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ValenceShift_6Aug2013
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1600 Commits

Author SHA1 Message Date
Greg Landrum
cc4a8e12ea passing all tests 2013-11-12 07:21:34 +01:00
Greg Landrum
deabce8146 sync with master 2013-11-12 04:32:03 +01:00
Greg Landrum
970e939523 Merge branch 'master' of github.com:rdkit/rdkit 2013-11-10 07:29:36 +01:00
Greg Landrum
6dd83d03f6 Fixes #151 2013-11-10 06:50:10 +01:00
Greg Landrum
00d350c000 Fixes #151 2013-11-10 06:07:49 +01:00
Greg Landrum
6c354852d1 small cleanups 2013-11-07 10:57:18 +01:00
Greg Landrum
38ca41c8ab remove another clang warning 
this also fixes a bug with topological torsions and client-provided invariants
 2013-11-06 05:03:07 +01:00
Greg Landrum
a92b7bd3c4 fix a clang compiler warning 2013-11-06 04:50:24 +01:00
Greg Landrum
3fec9346f5 Fixes #144 2013-11-05 05:17:29 +01:00
Greg Landrum
4bc59b863f aded swig output dir 2013-11-03 13:05:51 +01:00
Greg Landrum
b60b26039c add bondTypes and associated tests for FragmentOnBonds() 2013-11-02 07:54:10 +01:00
Greg Landrum
6d936e9d31 Merge branch 'master' of https://github.com/rdkit/rdkit 2013-11-02 07:23:31 +01:00
Greg Landrum
95c6c7f261 fragmentOnBonds() fix 2013-11-02 07:17:42 +01:00
Greg Landrum
85667c0fd6 Merge branch 'issue141' 2013-10-30 05:29:28 +01:00
Greg Landrum
05b3c95473 add docs 2013-10-30 05:25:38 +01:00
Greg Landrum
afb9f1ddfa add fragmentOnBonds() to python API 
Fixes #142
 2013-10-30 04:59:29 +01:00
Greg Landrum
b072fc4b42 Fixes #141 2013-10-29 05:57:10 +01:00
Greg Landrum
73657cd33f add to python wrapper 2013-10-27 14:42:57 +01:00
Greg Landrum
395608ffc6 add MolOps::renumberAtoms() 2013-10-27 14:19:28 +01:00
Greg Landrum
6d1231ae95 remove a debugging output 2013-10-25 05:02:41 +02:00
Greg Landrum
1501af51a5 PDB reader/writer fixes; 
add MolToMolFile() to python API
 2013-10-25 05:02:09 +02:00
Greg Landrum
7c4ead6d10 small changes in java wrappers 2013-10-23 08:09:18 +02:00
Greg Landrum
fd1bdd395f cartridge version bump 2013-10-22 06:10:04 +02:00
Greg Landrum
ca4b695152 remove the pdb_test dir 2013-10-22 05:48:49 +02:00
Greg Landrum
158c9b9e45 Fixes #136 2013-10-21 05:55:42 +02:00
Greg Landrum
fe92ada122 the mol writer should take const mols 2013-10-18 14:44:31 +01:00
Greg Landrum
cdd096a616 fix a bad test filename 2013-10-18 01:31:46 -07:00
Greg Landrum
c1836ae28a modify the monomer info interface so that it works with older boost versions 2013-10-17 23:00:26 -07:00
Greg Landrum
da9de0b520 Fixes #103 2013-10-18 05:41:02 +02:00
Greg Landrum
99f90961d7 more help for gcc 4.1 2013-10-17 04:05:14 +02:00
Greg Landrum
eba9bf60bf help older versions of g++ compile this 2013-10-17 03:56:49 +02:00
Greg Landrum
62efc6ab42 Fixes #133 2013-10-17 02:51:39 +02:00
Greg Landrum
0639f0c3d4 Merge branch 'PDB_29September2013' 2013-10-16 05:35:12 +02:00
Greg Landrum
9c7369b8a4 some cleanup 2013-10-16 03:40:34 +02:00
ptosco
865175104b - added getters/setters for bond lengths, angles, dihedrals 
in the MolTransforms namespace:

  * getBondLength(conf, iAtomId, jAtomId)
                 (only in this case, atoms need not be covalently bonded)
  * setBondLength(conf, iAtomId, jAtomId, value)
  * getAngleRad(conf, iAtomId, jAtomId, kAtomId)
  * setAngleRad(conf, iAtomId, jAtomId, kAtomId, value)
  * getAngleDeg(conf, iAtomId, jAtomId, kAtomId)
  * setAngleDeg(conf, iAtomId, jAtomId, kAtomId, value)
  * getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
  * getDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId)
  * setDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)

- added the corresponding Python wrappers in rdMolTransforms
  (same prototype as C++; as usual all Python methods
  have an uppercase initial)

- added relevant C++/Python tests
 2013-10-15 11:59:08 +02:00
Greg Landrum
d5fac5501b add basic support for O3A to Java wrapper 2013-10-12 16:54:49 +02:00
Greg Landrum
40908a43da mmff into SWIG wrapper. first tests 
note: these changes remove some direct ff-manipulation functionality that was
present previously
 2013-10-12 16:24:18 +02:00
Greg Landrum
64d389c517 fix a bunch of include guards 2013-10-12 16:06:21 +02:00
Greg Landrum
31e310cd3a merge an O3A patch from Paolo T. 2013-10-12 06:35:21 +02:00
Greg Landrum
d7c5d7a4ea basic pdb testing in python 2013-10-11 18:13:24 +02:00
Greg Landrum
21393521a3 first java wrappers of pdb stuff 2013-10-11 18:06:09 +02:00
Greg Landrum
e0e741bd49 very minimal testing of pdb reading/writing 2013-10-11 16:58:20 +02:00
Greg Landrum
5ce9c06d68 initial pass at adding pdb support into the swig wrappers 2013-10-11 05:51:01 +02:00
Greg Landrum
cee480b1e6 add MolToPDBFile() 2013-10-11 05:50:18 +02:00
Greg Landrum
03df082c42 copyright cleanup 2013-10-11 05:28:45 +02:00
Greg Landrum
6736192f7e a couple of small vector modifications 2013-10-08 13:38:47 +02:00
Greg Landrum
1acae67cba Merge branch 'master' into PDB_29September2013 2013-10-08 05:51:57 +02:00
Greg Landrum
0726c3ea9d changes suggested by Roger S: 
add residueNumber
serialNumber -> int
add segmentNumber
 2013-10-08 05:49:54 +02:00
Greg Landrum
3fd5df8a22 remove USR references from SWIG wrappers 2013-10-08 05:48:40 +02:00
ptosco
d402867610 - fixed a bug in the MMFF stretch-bend gradient calculation 
- put in better evidence the extents of the UFF hack so that it can be
  easily commented out if required
 2013-10-07 17:53:20 +02:00