80 Commits

Author	SHA1	Message	Date
Greg Landrum	d80ab78f70	initial pass at this	2013-07-15 17:04:15 +02:00
Greg Landrum	c36547010a	Fix #64	2013-07-09 05:40:55 +02:00
Greg Landrum	213e161b0c	remove some warnings from clang. ... At this point the only warnings are connected to the RNG parameterization in Fingerprints.cpp	2013-03-29 17:22:28 +00:00
Greg Landrum	b6a26aca44	fix and test sf.net issue273	2012-12-12 09:10:05 +00:00
Greg Landrum	2c3d7eb2f2	re-enable tests	2012-12-03 08:44:29 +00:00
Greg Landrum	3aa651d167	fix and test sf.net issue 269	2012-11-23 06:52:30 +00:00
Greg Landrum	894be3cf8b	adjust to the SMILES changes for unknown bonds	2012-10-18 12:19:04 +00:00
Greg Landrum	33d571850d	support skip lines in ctabs; ... get sdf property lines that contain only white space working	2012-10-10 10:16:13 +00:00
Greg Landrum	4a3933ed00	fix and test Issue 3557675	2012-08-15 04:21:33 +00:00
Greg Landrum	cfc14230e1	fix issues 3525799 and 3526810 ... this changes some canonical SMILES and removes support for "[Xa]" dummy atoms in SMILES	2012-05-18 05:56:45 +00:00
Greg Landrum	461353b299	remove a test that is not being used	2012-05-15 08:26:45 +00:00
Greg Landrum	807a410903	additional testing for issue 3525673	2012-05-12 05:39:33 +00:00
Greg Landrum	03ecdbc1cc	fix and test issue 3525000	2012-05-09 13:13:46 +00:00
Greg Landrum	e7d25d7973	tests passing except reactions	2012-04-21 04:40:55 +00:00
Greg Landrum	c6aefe9912	fix and test issue 3514824	2012-04-10 04:14:52 +00:00
Greg Landrum	ee95f8ba65	fix and test issue 3484552	2012-02-05 07:27:01 +00:00
Greg Landrum	dbd78604c8	fix and test issue 3477283 ... add a new option for ctab parsing to cause the parser to be less strict about errors in the file syntax.	2012-01-22 09:40:54 +00:00
Greg Landrum	510f68b102	initial pass at fixing issue 3432136	2011-11-03 04:13:02 +00:00
Greg Landrum	59c05266b7	fix and test issue 3392107. Add first pass at being able to write atom list queries to mol files	2011-08-16 06:03:27 +00:00
Greg Landrum	d512e49fff	partial solution to the chiral phosphorus problem	2011-07-28 05:22:55 +00:00
Greg Landrum	f6ff447b0b	fix and test issue 3376319 ... NOTE: the R/S labels that one gets for phosphates do not match those from chemdraw/marvin	2011-07-23 16:53:04 +00:00
Greg Landrum	8b077509e9	another piece of Issue3375684	2011-07-23 04:47:17 +00:00
Greg Landrum	67eccc1620	fix and tests Issue3375684	2011-07-23 03:49:36 +00:00
Greg Landrum	951f4b7fd3	fix and tests sf.net issue3375647	2011-07-22 15:53:05 +00:00
Greg Landrum	f61d48cadf	add some of the inchi rules for ignoring mol file stereochemistry	2011-07-22 14:21:39 +00:00
Greg Landrum	10cb677b33	fix and test Issue3374639	2011-07-22 10:55:40 +00:00
Greg Landrum	c7a9903e41	fix and test issue 3359739	2011-07-09 04:46:55 +00:00
Greg Landrum	1df2618213	fix and test issue 3316600	2011-06-15 05:34:15 +00:00
Greg Landrum	f0c0a060a2	fix and test Issue 3313540	2011-06-10 03:27:46 +00:00
Greg Landrum	a7cbd1a818	better fix for sf.net issue 3313539	2011-06-09 05:30:45 +00:00
Greg Landrum	deae1affcb	provisional fix and test sf.net issue 3313539	2011-06-08 05:18:14 +00:00
Greg Landrum	2ffaa92cf7	fix and test issue3228150; ... note that as part of these changes MolToSmiles and MolToSmarts no longer have side effects on the original molecule.	2011-03-26 06:51:50 +00:00
Greg Landrum	5c14f36de7	partial fix for Issue3228150	2011-03-25 03:26:03 +00:00
Greg Landrum	3b3d44db16	remove exe property from source files	2011-01-13 04:22:56 +00:00
Greg Landrum	e703428743	canonicalization test connected with issue 3154208	2011-01-11 05:12:19 +00:00
Greg Landrum	5592e31464	initial fix and tests for issue 3154208	2011-01-10 07:11:44 +00:00
Greg Landrum	f3fbef45c5	update copyright statements	2010-09-26 17:04:37 +00:00
Greg Landrum	5cc9d6ddeb	fixes and tests for two isotope-related problems: ... 1) issue 3073163 2) incorrect calculation of AMW with isotopes present	2010-09-22 13:26:30 +00:00
Greg Landrum	a09fd9f63a	cleanup work on file parsers code; add v3K rxn support	2010-06-03 06:59:48 +00:00
Greg Landrum	e448b5b7a4	expand capabilities of v3k ctab parser	2010-06-02 17:55:35 +00:00
Greg Landrum	80c0a8825e	fix issue 3009836; partial fix for issue 3009911	2010-06-01 17:54:49 +00:00
Greg Landrum	c235b26126	fix and test issues 3009756 and 3009836	2010-06-01 09:39:42 +00:00
Greg Landrum	2805355f34	First pass at the rewrite: ... this gets rid of all the "preceding atom" code and passes all tests on linux builds on other OS's and more extensive regression testing is required	2010-05-31 14:08:11 +00:00
Greg Landrum	5ac2d19bfa	resolve sf.net issue 2963522	2010-03-10 06:47:33 +00:00
Greg Landrum	9eccc4521d	add more flexibility to the R group labelling from mol files	2010-03-10 05:14:52 +00:00
Greg Landrum	4b3185e330	fix a v3k mol file problem	2010-02-15 12:43:38 +00:00
Greg Landrum	96adbc11ea	remove the deprecated assign{Atom,Bond}ChiralCodes functions	2009-08-02 15:33:08 +00:00
Greg Landrum	268b08ec17	fix and test sf.net issue 2804599	2009-06-11 04:55:44 +00:00
Greg Landrum	d397d7d7ed	preliminary handling of v3000 mol blocks	2009-06-05 06:12:51 +00:00
Greg Landrum	cfc14cbb8e	robustify multiple query handling	2009-05-28 14:14:15 +00:00