f051e2f342e3a0f9e49cc3543597c596ab676bf0 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/2b2c0f3fc82ad09a243fba36b8eda954c5ecfd79 2b2c0f3fc82ad09a243fba36b8eda954c5ecfd79 2009-01-22T07:38:00-08:00 2009-01-22T07:38:00-08:00 copyright, license, cleanup f1ea8d62dfec91c0d51c85b0b3e94517c1a4e291 Rich Apodaca rapodaca@metamolecular.com d604780a7a1a73cbaa82f0ecdb2a806b53ebbd2e Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/f051e2f342e3a0f9e49cc3543597c596ab676bf0 f051e2f342e3a0f9e49cc3543597c596ab676bf0 2009-01-22T06:57:51-08:00 2009-01-22T06:57:51-08:00 added substructure search benchmark a4085638708d76439a9170e9398ae1e36d3fc69f Richard Apodaca rapodaca@metamolecular.com b4390dd9c4b69d331cf7bc49dd96d9e1ac415428 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/d604780a7a1a73cbaa82f0ecdb2a806b53ebbd2e d604780a7a1a73cbaa82f0ecdb2a806b53ebbd2e 2009-01-21T09:02:40-08:00 2009-01-21T09:02:40-08:00 added pubchem query used to create test dataset 79a7d81a49ba34db61f92d0c9cde993bb7fa856b Rich Apodaca rapodaca@metamolecular.com a6b59dea87d931878393f2024444f296d18b127b Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/b4390dd9c4b69d331cf7bc49dd96d9e1ac415428 b4390dd9c4b69d331cf7bc49dd96d9e1ac415428 2009-01-21T08:57:45-08:00 2009-01-21T08:57:45-08:00 changed ring test data to be more representative 331d1544ed4bfc4dc111f5534745eeb9901d6aa0 Rich Apodaca rapodaca@metamolecular.com 4b98f42cdab866e73fb114a38825da561dde34fa 427636b768598a68c1432065b697942f58ceeff4 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/a6b59dea87d931878393f2024444f296d18b127b a6b59dea87d931878393f2024444f296d18b127b 2009-01-20T08:05:10-08:00 2009-01-20T08:05:10-08:00 resolved conflict with egon/master branch 343542f421fcaa9527c3bcc6fbd3fb7840fd0e05 Rich Apodaca rapodaca@metamolecular.com c9c0479dbb7a1c50e5a380a0141a65748a93d2c2 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/427636b768598a68c1432065b697942f58ceeff4 427636b768598a68c1432065b697942f58ceeff4 2009-01-20T03:36:23-08:00 2009-01-19T07:15:01-08:00 Updated README to indicate how to run a test Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> b0e287d90e487c46311aa4b18e4b2fd0e7329d2e Egon Willighagen egon.willighagen@gmail.com 0f743214f4921ea4ea5881e740c2e55a6c35c1af Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/c9c0479dbb7a1c50e5a380a0141a65748a93d2c2 c9c0479dbb7a1c50e5a380a0141a65748a93d2c2 2009-01-20T03:36:22-08:00 2009-01-19T07:10:06-08:00 Got rid of print statements from the SDF benchmark Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 713b83e2b5aa7ff26a913b33dc60a836c0ea26db Egon Willighagen egon.willighagen@gmail.com 8afe858b4e788169dc82e7e695f218335a535936 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/0f743214f4921ea4ea5881e740c2e55a6c35c1af 0f743214f4921ea4ea5881e740c2e55a6c35c1af 2009-01-20T03:36:20-08:00 2009-01-19T07:02:24-08:00 Got rid of print statements from the SDF benchmark Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> b24d0b652d2f114eac9c1aec33efd398fe25a5d9 Egon Willighagen egon.willighagen@gmail.com 8fd4088e99d72620d70893bd83e6596347d98940 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/4b98f42cdab866e73fb114a38825da561dde34fa 4b98f42cdab866e73fb114a38825da561dde34fa 2009-01-20T01:08:25-08:00 2009-01-20T01:08:25-08:00 added steroids dataset for use with mx-cdk-ring benchmark a665448c5dfd6c84aaa1d901e81548db1ffb34f0 Richard Apodaca rapodaca@metamolecular.com e7debe5c024804794c4106b92af34b1d6fd254a5 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/8fd4088e99d72620d70893bd83e6596347d98940 8fd4088e99d72620d70893bd83e6596347d98940 2009-01-20T00:11:17-08:00 2009-01-20T00:11:17-08:00 added cdk/mx ring comparison benchmark b3e5150240f45b1e45c2fd9a785e912d9c2cea04 Richard Apodaca rapodaca@metamolecular.com 00db6bbfd00c7f3ed6b3923b8bb6aacb63af5638 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/e7debe5c024804794c4106b92af34b1d6fd254a5 e7debe5c024804794c4106b92af34b1d6fd254a5 2009-01-19T22:38:04-08:00 2009-01-19T22:38:04-08:00 copyright, author notices f648f5a3db30b0f8dd8bbfc657847045af463025 Richard Apodaca rapodaca@metamolecular.com af0543774c0b2dd018be8ff12bdb458756e3eb54 ff02829c77332e6d9e0a14b47faf5f5cb015ad3d Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/00db6bbfd00c7f3ed6b3923b8bb6aacb63af5638 00db6bbfd00c7f3ed6b3923b8bb6aacb63af5638 2009-01-19T22:32:56-08:00 2009-01-19T22:32:56-08:00 Merge branch 'master' of git://github.com/rajarshi/cheminfbenchmark * 'master' of git://github.com/rajarshi/cheminfbenchmark: Updated README to indicate how to run a test Got rid of print statements from the SDF benchmark Got rid of print statements from the SDF benchmark 4c4e86bed03e40ed0303a3be2a6957b2ad5f8236 Richard Apodaca rapodaca@metamolecular.com 9e7915b35c8da460ed6efed4f931ede6751d5baf Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/af0543774c0b2dd018be8ff12bdb458756e3eb54 af0543774c0b2dd018be8ff12bdb458756e3eb54 2009-01-19T22:32:48-08:00 2009-01-19T22:32:48-08:00 removed printlns 36c6f570b3c194f45fc21022b36fec92119c7e52 Richard Apodaca rapodaca@metamolecular.com 0739dfde30440502ae42f4e3ab2e21e9153f326e Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/ff02829c77332e6d9e0a14b47faf5f5cb015ad3d ff02829c77332e6d9e0a14b47faf5f5cb015ad3d 2009-01-19T07:15:01-08:00 2009-01-19T07:15:01-08:00 Updated README to indicate how to run a test b0e287d90e487c46311aa4b18e4b2fd0e7329d2e Rajarshi Guha rajarshi.guha@gmail.com fb710da1b5a3ab86eac682f8134bf6c971c4f195 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/0739dfde30440502ae42f4e3ab2e21e9153f326e 0739dfde30440502ae42f4e3ab2e21e9153f326e 2009-01-19T07:10:06-08:00 2009-01-19T07:10:06-08:00 Got rid of print statements from the SDF benchmark 713b83e2b5aa7ff26a913b33dc60a836c0ea26db Rajarshi Guha rajarshi.guha@gmail.com 9e7915b35c8da460ed6efed4f931ede6751d5baf Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/fb710da1b5a3ab86eac682f8134bf6c971c4f195 fb710da1b5a3ab86eac682f8134bf6c971c4f195 2009-01-19T07:02:24-08:00 2009-01-19T07:02:24-08:00 Got rid of print statements from the SDF benchmark b24d0b652d2f114eac9c1aec33efd398fe25a5d9 Rajarshi Guha rajarshi.guha@gmail.com 1e0480510df633d3958d3e4f22255f14703d5ffc Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/8afe858b4e788169dc82e7e695f218335a535936 8afe858b4e788169dc82e7e695f218335a535936 2009-01-19T04:13:37-08:00 2009-01-18T07:53:29-08:00 got rif of old 1.2.x jar file Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 8579971437d12b471ab6974a3023025a4163f5cf Egon Willighagen egon.willighagen@gmail.com 3cdc458fc902555cdebf843b26af6fc94c94be79 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/1e0480510df633d3958d3e4f22255f14703d5ffc 1e0480510df633d3958d3e4f22255f14703d5ffc 2009-01-19T04:13:33-08:00 2009-01-17T18:58:03-08:00 version of fp benchmark that runs in reasonable time. Also updated to take fp params via the config file, so we can test multiple fingerprints and parameters Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> fc8729202c3d362744986cd52d8bc5f274ce8ef6 Egon Willighagen egon.willighagen@gmail.com 5014ca54eab059be2424701837f220aa7cda6414 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/3cdc458fc902555cdebf843b26af6fc94c94be79 3cdc458fc902555cdebf843b26af6fc94c94be79 2009-01-19T04:13:31-08:00 2009-01-17T18:05:35-08:00 Renamed isomorphism benchmark config file Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 3b230d4f3507ea376f2974d0504e6267e32e509f Egon Willighagen egon.willighagen@gmail.com c1a5c25ef43ed8877ffcdd5ba0e65b362893ccb4 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/5014ca54eab059be2424701837f220aa7cda6414 5014ca54eab059be2424701837f220aa7cda6414 2009-01-19T04:13:31-08:00 2009-01-17T18:01:41-08:00 added data for fp benchmark, derived from the pubchem smiles Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 0beea6f498ea2ad8b71e8cfa57c56a2e6f3562e8 Egon Willighagen egon.willighagen@gmail.com 41c118bcb763696338a8c10bdacccab0e72ab7b4 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/c1a5c25ef43ed8877ffcdd5ba0e65b362893ccb4 c1a5c25ef43ed8877ffcdd5ba0e65b362893ccb4 2009-01-19T04:13:30-08:00 2009-01-17T17:57:04-08:00 Updated config files to use the latest 1.2.x version Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 2e7b56e98787118183dc3b570867f05592a7b0b9 Egon Willighagen egon.willighagen@gmail.com 649609e9b64aa679b4b35550780a62e18aa8c340 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/41c118bcb763696338a8c10bdacccab0e72ab7b4 41c118bcb763696338a8c10bdacccab0e72ab7b4 2009-01-19T04:13:27-08:00 2009-01-17T17:56:46-08:00 Added config file for fp benchmark Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 4e1c8d14dc876e8ef68a85293b505e79f8e9b9c8 Egon Willighagen egon.willighagen@gmail.com b904fc0b2e5aef54814baebca92649ade1890582 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/649609e9b64aa679b4b35550780a62e18aa8c340 649609e9b64aa679b4b35550780a62e18aa8c340 2009-01-19T04:13:26-08:00 2009-01-17T17:56:25-08:00 Added code to benchmark fingerprints Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 99b32bbfd34f70b5b8e9bd94fb67489282ca3dfd Egon Willighagen egon.willighagen@gmail.com b7dc1324fbeb0a1d6ccf4712d2dc1c520303bdd9 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/b904fc0b2e5aef54814baebca92649ade1890582 b904fc0b2e5aef54814baebca92649ade1890582 2009-01-19T04:13:24-08:00 2009-01-16T13:08:57-08:00 Added latest cdk 1.2.x jar file Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> dac7e66648a1a7f4a3b0da1083e4d0505f6e2ce5 Egon Willighagen egon.willighagen@gmail.com 24c936c00980f3831a81bd07a473506b6ed1dca5 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/b7dc1324fbeb0a1d6ccf4712d2dc1c520303bdd9 b7dc1324fbeb0a1d6ccf4712d2dc1c520303bdd9 2009-01-19T04:12:59-08:00 2009-01-19T00:33:29-08:00 tweaked config file Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 3f8c661539ac9f449abdf1074188fdeea0753864 Egon Willighagen egon.willighagen@gmail.com 046d03cdd8ed0cbb063374b2cfdd1f1470ff8d1e Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/24c936c00980f3831a81bd07a473506b6ed1dca5 24c936c00980f3831a81bd07a473506b6ed1dca5 2009-01-19T04:12:57-08:00 2009-01-19T00:13:24-08:00 added mx, mx/cdk mw/sdf comparison Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> 10a5df0f4d6f5f5f1722fa810e0523713b4b40d0 Egon Willighagen egon.willighagen@gmail.com 343f3e9f8a6a149719ed0cdd0c83c2e298fa0f32 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/046d03cdd8ed0cbb063374b2cfdd1f1470ff8d1e 046d03cdd8ed0cbb063374b2cfdd1f1470ff8d1e 2009-01-19T04:12:53-08:00 2009-01-12T23:33:24-08:00 changing which config file gets loaded Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> bce608ab7abaa605f6f2dfa44f81fbb5478ec1a2 Egon Willighagen egon.willighagen@gmail.com 106b561b9f7df7316bf31a3f25ef619e845d3efd Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/9e7915b35c8da460ed6efed4f931ede6751d5baf 9e7915b35c8da460ed6efed4f931ede6751d5baf 2009-01-19T00:33:29-08:00 2009-01-19T00:33:29-08:00 tweaked config file 8579971437d12b471ab6974a3023025a4163f5cf Richard Apodaca rapodaca@metamolecular.com a34b44fef2524552ccd41fa77749a4a320aed73a Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/106b561b9f7df7316bf31a3f25ef619e845d3efd 106b561b9f7df7316bf31a3f25ef619e845d3efd 2009-01-19T00:13:24-08:00 2009-01-19T00:13:24-08:00 added mx, mx/cdk mw/sdf comparison 646323ad057199da336289dfab03b41d69fbab62 Richard Apodaca rapodaca@metamolecular.com 9b7be7b0934b893adda9853074bd3fa673f27b2b 5f2aa28f2878c6d6bea7579253ffcd2c33c33151 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/cheminfbenchmark/commit/a34b44fef2524552ccd41fa77749a4a320aed73a a34b44fef2524552ccd41fa77749a4a320aed73a 2009-01-18T22:33:54-08:00 2009-01-18T22:33:54-08:00 Merge branch 'master' of git://github.com/rajarshi/cheminfbenchmark * 'master' of git://github.com/rajarshi/cheminfbenchmark: got rif of old 1.2.x jar file version of fp benchmark that runs in reasonable time. Also updated to take fp params via the config file, so we can test multiple fingerprints and parameters Renamed isomorphism benchmark config file added data for fp benchmark, derived from the pubchem smiles Updated config files to use the latest 1.2.x version Added config file for fp benchmark Added code to benchmark fingerprints Added latest cdk 1.2.x jar file Added class, config and data files for subgraph isomorphism test 0f935e2829c52137eae221f31f2b05440addfe96 Richard Apodaca rapodaca@metamolecular.com