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Commit Graph

2266 Commits

Author SHA1 Message Date
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
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
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
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
Brian Kelley
5f75cbe3a8 Fixes FilterHierarchyMatcher serialization 2016-04-25 17:22:56 -04:00
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
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
Greg Landrum
ec50bf6a9d Fix for github874 (#877) 
* Fixes #874

* minor cleanup

* test for 874
 2016-04-23 11:53:13 -04:00
Paolo Tosco
5e5069c86f Merge remote-tracking branch 'upstream/master' into traj 2016-04-23 09:01:08 +01:00
Brian Kelley
ecf03f79b5 Removes debugging code and unneeded enum checking 2016-04-20 08:04:06 -04:00
Brian Kelley
73d5f394b9 Fixes regression in python api CalcNumRotatableBonds 2016-04-19 21:52:08 -04:00
Paolo Tosco
6f8071f7a5 - Progress on Python wrappers 
- Some adjustments to the C++ API
 2016-04-19 20:53:39 +01:00
Paolo Tosco
5f86fb26e5 Merge remote-tracking branch 'upstream/master' into traj 2016-04-19 17:09:17 +01:00
Greg Landrum
c0f9be86c8 Get things building with gcc4.4 on centos6 
* Fixes exposing shared_ptr<const T> to python

* remove some of the pragmas for pre 4.5 versions of gcc

* get things working with centos6 and gcc4.4
 2016-04-17 11:48:35 -04:00
Paolo Tosco
249ae83694 - Implemented Trajectory::readGromos() and added relevant tests 2016-04-16 22:27:37 +01:00
Paolo Tosco
c05cf6da55 - removed debugging info 2016-04-16 20:43:29 +01:00
Paolo Tosco
a5de000c5c - fixed int/unsigned int 2016-04-16 20:41:40 +01:00
Paolo Tosco
b35538599f - Added AMBER trajectory reader and relevant tests 2016-04-16 20:28:45 +01:00
Greg Landrum
21cbc23783 remove debugging output 2016-04-15 15:10:42 +01:00
Greg Landrum
0ff9a758aa width is now right (at least much closer to it) 
height also looks good, but we still need a vertical shift if there is a subscript
 2016-04-15 15:09:19 +01:00