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Commit Graph

100 Commits

Author SHA1 Message Date
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
53a2937eb6 Fixes #194 2014-01-15 03:19:26 -05:00
Greg Landrum
c13a643e06 Fixes #191 2014-01-12 05:42:50 +01:00
Greg Landrum
0ce8f23c6e further R group handling 2014-01-10 04:24:22 +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
355556b7de get atom lists working 2013-12-29 07:05:25 +01:00
Greg Landrum
0b8bd3079d fix isotope handling in V3K 2013-12-28 07:37:52 +01:00
Greg Landrum
d280c90117 a few more tests and a fix to not print empty bond blocks 2013-12-26 07:40:16 +01:00
Greg Landrum
9e91538d64 get rgroups working 2013-12-25 08:18:44 +01:00
Greg Landrum
329841d9ba add some tests; add radicals to output 2013-12-24 06:56:12 +01:00
Greg Landrum
f6517b572e Fixes #166 2013-11-25 05:36:45 +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
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
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