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Commit Graph

113 Commits

Author SHA1 Message Date
Nadine Schneider
d3f9d7c6e1 RDKFingerprint: add an unfolded count-based version of the RDKFingerprint 
- add a bitinfo map to the RDKFingerprint
- refactor some code to largely avoid code duplicates
 2016-04-01 09:10:47 +02:00
Greg Landrum
f595f891f6 rename rdk_unique_ptr to rdk_auto_ptr 
add C++11 compatibility
 2016-02-13 14:58:35 +01:00
Greg Landrum
44c85749c9 get rdmolops building 2016-02-13 08:07:58 +01:00
Greg Landrum
4f2aa0f51e Fixes #758 2016-02-08 16:11:22 +01:00
Greg Landrum
79e1f8b1fa compiles without numpy warnings, all tests pass on ubuntu 15.04 with numpy 1.10 2015-11-28 06:49:34 +01:00
Greg Landrum
e08e0d16d8 first pass, using google style 2015-11-14 14:58:11 +01:00
Greg Landrum
e37296d7c7 post review 2015-11-14 08:08:14 +01:00
Brian Kelley
fbf9225172 Fixes more unused parameters 2015-10-18 16:07:57 -04:00
Brian Kelley
daa7e62258 Fixes signed conversion issues (use rdcast) 2015-10-18 15:16:38 -04:00
Brian Kelley
5f59333a56 Silences unused parameters 2015-10-18 14:02:29 -04:00
Brian Kelley
403a3d6b7c Suppresses Boost warnings 2015-10-18 13:41:03 -04:00
Greg Landrum
a743cff4d7 Fixes #573 2015-09-20 04:44:39 +02:00
Greg Landrum
0ed27ca9d4 add python docstrings 2015-08-22 07:51:13 +02:00
Greg Landrum
8596c6f9ad add support for converting dummies to queries 2015-08-22 05:43:42 +02:00
Brian Kelley
020a9a8f36 Change merge_unmappped_only to more consistent mergeUnmappedOnly 2015-04-26 09:03:28 -04:00
Brian Kelley
61dd0b16a5 Add merge_unmapped_only option to MergeQueryHs 
By default all atoms are merged, however when
this flag is true, any mapped atom will convert
explicit Hs to implicit.  This is due to not
wanting to convert mapped hydrogens taking
part in reactions.
 2015-04-23 09:54:23 -04:00
Greg Landrum
33d538242d switch GetShortestPath() to return a tuple instead of a list 2015-04-22 05:58:21 +02:00
Greg Landrum
63ceb09714 add range checking to the new GetShortestPath() 2015-04-22 05:51:17 +02:00
Paolo Tosco
a9c7a08467 - added a Python wrapper for getShortestPath() 
- added a relevant test to Code/GraphMol/Wrap/rough_test.py
 2015-04-22 00:39:09 +01:00
Greg Landrum
c1704daccd support supplying highlight radii 2015-03-04 07:21:03 +01:00
Greg Landrum
051ff124bb attend to the atom circling and line width multiplier arguments from python 2015-02-08 06:17:10 +01:00
Greg Landrum
f73307270b support confIds in drawing 2015-02-08 06:16:31 +01:00
Greg Landrum
7fa02f748b Fixes #430 2015-02-04 13:45:47 +01:00
Greg Landrum
c41ffea23b add full argument set to removeHs python wrapper 2015-01-30 07:20:06 +01:00
Greg Landrum
6dabc2b42f Replace the SVG generator exposed to python with the new one 2015-01-15 05:08:43 +01:00
Greg Landrum
4db5fcef52 initial pass at #163 2014-12-19 13:48:51 +01:00
Greg Landrum
69be35684f reorder the results for that cutsPerAtom case 2014-11-26 07:50:42 +01:00
Greg Landrum
3f23c91eba did not have the version for breakSomeBonds() quite right 2014-11-22 10:42:17 +01:00
Greg Landrum
1725e22cca allow tracking the number of cuts made by the fragmentation code on a per-atom basis 2014-11-22 07:57:39 +01:00
Greg Landrum
e6574531b7 update a couple docstrings 2014-10-26 05:18:32 +01:00
Greg Landrum
288feb7a8a support partial fragmentation on bonds; 
Fixes #288
 2014-07-02 05:47:02 +02:00
Greg Landrum
e4cfc340a4 support white and black lists for getMolFragsWithQuery 2014-03-25 08:18:30 -04:00
Greg Landrum
196c2278fb Fixes #234 2014-03-17 08:33:07 +01:00
Greg Landrum
9f4471f872 more on #204 
A few other cleanups
 2014-02-06 06:43:28 +01:00
Greg Landrum
d7971cc40c Fixes #171 2013-12-06 06:54:31 +01:00
Greg Landrum
8503b49b75 add MolOps::get3DDistanceMat() 2013-12-01 07:57:20 +01:00
Greg Landrum
b60b26039c add bondTypes and associated tests for FragmentOnBonds() 2013-11-02 07:54:10 +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
73657cd33f add to python wrapper 2013-10-27 14:42:57 +01:00
Greg Landrum
2e1bb83ea0 add in-place form of mergeQueryHs() 2013-10-04 08:56:38 +02:00
Greg Landrum
6a6205cf9e Fixes #39 2013-06-02 06:18:43 +02:00
Greg Landrum
5b67e9c3e0 rename layered fingerprint2 -> pattern fingerprint 
rearrange fingerprint code a bit
 2013-03-28 09:44:33 +00:00
Greg Landrum
286d414b66 remove unused arguments for LayeredFingerprintMol 2013-03-28 03:56:00 +00:00
Sereina Riniker
589aad4fa2 update MolOps.cpp for older boost version 2013-03-27 12:44:04 +00:00
Greg Landrum
c96bb8dca2 forgot to remove a debug print 2013-03-12 04:40:50 +00:00
Greg Landrum
d1cae9346f an initial version of the "atomBits" feature for RDKit fingerprints 2013-03-12 04:39:43 +00:00
Greg Landrum
a304cbab16 expose fragmentOnBRICS bonds to python 2013-01-31 04:55:05 +00:00
Greg Landrum
03ef0e6f1b Add support for merging recursive queries on the C++ side 
(contribution from Sereina Riniker)

A pure Python version of this was in the tutorial material from the RDKit UGM.
 2013-01-08 15:13:01 +00:00
Greg Landrum
57572918de add initial support for addRecursiveQueries to ChemTransforms. 
active and tested in C++ and python, in the SWIG wrapper but untested.
still needs linux and windows builds.
 2012-12-17 09:06:02 +00:00