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SimilarityMapsInCPP_Jan2014
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1170 Commits

Author SHA1 Message Date
Greg Landrum
acb9de553a svg generation bug fixes 2014-01-06 05:46:28 +01:00
Greg Landrum
ce60df22c0 get svg working as well 2014-01-06 04:58:07 +01:00
Greg Landrum
298e637a23 backup 2014-01-05 11:21:29 +01:00
Greg Landrum
63f1f4d752 update .cmake files corresponding to flex/bison source changes 2014-01-04 16:49:14 +01:00
Greg Landrum
fb4910b9fa cleanup a residual declaration so that the java builds work again 2014-01-02 07:33:06 +01:00
Greg Landrum
bf313e683f cleanup the AddFragToMol() code a bit to support multiple bookmarked atoms 2014-01-01 18:12:49 +01:00
Greg Landrum
11af614ebc more cleanups of this stuff 2014-01-01 17:35:35 +01:00
Greg Landrum
64366007e1 more C++ style cleanups 2014-01-01 17:16:25 +01:00
Greg Landrum
03b333734e some C++ style cleanups 2014-01-01 16:50:09 +01:00
Greg Landrum
7eca2ead35 Fixes #149 2014-01-01 09:24:06 +01:00
Greg Landrum
3f90cecd9c Fixes #164 2013-12-31 08:27:09 +01:00
Greg Landrum
924fc373ef Fixes #165 2013-12-31 07:52:08 +01:00
Greg Landrum
47afcc1f53 remove some debugging printing 2013-12-31 07:12:40 +01:00
Greg Landrum
0a421d8aa5 Fixes #182 2013-12-31 07:11:31 +01:00
Greg Landrum
6dbd804121 clean up the way the unicode strings are handled and broaden suport a bit 2013-12-30 16:11:09 +01:00
Greg Landrum
e7ad13929b Fixes #179 
could be more elegant, but works for MolFromSmiles and MolFromSmarts
 2013-12-30 09:02:43 +01:00
Greg Landrum
ab35e4e08f fix typos 2013-12-20 05:30:04 +01:00
Greg Landrum
74ee2d5614 more query atom expansions for Issue #183 2013-12-19 05:33:17 +01:00
Greg Landrum
d779c850c9 further stereochemistry speedupb 2013-12-18 05:12:32 +01:00
Greg Landrum
4d47482f0f speed-up the stereochemistry cleanup 2013-12-18 04:59:30 +01:00
Greg Landrum
819272f375 initial batch of decent QueryAtom support for python; 
Fixes #181
 2013-12-17 05:55:18 +01:00
Greg Landrum
8076fefc17 add MatchingAtomIterator to C++ 2013-12-16 05:24:19 +01:00
Greg Landrum
4520ee1263 more progress towards #181; the problem now is that there is 
not really anyway to build a query atom from python
 2013-12-16 05:24:04 +01:00
Greg Landrum
aef75dced2 Progress towards #181 2013-12-14 15:45:45 +01:00
Greg Landrum
ccd08d353f Fixes #180 2013-12-14 10:41:35 +01:00
Greg Landrum
932d6606d5 typo fix 2013-12-14 10:41:25 +01:00
Greg Landrum
53e37810ba initial tests 2013-12-14 10:17:49 +01:00
Greg Landrum
36ec3ff809 move towards more flexible queries 2013-12-14 09:59:12 +01:00
Greg Landrum
2cbc96aec2 laying the groundwork for more generic atomic query functions 2013-12-14 09:32:12 +01:00
Greg Landrum
b45423be3e rename makeAtomNumEqualsQuery() to makeAtomNumQuery() 2013-12-14 09:14:57 +01:00
Greg Landrum
297f5d7877 minor optimization of chirality determination 2013-12-14 08:30:57 +01:00
Greg Landrum
a3a13a4173 docs clarification 
fix a typo with image size in MolsToGridImage
 2013-12-13 05:00:50 +01:00
Greg Landrum
9dca8636b7 Fixes #175 2013-12-07 08:26:58 +01:00
Greg Landrum
9d683b8401 remove debugs 2013-12-07 07:55:18 +01:00
Greg Landrum
7a586e9391 further robustification of the computed properties 2013-12-07 07:24:22 +01:00
Greg Landrum
c91b5b5ee1 Fixes #176 2013-12-07 03:18:40 +01:00
Greg Landrum
d7971cc40c Fixes #171 2013-12-06 06:54:31 +01:00
Greg Landrum
b8b5263fc3 update data 2013-12-06 05:10:51 +01:00
Greg Landrum
64f01f7506 sync with master 2013-12-06 03:56:07 +01:00
ptosco
170c88ae03 - the RMSD value returned by O3A::align() and O3A::trans() is now 
computed in the usual way, while previously the value computed
  by MolAlign::AlignMol(), which incorporates weights, was returned
- the C++ and Python test results were updated accordingly
 2013-12-04 23:18:21 +01:00
Greg Landrum
e3b7aa74d2 support providing a distance matrix to the O3A ctor 2013-12-04 15:22:15 +01:00
Greg Landrum
eec7c1c089 make sure there is ring info available 2013-12-03 04:12:46 +01:00
Greg Landrum
53ea3259c9 small SSS optimization 2013-12-02 06:21:32 +01:00
Greg Landrum
68b599c264 remove more clang warnings 2013-12-02 05:24:10 +01:00
Greg Landrum
4ace62f019 remove more clang warnings 2013-12-02 05:10:23 +01:00
Greg Landrum
60a68669da remove more clang warnings 2013-12-02 04:46:46 +01:00
Greg Landrum
18e251dda6 remove more extraneous preconditions 2013-12-02 04:15:43 +01:00
Greg Landrum
b25aaddfd5 clean up bug from that last fix; modify the distance histogram 
code so that it takes the distance matrix in the ctor
 2013-12-01 10:09:19 +01:00
Greg Landrum
65e72deb5c Merge branch 'master' of github.com:rdkit/rdkit 2013-12-01 08:07:15 +01:00
Greg Landrum
8503b49b75 add MolOps::get3DDistanceMat() 2013-12-01 07:57:20 +01:00