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AlternateValence_21Nov2012
Commit Graph

898 Commits

Author SHA1 Message Date
Greg Landrum
cdaaed4d56 sync back to trunk 2013-01-13 10:15:55 +00:00
Greg Landrum
2cbcfd8529 get windows build working 2013-01-13 03:49:54 +00:00
Greg Landrum
2a235f601c release notes update, build system tweak 2013-01-12 07:33:33 +00:00
Greg Landrum
fccbe02ce4 fix sf.net issue282 2013-01-11 03:39:33 +00:00
Greg Landrum
7610e1e6f5 additional help for sf.net issue 275 2013-01-10 05:10:40 +00:00
Greg Landrum
8890ecb792 initial fix and test for issue 281; 
this introduces some new shift/reduce warnings, so it is probably worth looking through
the parse in some detail again at some point to make sure there are not any hidden problems.
 2013-01-10 04:45:22 +00:00
Greg Landrum
e599ceca3c typo fix 2013-01-10 03:42:23 +00:00
Greg Landrum
052b87564c add one more test for issue 275 2013-01-09 13:12:27 +00:00
Greg Landrum
8ac59a261a continuation of cleanup from issue 279 [follow up from rev2355] 2013-01-09 04:11:15 +00:00
Greg Landrum
5e402f12ba fix possible overflow 2013-01-08 20:12:40 +00:00
Greg Landrum
7c9f658bb3 typo 2013-01-08 20:10:35 +00:00
Greg Landrum
73f8b2422c get the build working on the mac 2013-01-08 20:09:37 +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
e55d73fa57 fix and test sf.net issue 280. 2013-01-08 12:56:24 +00:00
Greg Landrum
b82a6b29a6 another swing at sf.net issue 279. This one is somewhat more efficient 2013-01-08 05:35:03 +00:00
Greg Landrum
772ef9199b fix and test sf.net issue 277; 2013-01-06 11:04:01 +00:00
Greg Landrum
4b69859f07 fix sf.net issue 276 2013-01-01 12:56:34 +00:00
Greg Landrum
586651341d docs fix 2012-12-31 11:57:43 +00:00
Greg Landrum
bae718e341 at this point all non-Python, non-Java tests pass 2012-12-26 12:23:19 +00:00
Greg Landrum
a4129c912a testChemTransforms works 2012-12-26 11:51:35 +00:00
Greg Landrum
6a7d998a8c graphmoltestPickler and MolOps test passing 2012-12-23 15:28:34 +00:00
Greg Landrum
f6b6af8a54 backup commmit 2012-12-23 07:48:16 +00:00
Greg Landrum
9bf1d492ed smaTest1 now passes 2012-12-23 06:26:20 +00:00
Greg Landrum
3ced784804 smiTest1 now passes 2012-12-23 06:14:56 +00:00
Greg Landrum
9965b3b0ef passes molops test; 
failing:
The following tests FAILED:
 16 - graphmoltestPickler (OTHER_FAULT)
 19 - smiTest1 (OTHER_FAULT)
 20 - smaTest1 (OTHER_FAULT)
 21 - fileParsersTest1 (OTHER_FAULT)
 25 - testMol2ToMol (OTHER_FAULT)
 28 - testChemTransforms (OTHER_FAULT)
 41 - testSLNParse (OTHER_FAULT)
 2012-12-23 06:06:15 +00:00
Greg Landrum
d0778ecb8c sync with trunk 2012-12-22 03:42:58 +00:00
Greg Landrum
68e370d581 initial pass at a fix for sf.net issu275 2012-12-18 17:16:06 +00:00
Greg Landrum
bef74c1c81 initial support for reading query files. Python wrapper still needs to be done. 2012-12-17 10:28:35 +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
Greg Landrum
14314b01ad add cmake configure variable to make multi-threaded stuff optional 2012-12-17 04:07:20 +00:00
Greg Landrum
f390b35580 sync back to trunk 2012-12-16 04:36:50 +00:00
Greg Landrum
50bc499c20 fix for sf.net bug 274 2012-12-15 03:29:03 +00:00
Greg Landrum
b6a26aca44 fix and test sf.net issue273 2012-12-12 09:10:05 +00:00
Greg Landrum
5324c9c783 fix and test sf.net issue 272 2012-12-12 04:39:55 +00:00
Greg Landrum
a5baf0239b more on the locale problem; this still needs testing on non-linux 2012-12-12 04:20:14 +00:00
Greg Landrum
3f6d82a4d1 start to take a swing at the locale problem; this still needs testing on non-linux 2012-12-12 03:24:54 +00:00
Greg Landrum
e145175047 remove getNumExplicitHs; change getTotalNumHs 2012-12-08 07:05:00 +00:00
Greg Landrum
ce083b7ec0 sync with trunk 2012-12-08 06:07:59 +00:00
Greg Landrum
df3f6e9d39 backup commit; not actually working yet 2012-12-08 06:06:53 +00:00
Greg Landrum
7f888bd6b0 remove some compiler warnings; patch from Roger S 2012-12-08 03:48:41 +00:00
Greg Landrum
2c591cced6 sync with trunk 2012-12-04 17:08:38 +00:00
Greg Landrum
0c635ea239 add a couple extra rings and fix a typo 2012-12-04 10:54:44 +00:00
Greg Landrum
96760b37de fix and test sf.net issue 270 2012-12-04 07:13:08 +00:00
Greg Landrum
175338d061 fix sf.net issue261: add isotope information to debugMol() 2012-12-04 05:40:55 +00:00
Greg Landrum
36981090e3 move the cairo drawing stuff in as well 2012-12-04 05:11:34 +00:00
Greg Landrum
560b994c7a fix triple bonds and the extra dashed line drawn in double bonds 2012-12-04 04:58:44 +00:00
Greg Landrum
ee28352889 move the svg drawing code into GraphMol too 2012-12-03 16:03:02 +00:00
Greg Landrum
2c3d7eb2f2 re-enable tests 2012-12-03 08:44:29 +00:00
Greg Landrum
38c5149c3e move c++ drawing code from Demo to GraphMol 2012-12-03 04:40:33 +00:00
Greg Landrum
01afbca87b add ClearProp() method to atoms and bonds; modify Mol.ClearProp() so that it no longer raises an exception when the property is not there 2012-12-01 06:28:00 +00:00