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1836 Commits

Author SHA1 Message Date
Greg Landrum
0ddfa00147 update to assertEqual (no reason to dig the python3 hole any deeper 2014-07-01 06:20:21 +02:00
Greg Landrum
f4da8d91d8 support completeRingsOnly and ringMatchesRingOnly from Python 2014-07-01 06:19:40 +02:00
Greg Landrum
8904465804 Merge branch 'master' into fmcs_port_21Feb2014 2014-07-01 05:57:37 +02:00
Greg Landrum
c9b91cd744 code formatting changes (indentation and untabify) 2014-07-01 05:48:51 +02:00
Greg Landrum
6e27eb3f1f remove some defs that were producing useless results anyway 
Fixes #277
 2014-06-29 15:39:29 +02:00
Greg Landrum
c19e52e2e3 Merge branch 'master' into fmcs_port_21Feb2014 2014-06-28 15:12:44 +02:00
Greg Landrum
9bf13137cf add explicit import of <algorithm> to resolve build problem on VS2013 2014-06-28 15:11:14 +02:00
Greg Landrum
38d9f00f84 merge 2014-06-28 15:02:52 +02:00
Greg Landrum
150c963630 fix a build problem 2014-06-28 15:01:13 +02:00
Greg Landrum
d4fc8d6d18 typo fix 2014-06-27 08:46:27 +02:00
Greg Landrum
5ed406a901 Merge remote-tracking branch 'origin/master' into fmcs_port_21Feb2014 2014-06-27 08:09:10 +02:00
Greg Landrum
2389ab4859 Merge remote-tracking branch 'origin/fmcs_port_21Feb2014' into fmcs_port_21Feb2014 2014-06-27 08:03:54 +02:00
Greg Landrum
76188798a2 Fixes #285 2014-06-27 08:02:53 +02:00
Alexander Savelyev
21b2ea4a68 improve prune() heuristic. the search speed was increased. mem leaks fixed 2014-06-26 19:05:55 +04:00
Greg Landrum
eb15c98f97 clean up some leaks in one of the tests 2014-06-23 21:14:54 +02:00
Greg Landrum
8905d71f7f Merge remote-tracking branch 'origin/fmcs_port_21Feb2014' into fmcs_port_21Feb2014 2014-06-20 14:06:38 +02:00
Alexander Savelyev
f9245ec8ac fix multiple atoms and bonds SMARTS for anyCompare 2014-06-20 13:31:12 +04:00
Greg Landrum
5a8cc10790 Merge remote-tracking branch 'origin/master' 2014-06-17 15:39:44 +02:00
Greg Landrum
8d651453b8 Fixes #281 2014-06-17 15:38:56 +02:00
Greg Landrum
d5bb6b2d70 add isotope match test 2014-06-12 02:07:58 -04:00
Greg Landrum
c67b71a4f6 stop matching SMARTS 2014-06-11 11:42:00 -04:00
Greg Landrum
189de60e45 get build working on the mac and python tests running 2014-06-11 11:04:54 -04:00
Alexander Savelyev
98e052bc8c bug with isotopes was fixed 2014-06-11 17:38:20 +04:00
Greg Landrum
07e9356c1e Merge remote-tracking branch 'origin' into fmcs_port_21Feb2014 2014-06-09 23:45:20 +02:00
Greg Landrum
ae0388cfba start to support atom and bond comparators 2014-06-09 23:43:44 +02:00
Greg Landrum
c6deb3f492 add some real python tests 2014-06-09 22:58:21 +02:00
f
009885306d seg fault was fixed 2014-06-02 19:17:39 +04:00
ptosco
ba4a48ce05 - fixed a bug in Code/ForceField/MMFF/testMMFFForceField.cpp 
- fixed a bug in Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp
  which caused misassignment of atom types in CYGUAN01 upon shuffling
  the order of atoms in the validation SDF files
- added checks for acos and asin function parameters to be within
  a (-1, 1) range
 2014-06-01 16:23:03 +01:00
f
be1a2dde81 query optimisation was implemented. Memory leak was fixed. Verbose cosmetic 2014-05-30 15:02:53 +04:00
Greg Landrum
f94ed4a1f5 get queries from SMARTS into CTABs more reasonably 2014-05-26 09:02:08 +02:00
Greg Landrum
b442e9ef32 Merge remote-tracking branch 'origin/master' 2014-05-25 06:56:19 +02:00
Greg Landrum
665872cb39 Fixes #268 2014-05-25 06:55:30 +02:00
Greg Landrum
3216435d73 Fixes #270 2014-05-24 06:16:52 +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
1567ec4462 add getFullDescription() to Query; 
Fixes #287
 2014-05-22 15:18:07 +02:00
Greg Landrum
12fd90c3c5 add test for bond iterators 2014-05-22 10:32:46 +02:00
Greg Landrum
209ada1cbe Merge pull request #261 from ptosco/master 
Fixed a weakness in the angular restraint code
 2014-05-19 23:41:24 -04:00
Greg Landrum
4665bbb9cf remove a compiler warning 2014-05-13 03:47:41 -04:00
Greg Landrum
a979cde58f merge in changes from trunk 2014-05-13 03:34:36 -04:00
Savelyev Alexander
604ee4c675 bug with empty MCS was fixed. MT stub 2014-05-12 21:39:55 +04:00
ptosco
8ed92e222a - fixed a weakness in the angular restraint code which misbehaved 
in case ranges involving negative angles were given as input
 2014-05-10 20:53:17 +01:00
Greg Landrum
d8c523352c fix a profoundly stupid mistake from an earlier commit 2014-05-10 07:43:30 +02:00
Greg Landrum
c26cbc26cb switch to using references to smart pointers for the Match functions; 
really ought to re-examine when/how we are passing smart pointers
 around in general, but that is a bigger job.
Ref: http://herbsutter.com/2013/06/05/gotw-91-solution-smart-pointer-parameters/
 2014-05-10 06:21:27 +02:00
Greg Landrum
ea6263008d add tests for indexing on maccs 2014-05-09 18:17:27 +02:00
Greg Landrum
a8a58342b9 Merge remote-tracking branch 'origin/master' 2014-05-09 17:38:43 +02:00
Greg Landrum
5a6c1c6a12 Fixes: #259 
Fixes: #260
 2014-05-09 12:39:21 +02:00
Greg Landrum
f5cf3322fe code cleanup: removing compiler warnings 2014-05-08 06:06:07 +02:00
Greg Landrum
7306903ef7 use boost::flyweight to ensure thread-safe construction of the pattern fingerprint queries 2014-05-08 04:27:06 +02:00
Greg Landrum
118306d1f9 expose useQueryQueryMatch info to python; 
Fixes #258
 2014-05-07 06:04:38 +02:00