68 Commits

Author	SHA1	Message	Date
Greg Landrum	ff872cdba7	add test for #378	2014-11-09 11:47:46 +01:00
Greg Landrum	a94ce46a43	smiles tests now pass as well	2014-08-27 22:32:49 +02:00
Greg Landrum	23076b1cdb	Fixes #298	2014-07-23 05:31:16 +02:00
Greg Landrum	0839cf41ad	Fixes #210	2014-02-03 05:25:27 +01:00
Greg Landrum	9e4ceef1bd	Fixes #206 but more testing is definitely required	2014-01-28 06:44:43 +01:00
Greg Landrum	47afcc1f53	remove some debugging printing	2013-12-31 07:12:40 +01:00
Greg Landrum	0a421d8aa5	Fixes #182	2013-12-31 07:11:31 +01:00
Greg Landrum	158c9b9e45	Fixes #136	2013-10-21 05:55:42 +02:00
Greg Landrum	dccf20b8c7	Fixes #45	2013-06-08 06:01:54 +02:00
Greg Landrum	e9d8cb1b99	fix and test github issue 12	2013-03-19 04:44:24 +00:00
Greg Landrum	ca5edda7fb	fix and test problems with reading aromatic Si from smiles ... (github issue 5)	2013-02-14 03:59:44 +00:00
Greg Landrum	24e269f8ac	I *think* that this fixes sf.net issue 40: ... the long-standing problem with ring stereochemistry and canonicalization	2012-11-02 06:33:11 +00:00
Greg Landrum	5c2a3f12ce	fix and test issue 257 ... Note that unknown bond types are now written to SMILES as "~" characters. The smiles parser has been modified to recognize these.	2012-10-12 08:58:38 +00:00
Greg Landrum	854dde8097	fix and test issue 253	2012-09-21 12:32:35 +00:00
Greg Landrum	14e396c26d	refactoring the SMILES parser to make it more efficient ... NOTE: this changes the ordering of bonds in molecules with branches.	2012-08-28 04:01:49 +00:00
Greg Landrum	f2d9755a65	at this point all tests pass	2012-06-29 03:40:28 +00:00
Greg Landrum	55ae9a6e26	start fixing some tests (note: this is not done)	2012-06-29 02:42:27 +00:00
Greg Landrum	0f3b84cd28	backup commit; we are not quite there yet	2012-06-26 06:15:08 +00:00
Greg Landrum	a3dc23c43c	more canonicalization improvements ... there are still some problems with double bonds	2012-06-11 03:21:30 +00:00
Greg Landrum	086cbd769c	fix a bug in MolFragmentToSmiles() without canonicalization	2012-05-23 04:37:03 +00:00
Greg Landrum	efc76f5bd5	clean up an uninitialized variable that was causing problems on the mac	2012-05-20 06:11:48 +00:00
Greg Landrum	700d60c94d	left out some tests	2012-05-19 04:34:45 +00:00
Greg Landrum	c293dc23da	initial version of MolFragmentToSmiles	2012-05-19 03:50:31 +00:00
Greg Landrum	7495b6248f	cleanup + tests for issue 3526815	2012-05-18 09:09:04 +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	a39187a528	fix and test issue 3526814	2012-05-16 05:29:34 +00:00
Greg Landrum	e77cfcf336	fix and test issue 3525776	2012-05-11 13:02:07 +00:00
Greg Landrum	8ffcfd7149	fix and test issue 35525671	2012-05-11 07:13:45 +00:00
Greg Landrum	f2bc7f77d2	fix and test issue 3525669	2012-05-11 06:42:08 +00:00
Greg Landrum	54f861e5ee	fix and test issue 3525668	2012-05-11 06:36:08 +00:00
Greg Landrum	e7d25d7973	tests passing except reactions	2012-04-21 04:40:55 +00:00
Greg Landrum	3520c441cb	add allBondsExplicit argument for SMILES writing	2012-03-26 03:12:37 +00:00
Greg Landrum	813f4863ed	fix and test Issue 3480481	2012-02-18 05:34:34 +00:00
Greg Landrum	d47f423009	support [HH]	2011-12-20 04:12:07 +00:00
Greg Landrum	9316758cec	improved handling of isotope specifications (still definitely not optimal)	2011-07-01 03:42:35 +00:00
Greg Landrum	faab610321	add string replacements to smiles and smarts parsers	2011-05-22 10:45:14 +00:00
Greg Landrum	3b3d44db16	remove exe property from source files	2011-01-13 04:22:56 +00:00
Greg Landrum	c6c7af1e6a	fix and test issue 3152751	2011-01-07 05:04:26 +00:00
Greg Landrum	e269703e0e	some more natural product tests for issue 3139534	2011-01-05 06:30:56 +00:00
Greg Landrum	f4a0012bc6	fix a residual problem with ring stereochem	2011-01-04 04:45:42 +00:00
Greg Landrum	c20376ad15	typo	2010-12-28 17:57:54 +00:00
Greg Landrum	5891b5edc8	further work on bug 3139534	2010-12-28 15:43:20 +00:00
Greg Landrum	006c696067	an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534); ... this needs a ton more testing, but it is worth getting a "working" version in	2010-12-28 10:38:14 +00:00
Greg Landrum	67dadac26e	fix and test bug 3145697	2010-12-27 07:20:34 +00:00
Greg Landrum	e977a642f6	add support for writing non-canonical SMILES; ... add support for atom-mapping information in plain SMILES	2010-12-20 03:59:56 +00:00
Greg Landrum	43fdf6db27	fix and test sf.net bug 3127883	2010-12-05 08:35:41 +00:00
Greg Landrum	f3fbef45c5	update copyright statements	2010-09-26 17:04:37 +00:00
Greg Landrum	d23bdac363	fix and test sf.net issue 3018558	2010-06-20 03:46:58 +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	96adbc11ea	remove the deprecated assign{Atom,Bond}ChiralCodes functions	2009-08-02 15:33:08 +00:00