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82 Commits

Author SHA1 Message Date
Greg Landrum
c6dd83a47c Fixes #360 2014-10-25 12:13:01 +02:00
Greg Landrum
cd03d877fb Fixes #337 2014-10-04 14:44:42 +02:00
Greg Landrum
6b26036f6a Fixes #269 2014-05-23 08:26:26 +02:00
Greg Landrum
684f451352 Fixes #266 2014-05-22 17:34:06 +02:00
Greg Landrum
196c2278fb Fixes #234 2014-03-17 08:33:07 +01:00
Greg Landrum
601c21f19d Fixes #189 2014-03-13 05:23:56 +01:00
Greg Landrum
75be63fd6b merge with trunk 2014-02-09 05:00:18 +01:00
Greg Landrum
0839cf41ad Fixes #210 2014-02-03 05:25:27 +01:00
Greg Landrum
deed4a9acf Merge branch 'Issue194_V3000MolWriter' 
Conflicts:
	Code/GraphMol/Chirality.cpp
	Code/GraphMol/FileParsers/test1.cpp
 2014-01-22 07:07:27 +01:00
Greg Landrum
aab11535e8 Fixes #196 2014-01-16 02:07:03 -05:00
Greg Landrum
c13a643e06 Fixes #191 2014-01-12 05:42:50 +01:00
Greg Landrum
e38e60d283 Fixes #186 2014-01-11 06:01:30 +01:00
Greg Landrum
5dca39e2f7 Fixes #187 2014-01-11 05:38:11 +01:00
Greg Landrum
f653e9e961 more isotope fixing 2014-01-08 06:51:48 +01:00
Greg Landrum
4b72d1b153 add (non-standard) handling of R groups to v3k mol parser 2014-01-08 05:22:15 +01:00
Greg Landrum
3f90cecd9c Fixes #164 2013-12-31 08:27:09 +01:00
Greg Landrum
ae14fa3bd9 add support for the ZCH and HYD elements in mol files 2013-12-07 17:40:04 +01:00
Greg Landrum
3b0c72c4bf initial pass at ZBO support. 
does not yet handle the HYD and ZCH lines
 2013-11-30 06:58:03 +01:00
Greg Landrum
1501af51a5 PDB reader/writer fixes; 
add MolToMolFile() to python API
 2013-10-25 05:02:09 +02:00
Greg Landrum
e0e741bd49 very minimal testing of pdb reading/writing 2013-10-11 16:58:20 +02:00
Greg Landrum
e51d2c1020 Fixes #118 2013-10-05 16:19:02 +02:00
malteseunderdog
83ada4c9ce Fixed GitHub Issue #114 
https://github.com/rdkit/rdkit/issues/114
 2013-10-05 11:10:32 +01:00
Greg Landrum
cc154d03ee handle isotopic H better from ctabs 2013-08-23 12:59:09 +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
6157ec6547 Fix #64 2013-07-09 07:19:24 +02:00
Greg Landrum
8462195001 fix and test GitHub issue 19 2013-04-21 05:22:57 +00:00
Greg Landrum
3aa651d167 fix and test sf.net issue 269 2012-11-23 06:52:30 +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
e16b345d8b fix and test issue 3525673 2012-05-12 05:31:54 +00:00
Greg Landrum
4b40a7d3f4 a bit more robustification around issue 3525000b 2012-05-09 13:41:22 +00:00
Greg Landrum
03ecdbc1cc fix and test issue 3525000 2012-05-09 13:13:46 +00:00
Greg Landrum
c6aefe9912 fix and test issue 3514824 2012-04-10 04:14:52 +00:00
Greg Landrum
207b1c181b fix and test issue 3482695 2012-02-02 03:28:48 +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
839104b2d0 forward progress; basic function is there; tests pass on the mac 2011-11-19 13:20:08 +00:00
Eddie Cao
a7ff9b3407 fix a bug that causes rdkit to hang when reading certain SD files not ending with a new line 2011-11-15 17:58:18 +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
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
5c14f36de7 partial fix for Issue3228150 2011-03-25 03:26:03 +00:00