the diversity picker in a performance boost of more than 75%! Co-authored-by: Manuel Schwarze <manuel.schwarze@novartis.com> commit 3afe684 Author: Greg Landrum <greg.landrum@gmail.com> Date: Fri Nov 20 04:40:56 2020 +0100 Two enhancements to existing nodes (#81) * Fixes #64 * add support to the molecule substruct filter too * update substruct counter * update tests * finish updating tests * Support additional options in Adjust Query Properties node * Bugfixes, documentation and test updates Added cleanup for RDKit objects to free memory. Added backward-compatibility for new parameters with call of registerSettings(xxx, true) to avoid ugly error when loading workflows with older node versions. Completed JavaDocs for new functionality and fixed some old one. Minor performance improvements. Cleanup some formatting. Simplified some test workflows, saved them with KNIME 4.2.3. Corrected TestFlowConfiguration nodes with old configurations. Co-authored-by: Manuel Schwarze <manuel.schwarze@novartis.com> commit 7794be3 Merge: 2cbe17a 59954f8 Author: greg landrum <greg.landrum@gmail.com> Date: Fri Oct 30 04:58:43 2020 +0100 Merge branch 'master' of github.com:rdkit/knime-rdkit commit 2cbe17a Author: greg landrum <greg.landrum@gmail.com> Date: Fri Oct 30 04:56:37 2020 +0100 bump version to 4.1.0 commit 59954f8 Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Oct 29 11:32:30 2020 +0100 bump min version of KNIME plugins commit 8f06745 Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Oct 29 08:59:54 2020 +0100 update rdkit binaries for the new release (#80) * Remove buckminsterhelpfile generation & adapt to batik changes in KNIME AP 4.2 (#79) * Remove knime helpfile generation buckminster instruction The helpfile generation is no longer supported by upcomming KNIME AP version (4.2) so this instruction needs to be removed so that the plugin can be build for this version. * Adapt to batik updates in KNIME AP 4.2 * backup, untested * update one test to get things working on windows * forgot to update a node configuration * update linux binary * some cleanup around the way conformers are handled Co-authored-by: Gabriel Einsdorf <gabriel.einsdorf@uni-konstanz.de> commit a13bec5 Author: greg landrum <greg.landrum@gmail.com> Date: Wed Jul 8 17:11:06 2020 +0200 Revert "Remove buckminsterhelpfile generation & adapt to batik changes in KNIME AP 4.2 (#79)" This reverts commit dcaa4b0.
greglandrum
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Mar 3, 2021
commit 575ca0b Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Feb 25 16:03:43 2021 +0100 simplify reaction copy in ChemicalTransformation node (#87) commit fa68610 Author: Greg Landrum <greg.landrum@gmail.com> Date: Tue Feb 23 13:50:42 2021 +0100 bump the version of opsin we are using to 2.5.0 (#86) commit 14696f5 Author: greg landrum <greg.landrum@gmail.com> Date: Mon Feb 22 05:52:06 2021 +0100 forgot one marvin dependency commit 3a14e54 Author: Greg Landrum <greg.landrum@gmail.com> Date: Fri Feb 12 05:54:21 2021 +0100 Add RDKit renderers for SMILES/SMARTS/MOL/SDF (#85) * version bump * initial pass at adding an RDKit renderer for mol, SDF, SMILES, and SMARTS commit f1a8105 Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Dec 17 15:20:14 2020 +0100 Remove dependency on ChemAxon nodes (#84) * remove MarvinSketch dependency in the tests * add TP defn for 4.3 commit aa80970 Author: Greg Landrum <greg.landrum@gmail.com> Date: Wed Dec 9 16:44:59 2020 +0100 remove freetype dependency from the mac binary commit 6972801 Author: Greg Landrum <greg.landrum@gmail.com> Date: Mon Nov 23 20:23:38 2020 +0100 A couple optimizations of the diversity picker (#82) * some optimization of the diversity picker * Performance tuning for fingerprint calculation or conversion Implemented multi-threading for time-consuming code * Central bugfix to unleash performance power of RDKit nodes in general The cleanup tracker for RDKit objects got a performance boost by using now a set instead of a list to track RDKit objects marked for future cleanup - this saves us from checking if an object was already contained in the list, and apparently the set implementation is much better and faster, internally using hashes (for RDKit objects probably direct pointers) to compare objects. This resulted in the diversity picker in a performance boost of more than 75%! Co-authored-by: Manuel Schwarze <manuel.schwarze@novartis.com> commit 3afe684 Author: Greg Landrum <greg.landrum@gmail.com> Date: Fri Nov 20 04:40:56 2020 +0100 Two enhancements to existing nodes (#81) * Fixes #64 * add support to the molecule substruct filter too * update substruct counter * update tests * finish updating tests * Support additional options in Adjust Query Properties node * Bugfixes, documentation and test updates Added cleanup for RDKit objects to free memory. Added backward-compatibility for new parameters with call of registerSettings(xxx, true) to avoid ugly error when loading workflows with older node versions. Completed JavaDocs for new functionality and fixed some old one. Minor performance improvements. Cleanup some formatting. Simplified some test workflows, saved them with KNIME 4.2.3. Corrected TestFlowConfiguration nodes with old configurations. Co-authored-by: Manuel Schwarze <manuel.schwarze@novartis.com> commit 7794be3 Merge: 2cbe17a 59954f8 Author: greg landrum <greg.landrum@gmail.com> Date: Fri Oct 30 04:58:43 2020 +0100 Merge branch 'master' of github.com:rdkit/knime-rdkit commit 2cbe17a Author: greg landrum <greg.landrum@gmail.com> Date: Fri Oct 30 04:56:37 2020 +0100 bump version to 4.1.0 commit 59954f8 Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Oct 29 11:32:30 2020 +0100 bump min version of KNIME plugins commit 8f06745 Author: Greg Landrum <greg.landrum@gmail.com> Date: Thu Oct 29 08:59:54 2020 +0100 update rdkit binaries for the new release (#80) * Remove buckminsterhelpfile generation & adapt to batik changes in KNIME AP 4.2 (#79) * Remove knime helpfile generation buckminster instruction The helpfile generation is no longer supported by upcomming KNIME AP version (4.2) so this instruction needs to be removed so that the plugin can be build for this version. * Adapt to batik updates in KNIME AP 4.2 * backup, untested * update one test to get things working on windows * forgot to update a node configuration * update linux binary * some cleanup around the way conformers are handled Co-authored-by: Gabriel Einsdorf <gabriel.einsdorf@uni-konstanz.de> commit a13bec5 Author: greg landrum <greg.landrum@gmail.com> Date: Wed Jul 8 17:11:06 2020 +0200 Revert "Remove buckminsterhelpfile generation & adapt to batik changes in KNIME AP 4.2 (#79)" This reverts commit dcaa4b0.
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We've been using an ancient version of opsin (v1.3.0). This bumps the version to the most recent one: 2.5.0