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80 Commits

Author SHA1 Message Date
Greg Landrum
47c222e3d5 clear up some compiler warnings 2007-05-04 04:59:30 +00:00
Greg Landrum
b176a0dc70 working towards a fix for Issue 1695221 (http://sourceforge.net/tracker/index.php?func=detail&aid=1695221&group_id=160139&atid=814650) 2007-04-27 05:21:23 +00:00
Greg Landrum
823f64f192 Issue 1702647 fix for TDTMolSupplier (http://sourceforge.net/tracker/index.php?func=detail&aid=1702647&group_id=160139&atid=814650) 2007-04-27 05:20:46 +00:00
Greg Landrum
bfc7a1ff20 Issue 1702647 fix for TDTMolSupplier (http://sourceforge.net/tracker/index.php?func=detail&aid=1702647&group_id=160139&atid=814650) 2007-04-27 05:20:24 +00:00
Greg Landrum
35204ea378 Issue 1702647 fix for TDTMolSupplier (http://sourceforge.net/tracker/index.php?func=detail&aid=1702647&group_id=160139&atid=814650) 2007-04-27 05:20:10 +00:00
Greg Landrum
e9e865d33f some rather embarassing typos preventing a linux build were fixed 2007-04-24 17:50:18 +00:00
Greg Landrum
c3dc1fd914 These are mostly documentation changes. Exceptions are noted below. 
Wrap/MolChemicalFeature.cpp: expose ClearCache() method.
RDCode.sln: fix a dependency
 2007-04-24 04:24:22 +00:00
Greg Landrum
7407f8cfc8 this is a partial fix for issue 1702647, TDTMolSuppliers still need to be tested and probably fixed 
http://sourceforge.net/tracker/index.php?func=detail&aid=1702647&group_id=160139&atid=814650
 2007-04-18 17:34:36 +00:00
Greg Landrum
783f220443 removed extraneous printing 2007-04-18 03:35:44 +00:00
Greg Landrum
4fff15fedf fixes (and tests) for sf.net bug 1694023 (http://sourceforge.net/tracker/index.php?func=detail&aid=1694023&group_id=160139&atid=814650) 2007-04-04 06:07:31 +00:00
Greg Landrum
012654895a remove a compile error 2007-03-24 05:43:42 +00:00
Greg Landrum
9bd4c59606 substantial optimization of SD/mol file parsing;some reformattig 2007-03-20 21:06:37 +00:00
Greg Landrum
765561036d update project files 2007-03-18 17:57:28 +00:00
Santosh Putta
bc0958a6ad test data for structure sampling and mimic 3D 2007-03-13 02:47:52 +00:00
Santosh Putta
5cf8958732 Functionality to sample rotatable bonds and bond flips at degree 4 nodes to either spread the drawing more or mimic a specified distance matrix 2007-03-13 02:46:15 +00:00
Greg Landrum
547f71ec7c further work on the TPL reader/writer 2007-03-04 16:22:11 +00:00
Greg Landrum
804b3dbf88 TPL reading is now getting close to being done 2007-03-03 06:38:03 +00:00
Greg Landrum
3f8e053b31 again, just a backup commit; 2007-03-02 06:40:25 +00:00
Greg Landrum
9d6d55b523 just a backup commit; this isn't quite done yet 2007-03-02 06:21:59 +00:00
Greg Landrum
4006f25d58 fix isotope handling in SMILES 2007-02-28 17:51:17 +00:00
Greg Landrum
2c96cd54dd fix and test SF.net issue 1670149 
http://sourceforge.net/tracker/index.php?func=detail&aid=1670149&group_id=160139&atid=814650
 2007-02-27 18:07:43 +00:00
Greg Landrum
8023683f96 the ChemReactions stuff was not being built properly on linux 2007-02-25 11:43:17 +00:00
Greg Landrum
80c76c59ac merge in chemical reactions branch (r173:183) 2007-02-23 18:05:50 +00:00
Greg Landrum
bbe6387c74 doc updates 
fixed a core leak in MolCatalogEntry.cpp
 2007-02-16 05:31:01 +00:00
Greg Landrum
f3f0866ea6 test MolCatalogs 2007-02-13 20:05:36 +00:00
Greg Landrum
17e863b667 Merge in changes from MolCatalog branch (r109:169) 
This needs some massive testing.
 2007-02-13 18:56:04 +00:00
Greg Landrum
5e4f23fbe2 fix and test SF.net issue 1653802 
https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1653802&group_id=160139
This fix may well cause problems in other regressions, but it passes
all code/GraphMol tests on windows as of this point.
 2007-02-07 06:32:40 +00:00
Greg Landrum
2c603a1abf fix the build 2007-01-26 05:07:55 +00:00
Greg Landrum
cf728dbc7c primarily project file changes to make things work 
with python 2.5
Also includes a slackening of the tolerance for a distgeomhelpers test.
 2007-01-15 20:30:01 +00:00
Santosh Putta
5b98198322 fix for 1607290 on VC8. Use resize instead of reserve in getShortestPath function for couple of std::vectors 2006-12-29 19:06:23 +00:00
Greg Landrum
28c3224c9b MolFileParser: move the chirality setting inside the sanitization test 
FileParsers.vcproj: remove optimization (under vc++) for two files. This is a "fix" for what I believe to be a vc++ compiler bug. See issue 1607290 (http://sourceforge.net/tracker/index.php?func=detail&aid=1607290&group_id=160139&atid=814650)

testMolWriter.cpp: update memory corruption test
 2006-12-21 04:45:37 +00:00
Greg Landrum
fedc0d6df3 up the tolerance a bit to get this passing on windows 2006-12-17 15:55:57 +00:00
Greg Landrum
cf1fa4fb06 minor cleanups... this seems to fix the memory corruption problems I found earlier, but there's no particular reason whey it should. 
http://sourceforge.net/tracker/index.php?func=detail&aid=1607290&group_id=160139&atid=814650
 2006-12-17 15:33:57 +00:00
Greg Landrum
47a62846e7 test for memory corruption 2006-12-17 15:32:48 +00:00
Greg Landrum
cab9793963 small cleanups 2006-12-17 15:00:41 +00:00
Greg Landrum
1378a5c934 small cleanups 2006-12-17 14:58:54 +00:00
Greg Landrum
730e69fc59 this typo caused problems on a newer linux version 2006-12-06 20:14:25 +00:00
Santosh Putta
218032f32b letting hydrogens in the graph be part of chiral volume calculation atoms 2006-11-30 00:24:34 +00:00
Greg Landrum
688ed25c88 fix and test SF.net bug 1603923 
(https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1603923&group_id=160139)
 2006-11-27 17:53:02 +00:00
Greg Landrum
1bca002c97 fix a minor coordinate problem in the regressions (connected to new chirality handling) 2006-11-22 04:25:24 +00:00
Santosh Putta
5cccfa3870 new test for chirality stuff 2006-11-22 00:54:12 +00:00
Santosh Putta
086faee1a9 changes related to chirality addition 2006-11-22 00:53:26 +00:00
Greg Landrum
e35d093dc3 modify the depickler so that it no longer has to seek within the stream; 
this increases our flexibility a LOT
 2006-11-21 17:48:48 +00:00
Greg Landrum
a023b862aa support direct passing of streams 2006-11-19 06:46:58 +00:00
Greg Landrum
05efa716e3 fix a core leak 2006-11-16 05:00:02 +00:00
Greg Landrum
d5ffea669d add support for chirality in substructure searches; 
this only is going to work in cases where CIP codes have been (i.e. can be)
assigned to atoms.
 2006-11-03 06:35:14 +00:00
Greg Landrum
e66c87a322 we shouldn't have been labelling things 'Xe' 2006-10-31 17:47:55 +00:00
Greg Landrum
e56716953d throw an exception with zero-atom molecules; untabify 2006-10-29 07:01:39 +00:00
Greg Landrum
419dd173b4 fixed a typo 2006-10-24 04:54:42 +00:00
Greg Landrum
393f394e9f add _SetStreamIndices() to SDMolSupplier 2006-10-24 04:08:07 +00:00