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241 Commits

Author SHA1 Message Date
Greg Landrum
924fc373ef Fixes #165 2013-12-31 07:52:08 +01:00
Greg Landrum
12ecae962e merge 2013-12-07 10:51:19 +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
0f92877061 stop messing up aromaticity and hybridization; 
all tests pass, but this is definitely not the most efficient thing.
 2013-11-30 08:07:09 +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
1acae67cba Merge branch 'master' into PDB_29September2013 2013-10-08 05:51:57 +02:00
Greg Landrum
f629c1ea6d Fixes #116 2013-10-06 07:49:54 +02:00
Greg Landrum
2e1bb83ea0 add in-place form of mergeQueryHs() 2013-10-04 08:56:38 +02:00
Greg Landrum
c95d57aa54 add in-place form of addHs() 2013-10-04 07:58:53 +02:00
Greg Landrum
937ee9f60a add in-place form of removeHs() 2013-10-04 07:19:01 +02:00
ptosco
ec8eb5a1bf - Changed all occurrences of RDKit::PI into M_PI 
- added #ifdef M_PI (...) #endif in all relevant places
- made length() and sqLength() method consistent
  with respect to usage of pow(x, 2) vs x*x in
  Code/Geometry/point.h
- removed gzip-related boost.iostreams dependency and
  replaced with portable "cmake -E tar xzf" command
  in Code/ForceField/MMFF/CMakeLists.txt
 2013-09-20 17:45:41 +02:00
Greg Landrum
86b9e6b089 Fixes #72 2013-08-25 06:36:10 +02:00
Greg Landrum
0091417965 Fix #65 2013-07-09 14:54:32 +02:00
Greg Landrum
2cde2aae9f remove premature commit 2013-07-09 07:23:25 +02:00
Greg Landrum
6157ec6547 Fix #64 2013-07-09 07:19:24 +02:00
Greg Landrum
61f333db07 a couple copyright cleanups 2013-07-04 09:21:03 +02:00
Greg Landrum
6bc9a88b8b this was broken by the fix for #42 2013-07-04 08:19:57 +02:00
Greg Landrum
c53196e068 Fixes #42 2013-06-05 05:44:03 +02:00
Greg Landrum
0b45f3c320 fix GitHub issue 8 
This breaks the InChI python unit tests, so those need to be cleaned up.
 2013-03-01 06:54:33 +00:00
Greg Landrum
50bc499c20 fix for sf.net bug 274 2012-12-15 03:29:03 +00:00
Greg Landrum
5324c9c783 fix and test sf.net issue 272 2012-12-12 04:39:55 +00:00
Greg Landrum
294cb24de4 fix and test issue 266 2012-11-17 07:39:39 +00:00
Greg Landrum
8d9fd053b2 fix and test issue 256; 
this is a change that affects backwards compatibility.
 2012-10-08 03:18:05 +00:00
Greg Landrum
6555d2062f more changes connected to sf.net issue 249 2012-09-16 05:40:17 +00:00
Greg Landrum
b67dd0f437 another bit of fixing sf.net issue 249 2012-09-01 04:06:02 +00:00
Greg Landrum
2d7315e8d4 fix and test sf.net issue 249 2012-08-30 05:45:59 +00:00
Greg Landrum
b5d1ad394e accelerate FastFindRings 2012-08-29 02:28:03 +00:00
Greg Landrum
14e396c26d refactoring the SMILES parser to make it more efficient 
NOTE: this changes the ordering of bonds in molecules with branches.
 2012-08-28 04:01:49 +00:00
Greg Landrum
f5eb640766 fix and test Issue3549146 2012-07-26 14:34:35 +00:00
Greg Landrum
8690fb99b9 add a test for issue 3526831 (already fixed) 2012-07-02 03:16:15 +00:00
Greg Landrum
ebfe1b1ec8 add a test for issue 3528556 (already fixed) 2012-07-02 03:12:56 +00:00
Greg Landrum
2785c7a251 update expected canonical smiles 2012-06-28 11:21:45 +00:00
Greg Landrum
6157345dde this version passes the ZINC natural-products torture test 2012-06-28 06:45:42 +00:00
Greg Landrum
0f3b84cd28 backup commit; we are not quite there yet 2012-06-26 06:15:08 +00:00
Greg Landrum
ee43d3e8f8 another step forward 2012-06-13 05:20:39 +00:00
Greg Landrum
a3dc23c43c more canonicalization improvements 
there are still some problems with double bonds
 2012-06-11 03:21:30 +00:00
Greg Landrum
0085012701 fix and test issue 3525076 2012-05-10 05:35:20 +00:00
Greg Landrum
5d48f52545 a quick optimization of the stereochemistry code 
(thanks to Roger Sayle for the suggestion
 2012-03-27 10:27:18 +00:00
Greg Landrum
e38ef02346 initial pass at changing atom-atom matching behavior; 
fix for issue 3495370
 2012-03-02 07:20:16 +00:00
Greg Landrum
bb4acb5495 merge with the trunk rev1977 2012-02-26 19:19:16 +00:00
Greg Landrum
7ba9571e3c further refinements 2012-02-26 08:47:14 +00:00
Greg Landrum
813f4863ed fix and test Issue 3480481 2012-02-18 05:34:34 +00:00
Greg Landrum
fe071d1aa5 fix and test issue 3487473 2012-02-14 17:58:04 +00:00
Greg Landrum
3eeb1bf30c initial version of a DFS-based ring finder 2012-01-02 15:34:43 +00:00
Greg Landrum
b434870824 tests for the already fixed issue 3415206 2011-09-29 03:59:31 +00:00
Greg Landrum
164a9b19c8 update the way query Hs are merged 2011-09-28 05:24:38 +00:00
Greg Landrum
dad3885839 fix and test sf.net issue 3349243 2011-07-02 04:25:59 +00:00