d4f2ad4a2e1fbc6465b302a79ed59d2c7011c181 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/6c4a459ec2b65dcf18d6231af1252bbaa0f828f2 6c4a459ec2b65dcf18d6231af1252bbaa0f828f2 2008-12-07T20:39:50-08:00 2008-12-07T20:39:50-08:00 test/data/impl for sdfilereader 8524734abd36cf1d6211e1fea7eccb0dddc24886 Rich Apodaca rapodaca@metamolecular.com c3f8bf2cab332a9295b6310e3345b941c6ea1221 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/d4f2ad4a2e1fbc6465b302a79ed59d2c7011c181 d4f2ad4a2e1fbc6465b302a79ed59d2c7011c181 2008-12-07T17:51:31-08:00 2008-12-07T17:51:31-08:00 added sdfilereader/test 1f51fdd2d018e248ef2a991c1bb7e24cb8f9936e Rich Apodaca rapodaca@metamolecular.com d458691f22d7a41c8472db475b8b3fc205073c2f Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/c3f8bf2cab332a9295b6310e3345b941c6ea1221 c3f8bf2cab332a9295b6310e3345b941c6ea1221 2008-12-06T22:31:06-08:00 2008-12-06T22:31:06-08:00 added mass calc test 051942b2e54ad2714c9498920dfc5e437ab73d09 Richard Apodaca rapodaca@metamolecular.com 8d90a8256eae52a24a91fb499814d5294ac22de9 afca6df7e862a15a11efa1c7fa4a51066fb7e29c Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/d458691f22d7a41c8472db475b8b3fc205073c2f d458691f22d7a41c8472db475b8b3fc205073c2f 2008-12-06T22:17:58-08:00 2008-12-06T22:17:58-08:00 Merge branch 'masses' * masses: add dsstore to gitignore added new testcase cleanup from atomicsystem cleanup from atomicsystem added first test/impl for MassCalculator replaced atomicsystem with atomicmass system added test/impl for detecting valid atomic symbol refactored Entry access refactored Entry access added tests/logic for invalid input minor cleanup refactored handling of measurement nodes copyright notice and author tag specific isotope mass/abundance tests and impl added test/implementaiton for getting masses now loading atomic masses file and passing first test first test/impl for AtomicMassSystem 987061bc0a9a87b38b662973bfbbf16db0d8f57c Richard Apodaca rapodaca@metamolecular.com 0004e1e640bc3f7ec9e245d0fb5033e47949dd79 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/afca6df7e862a15a11efa1c7fa4a51066fb7e29c afca6df7e862a15a11efa1c7fa4a51066fb7e29c 2008-12-06T22:14:35-08:00 2008-12-06T22:14:35-08:00 add dsstore to gitignore f5dbb8a766ee3b94be93ba408efb4e9c22e500c8 Richard Apodaca rapodaca@metamolecular.com d585e01134cc2e2443d6c31606367869a4dc9c6d Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/8d90a8256eae52a24a91fb499814d5294ac22de9 8d90a8256eae52a24a91fb499814d5294ac22de9 2008-12-05T18:01:46-08:00 2008-12-05T18:01:46-08:00 minor++ f530df3626a6088d3bf94956771894e9c0439e4a Rich Apodaca rapodaca@metamolecular.com e540d54de2503402a062b6513a5a2e63dd556885 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/d585e01134cc2e2443d6c31606367869a4dc9c6d d585e01134cc2e2443d6c31606367869a4dc9c6d 2008-12-05T17:57:11-08:00 2008-12-05T17:57:11-08:00 closes issue 5 (http://code.google.com/p/mx-java/issues/detail?id=5) 8a2cc84243a60b07520f37a1639a24fb831a768c Rich Apodaca rapodaca@metamolecular.com 371841c9ab43405ec5076ff37430251e607f8ed9 Rich Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/e540d54de2503402a062b6513a5a2e63dd556885 e540d54de2503402a062b6513a5a2e63dd556885 2008-12-03T07:52:03-08:00 2008-12-03T07:52:03-08:00 updated README ea4652c81c131856a8cff3262188a1d6bbb0005f Rich Apodaca rapodaca@metamolecular.com 1b7564065c888ea616b68f7404c0564d746753c6 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/371841c9ab43405ec5076ff37430251e607f8ed9 371841c9ab43405ec5076ff37430251e607f8ed9 2008-12-03T01:26:30-08:00 2008-12-03T01:26:30-08:00 static method to read SMILES 0373dcbf755ac67991b636ce5786cc72f2e9faa5 Richard Apodaca rapodaca@metamolecular.com 6893116343948eeb799e2944f13e41abff7f801d Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/1b7564065c888ea616b68f7404c0564d746753c6 1b7564065c888ea616b68f7404c0564d746753c6 2008-12-03T01:03:23-08:00 2008-12-03T01:03:23-08:00 tests for reading double and triple bond smiles 0b20a7cd38bcdfbaf32cfb971c0dd6294f991c4a Richard Apodaca rapodaca@metamolecular.com 5375d5fbaee275df996dc7ad834980efd35bface Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/0004e1e640bc3f7ec9e245d0fb5033e47949dd79 0004e1e640bc3f7ec9e245d0fb5033e47949dd79 2008-12-03T00:42:44-08:00 2008-12-03T00:42:44-08:00 added new testcase a5cf197a409a919a4f77ee623d9ff3235d6dc621 Richard Apodaca rapodaca@metamolecular.com 691c5f499fdc96c3e7ef660ba3af47706c479d9d Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/5375d5fbaee275df996dc7ad834980efd35bface 5375d5fbaee275df996dc7ad834980efd35bface 2008-12-03T00:31:32-08:00 2008-12-03T00:31:32-08:00 cleanup from atomicsystem 665d8e96c40c7d650c08b94ff9008977af2aa899 Richard Apodaca rapodaca@metamolecular.com f775c757ed50c69c5bd51e3be57075fca2c1bdbd Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/691c5f499fdc96c3e7ef660ba3af47706c479d9d 691c5f499fdc96c3e7ef660ba3af47706c479d9d 2008-12-03T00:22:12-08:00 2008-12-03T00:22:12-08:00 cleanup from atomicsystem 7bd8e56a1d9ee03a1293bfc76657a79d36aac0b6 Richard Apodaca rapodaca@metamolecular.com 035c8fd12e5fc8729084e69d724c2ff25b39226d Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/f775c757ed50c69c5bd51e3be57075fca2c1bdbd f775c757ed50c69c5bd51e3be57075fca2c1bdbd 2008-12-03T00:19:53-08:00 2008-12-03T00:19:53-08:00 added first test/impl for MassCalculator 3114848691cdaef12944c325fee4b10080e029b8 Richard Apodaca rapodaca@metamolecular.com 3cf0eaff10a7122df01bf8e7ceca37c7205820ea Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/035c8fd12e5fc8729084e69d724c2ff25b39226d 035c8fd12e5fc8729084e69d724c2ff25b39226d 2008-12-01T23:58:55-08:00 2008-12-01T23:58:55-08:00 replaced atomicsystem with atomicmass system 97365ab858aeede5114186896d706b1ecea20799 Richard Apodaca rapodaca@metamolecular.com b0410a83c525cbfec8e551f82c36ede9b3c6011c Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/3cf0eaff10a7122df01bf8e7ceca37c7205820ea 3cf0eaff10a7122df01bf8e7ceca37c7205820ea 2008-12-01T23:52:33-08:00 2008-12-01T23:52:33-08:00 added test/impl for detecting valid atomic symbol f9b9f426c6269f5be7c6dcbf67dc218d88027e86 Richard Apodaca rapodaca@metamolecular.com fd2b2f3357879445812c7faa49f749ace0921230 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/b0410a83c525cbfec8e551f82c36ede9b3c6011c b0410a83c525cbfec8e551f82c36ede9b3c6011c 2008-12-01T23:48:54-08:00 2008-12-01T23:48:54-08:00 refactored Entry access 0f2f5b99034a75e1de1564f5dac303ae776064e2 Richard Apodaca rapodaca@metamolecular.com 098fa7b93eacd1aacd42856f86bb4cf295bb15a6 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/fd2b2f3357879445812c7faa49f749ace0921230 fd2b2f3357879445812c7faa49f749ace0921230 2008-12-01T23:46:03-08:00 2008-12-01T23:46:03-08:00 refactored Entry access 90b5a66c10fd65ab8b453b676294cc51bf8383d1 Richard Apodaca rapodaca@metamolecular.com 3f960c28caf34d30c644be288ed9263e7f80d4ec Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/098fa7b93eacd1aacd42856f86bb4cf295bb15a6 098fa7b93eacd1aacd42856f86bb4cf295bb15a6 2008-12-01T23:43:25-08:00 2008-12-01T23:43:25-08:00 added tests/logic for invalid input b91c0f551c3293c10e1566b2dabdd58ce8cea462 Richard Apodaca rapodaca@metamolecular.com c0726dc709fdfa42be79f8899e8f4e18280abc73 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/3f960c28caf34d30c644be288ed9263e7f80d4ec 3f960c28caf34d30c644be288ed9263e7f80d4ec 2008-12-01T23:18:00-08:00 2008-12-01T23:18:00-08:00 minor cleanup 4c3745776332210f9a5a03b7c0b12941ccf84a67 Richard Apodaca rapodaca@metamolecular.com 27e516991346e4ca37fdcd33ecccaa1405a9f163 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/c0726dc709fdfa42be79f8899e8f4e18280abc73 c0726dc709fdfa42be79f8899e8f4e18280abc73 2008-12-01T23:17:11-08:00 2008-12-01T23:17:11-08:00 refactored handling of measurement nodes 90f92bdb86299f33b60c85becdb6ec9df1339434 Richard Apodaca rapodaca@metamolecular.com 7a25174500cb48c4258643598369b9fdc05d32af Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/27e516991346e4ca37fdcd33ecccaa1405a9f163 27e516991346e4ca37fdcd33ecccaa1405a9f163 2008-12-01T23:09:28-08:00 2008-12-01T23:09:28-08:00 copyright notice and author tag b504ff090a356034a39092b0d79394ba2a4ab164 Richard Apodaca rapodaca@metamolecular.com f3f6f5c094b60acdf8e0a46567e35ecb79b30557 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/7a25174500cb48c4258643598369b9fdc05d32af 7a25174500cb48c4258643598369b9fdc05d32af 2008-12-01T23:07:54-08:00 2008-12-01T23:07:54-08:00 specific isotope mass/abundance tests and impl b0cf0a8b5b5fe8f91cd7fe2852976e783b8dbbcd Richard Apodaca rapodaca@metamolecular.com 24d8b2a1a8f04728deca5fd05d32f4ed43b3d24d Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/f3f6f5c094b60acdf8e0a46567e35ecb79b30557 f3f6f5c094b60acdf8e0a46567e35ecb79b30557 2008-12-01T21:40:18-08:00 2008-12-01T21:40:18-08:00 added test/implementaiton for getting masses 0f9073a627a7c95b8da3f38b75baf23a175dedd7 Richard Apodaca rapodaca@metamolecular.com 73deb09d488ca1a80ac82c7f66cc435c96bc9965 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/24d8b2a1a8f04728deca5fd05d32f4ed43b3d24d 24d8b2a1a8f04728deca5fd05d32f4ed43b3d24d 2008-12-01T00:19:59-08:00 2008-12-01T00:19:59-08:00 now loading atomic masses file and passing first test 429f4ce92132492b1e0d203245e2012f8be321c5 Richard Apodaca rapodaca@metamolecular.com 6893116343948eeb799e2944f13e41abff7f801d Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/73deb09d488ca1a80ac82c7f66cc435c96bc9965 73deb09d488ca1a80ac82c7f66cc435c96bc9965 2008-11-30T23:29:45-08:00 2008-11-30T23:29:45-08:00 first test/impl for AtomicMassSystem 41e9fbae4946ab7be57c0646ee6b0c5ff046f98f Richard Apodaca rapodaca@metamolecular.com 439aafe3533099c91d3ddfac92b6de6cc238e2b6 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/6893116343948eeb799e2944f13e41abff7f801d 6893116343948eeb799e2944f13e41abff7f801d 2008-11-30T23:07:34-08:00 2008-11-30T23:07:34-08:00 test and impl for smiles nested branching c51ea902a2c2e3de364ce9e771402c9646526e0b Richard Apodaca rapodaca@metamolecular.com 118fc6b212c63a9cdd58662c2df0c1de4f07e9d5 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/439aafe3533099c91d3ddfac92b6de6cc238e2b6 439aafe3533099c91d3ddfac92b6de6cc238e2b6 2008-11-30T22:57:24-08:00 2008-11-30T22:57:24-08:00 tests and implementation for smiles branching 4747c6c0a8a882cb6f113a4241160f2f2f815131 Richard Apodaca rapodaca@metamolecular.com 8e551ca565fbbfebf9406d2dc5f9988a9b907129 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/118fc6b212c63a9cdd58662c2df0c1de4f07e9d5 118fc6b212c63a9cdd58662c2df0c1de4f07e9d5 2008-11-30T16:19:51-08:00 2008-11-30T16:19:51-08:00 revision++ 22926b2502216838200650cf1ddaf21190cff093 Richard Apodaca rapodaca@metamolecular.com d3e110004a49042f45e9183c2bb95c7a9af47032 Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/8e551ca565fbbfebf9406d2dc5f9988a9b907129 8e551ca565fbbfebf9406d2dc5f9988a9b907129 2008-11-30T16:13:44-08:00 2008-11-30T16:13:44-08:00 moved molfile classes to mdl package 3221f21f30b4cf30fb4c7fd97b1cdbdc00240b29 Richard Apodaca rapodaca@metamolecular.com