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088256bfb13d14f998f6325669c2cfbabc498308
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3080 Commits

Author SHA1 Message Date
Paolo Tosco
088256bfb1 - fixed a typo in the Python docs 2016-05-11 23:45:37 +01:00
Paolo Tosco
779ec747ac - put SnapshotVect in the RDKit namespace 2016-05-11 23:41:31 +01:00
Paolo Tosco
471fd9a3c3 - added missing libraries 2016-05-11 23:13:04 +01:00
Paolo Tosco
06d2dfbba6 Merge branch 'traj' of https://github.com/ptosco/rdkit into traj 2016-05-11 22:24:13 +01:00
Paolo Tosco
2dcedcbbf9 - added missing Code/GraphMol/Trajectory/Snapshot.h 2016-05-11 22:23:46 +01:00
Paolo Tosco
27fa3f1745 Merge branch 'traj' of https://github.com/ptosco/rdkit into traj 2016-05-11 19:56:55 +01:00
Paolo Tosco
95ebdbd55d - added miising Code/GraphMol/Wrap/rdTrajectory.cpp 2016-05-11 19:56:32 +01:00
Paolo Tosco
cbe5358b64 Merge branch 'traj' of https://github.com/ptosco/rdkit into traj 2016-05-11 19:55:37 +01:00
Paolo Tosco
8a2623e128 - added missing Code/GraphMol/Trajectory/CMakeLists.txt 2016-05-11 19:55:06 +01:00
Paolo Tosco
158911ace9 Merge remote-tracking branch 'upstream/master' into traj 2016-05-11 19:51:50 +01:00
Paolo Tosco
2b3a818f84 - removed the dependency on Trajectory from ROMol and ForceField 2016-05-11 19:37:09 +01:00
Paolo Tosco
8b5176f8c9 - initial work to put the Trajectory code into a separate object 2016-05-09 19:05:15 +01:00
Greg Landrum
fc537d6128 Fixes #904 (#905) 2016-05-09 12:06:58 -04:00
Paolo Tosco
3bfe792653 Updated copyright notices and docs for Trajectory 2016-05-07 22:03:53 +01:00
Paolo Tosco
d1d40ec27c Merge remote-tracking branch 'upstream/master' into traj 2016-05-07 21:05:43 +01:00
Paolo Tosco
9d0f688e87 - linked additional libs to fix a build failure on Windows (#901) 2016-05-05 09:52:55 -04:00
Paolo Tosco
a2eca41365 - the Trajectory object now holds a vector of Snapshots rather than 
a vector of shared_ptr to Snapshots
- The PySnapshot class was removed
- the Trajectory::readAmber and Trajectory::readGromos member functions
  were converted into non-member functions
- tests were modified accordingly
 2016-05-04 18:42:23 +01:00
Paolo Tosco
d24a7abcda Merge remote-tracking branch 'upstream/master' into traj 2016-05-03 18:40:44 +01:00
Greg Landrum
db0db2e4e4 expose FPS functions to java; add tests for that (#897) 2016-05-02 14:39:48 -04:00
Greg Landrum
6709ed553d Merge pull request #892 from bp-kelley/dev/preprocessrxn-cpp 
Dev/preprocessrxn cpp
 2016-05-02 13:21:20 +02:00
Greg Landrum
da579451ee Merge pull request #895 from bp-kelley/fix/2016-04-warning-squash-rollup 
Rollup of warning squashing (with some tests diagnostics thrown in)
 2016-05-01 06:33:47 +02:00
Brian Kelley
34fef8baaf Rollup of warning squashing (with some tests diagnostics thrown in) 2016-04-30 13:25:48 -04:00
Greg Landrum
116bfc9c40 Fixes depictor problem with empty fragments (#894) 
@rvianello caught that this one was causing intermittent problems on windows.
 2016-04-30 13:16:43 -04:00
Brian Kelley
eb879081bf Removes unecessary find step 2016-04-29 09:34:09 -04:00
Brian Kelley
db73c1e237 Fixes typo 2016-04-29 09:26:40 -04:00
Brian Kelley
5f96121d0d Readds turned off tests 2016-04-29 09:24:45 -04:00
Brian Kelley
1b9368571b Adds python3 support 2016-04-28 17:31:48 -04:00
Brian Kelley
0f78fe97e8 Reverts change in library order 2016-04-28 16:34:21 -04:00
Brian Kelley
5561ca9d0b Adds PreprocessReactions 2016-04-28 16:33:50 -04:00
Brian Kelley
ecec4fad2b Changes dependency order 2016-04-28 15:51:13 -04:00
Brian Kelley
aaa23995cc Updates PreprocessReaction to the C++ version 
Fixes doctests
  Add normalize param to GetFlattenedFunctionalGroupHierarchy
 2016-04-28 15:21:11 -04:00
Paolo Tosco
b6deabb4a7 Merge remote-tracking branch 'upstream/master' into traj 2016-04-27 14:03:26 +01:00
Greg Landrum
6271682527 Merge pull request #885 from bp-kelley/dev/filtercatalog-functional-groups 
Dev/filtercatalog functional groups
 2016-04-27 11:09:07 +02:00
Brian Kelley
1199c9f2a8 Updates with BOOST_FOREACH 2016-04-26 21:34:50 -04:00
Brian Kelley
12ef2b31fe Add max depth check 2016-04-26 21:26:15 -04:00
Brian Kelley
0b44366e73 Fixes issues, updates docs 2016-04-26 21:13:57 -04:00
Paolo Tosco
5538cef587 No change 2016-04-26 21:58:22 +01:00
Paolo Tosco
fdd9b7b38f No change 2016-04-26 21:57:06 +01:00
Paolo Tosco
a47cf48624 - added a test to check adding Snapshots to a Trajectory from Python 
- removed a spurious NOGIL residuated from a copy/paste
 2016-04-26 19:36:36 +01:00
Paolo Tosco
9ffd1670f0 - added a few tests 
- changed a few PRECONDITION into URANGE_CHECK
 2016-04-26 09:00:22 +01:00
Paolo Tosco
96d585957e - switched from a vector of Snapshot* to a vector of boost::shared_ptr<Snapshot> 
- added a test case for Snapshot to C++ and Python
 2016-04-25 22:39:27 +01:00
Brian Kelley
5f75cbe3a8 Fixes FilterHierarchyMatcher serialization 2016-04-25 17:22:56 -04:00
Paolo Tosco
48b8e616ad Merge remote-tracking branch 'upstream/master' into traj 2016-04-25 21:54:20 +01:00
Paolo Tosco
3f4c6ec9ff - switch to boost::shared_array 2016-04-25 21:53:04 +01:00
Brian Kelley
4c497c495e Tests FilterCatalog with addRecursiveQueries 2016-04-25 16:20:35 -04:00
Brian Kelley
eba6762d71 Adds FunctionalGroups to the FilterCatalog 2016-04-25 16:02:00 -04:00
Greg Landrum
ffe829d5da adjust cartridge tests after the fix for #874 (#884) 2016-04-25 14:19:01 -04:00
Paolo Tosco
605ff9264c - fixed a typo in the headers 2016-04-25 07:16:22 +01:00
Paolo Tosco
d16b312ee6 - Completely revised coordinate ownership 
- Implemented Python wrappers
- prepared relevant test cases
 2016-04-24 23:30:25 +01:00
Paolo Tosco
a7e54bc25e Merge remote-tracking branch 'upstream/master' into traj 2016-04-24 23:29:49 +01:00