78 Commits

Author	SHA1	Message	Date
Greg Landrum	b45423be3e	rename makeAtomNumEqualsQuery() to makeAtomNumQuery()	2013-12-14 09:14:57 +01:00
Greg Landrum	60a68669da	remove more clang warnings	2013-12-02 04:46:46 +01:00
Greg Landrum	1acae67cba	Merge branch 'master' into PDB_29September2013	2013-10-08 05:51:57 +02:00
Greg Landrum	e51d2c1020	Fixes #118	2013-10-05 16:19:02 +02:00
Greg Landrum	937ee9f60a	add in-place form of removeHs()	2013-10-04 07:19:01 +02:00
Greg Landrum	2546ea0d7a	Fixes #82	2013-08-23 09:18:04 +02:00
Greg Landrum	8c70417690	Fixes #88	2013-08-21 20:45:54 +02:00
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	581695da0f	support R values greater than 9 in ctabs	2013-07-04 08:21:13 +02:00
Greg Landrum	8ac59a261a	continuation of cleanup from issue 279 [follow up from rev2355]	2013-01-09 04:11:15 +00:00
Greg Landrum	b82a6b29a6	another swing at sf.net issue 279. This one is somewhat more efficient	2013-01-08 05:35:03 +00:00
Greg Landrum	b6a26aca44	fix and test sf.net issue273	2012-12-12 09:10:05 +00:00
Greg Landrum	a5baf0239b	more on the locale problem; this still needs testing on non-linux	2012-12-12 04:20:14 +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	e16b345d8b	fix and test issue 3525673	2012-05-12 05:31:54 +00:00
Greg Landrum	e7d25d7973	tests passing except reactions	2012-04-21 04:40:55 +00:00
Greg Landrum	162662186d	not working yet	2012-04-19 06:15:40 +00:00
Greg Landrum	207b1c181b	fix and test issue 3482695	2012-02-02 03:28:48 +00:00
Greg Landrum	51991c7619	add line numbers to all error messages/warnings from ctab parsing	2012-01-29 08:41:30 +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	82129c3e13	fix and test Issue3399798	2011-08-30 09:13:07 +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
Eddie Cao	adbd5c7b18	Several InChI generation fixes, including perchloric acid, isotopic property, chirality loss, stereoany	2011-07-25 06:41:47 +00:00
Greg Landrum	d34f3dd6b2	do isotope work relative to the most common isotope	2011-07-01 04:34:14 +00:00
Greg Landrum	9316758cec	improved handling of isotope specifications (still definitely not optimal)	2011-07-01 03:42:35 +00:00
Greg Landrum	1df2618213	fix and test issue 3316600	2011-06-15 05:34:15 +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	3b3d44db16	remove exe property from source files	2011-01-13 04:22:56 +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	4d168b2637	further leak stoppage	2010-06-09 18:30:22 +00:00
Greg Landrum	e4b215a6b0	properly handle quoted NOT atom lists	2010-06-04 10:06:50 +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	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	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
Greg Landrum	477a26b84a	better handling of Q, A and * queries from CTABs ... sf.net issue 2797708	2009-05-28 04:37:12 +00:00
Greg Landrum	305bf237b4	add the ForwardSDMolSupplier to allow use of gzipped sd files; ... remove the long-obsolete SDFileParser stuff.	2009-05-14 18:07:57 +00:00
Greg Landrum	6e0d5c0e67	support parsing atom properties; fix ordering "bug" in property parsing	2009-05-11 15:27:39 +00:00
Greg Landrum	35de73dff0	prelim parity handling, no testing yet	2009-01-20 06:40:36 +00:00
Greg Landrum	1a186a2d82	fix and test issue2413431	2008-12-10 09:09:02 +00:00
Greg Landrum	bc580ac2e3	fix and test issue 2337369	2008-11-24 07:40:53 +00:00
Greg Landrum	6d3a9f6fb3	Check in a bunch of changes to fix radical handling. ... These are connected to issues 2093420, 2091890, and 2091839 this still needs more testing.	2008-09-23 06:02:02 +00:00