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54 Commits

Author SHA1 Message Date
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
Greg Landrum
5592e31464 initial fix and tests for issue 3154208 2011-01-10 07:11:44 +00:00
Greg Landrum
e4b215a6b0 properly handle quoted NOT atom lists 2010-06-04 10:06:50 +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
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
2f3b3e251c support parity with implicit hs 2009-01-26 05:56:28 +00:00
Greg Landrum
73fccfd26f add a few simple tests for the mol file parity handling 2009-01-21 06:05:13 +00:00
Greg Landrum
1a186a2d82 fix and test issue2413431 2008-12-10 09:09:02 +00:00
Greg Landrum
cfc3fcbd08 merge sybyl file parsers into trunk. These are revs831:895 from the branch 2008-11-25 06:04:17 +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
Greg Landrum
023f7b4f0f Merge changes from the iterative chirality branch: 
https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/IterativeChirality_20Aug2008
into the trunk.
This covers revs 798-828.

Dependent chirality should now be correctly handled, but the
handling of ring stereochemistry, i.e. things like:
C[C@H]1CC[C@H](C)CC1
is still not 100% correct.
 2008-09-19 09:40:15 +00:00
Greg Landrum
5e9d1e8307 fix and test issue 1965035 2008-05-16 05:35:50 +00:00
Greg Landrum
562c18fdfa further progress towards supporting MDL mol file queries (sf.net issue 1756962) 2008-02-26 18:06:20 +00:00
Greg Landrum
a788e29511 merge the changes from the CanonicalizerRework30Nov branch in. 
The changes are revs 451:498.
 2008-01-30 14:53:04 +00:00
Greg Landrum
ae959f6326 test the removeHs stuff a bit better 2007-08-13 03:59:58 +00:00
Greg Landrum
168d45ebc9 further improvements in handling queries from MDL mol files 2007-08-07 17:32:30 +00:00
Greg Landrum
3e7dbcf66a start to add better support for MDL mol files. 
this is sf.net issue 1756962: https://sourceforge.net/tracker/?func=detail&atid=814653&aid=1756962&group_id=160139
 2007-07-19 16:41:11 +00:00
Greg Landrum
66ec16dedf Fix and test sf.net bug 1725068: 
http://sourceforge.net/tracker/index.php?func=detail&aid=1725068&group_id=160139&atid=814650
 2007-06-06 17:25:08 +00:00
Greg Landrum
ee60199400 continue fix and test for sf.net issue 1718794 
http://sourceforge.net/tracker/index.php?func=detail&aid=1718794&group_id=160139&atid=814650
 2007-05-14 17:41:17 +00:00