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61 Commits

Author SHA1 Message Date
Greg Landrum
05840816cd Add Rogot Goldberg and AllBit similarity to C++ and the python wrapper. 
(contribution from Sereina Riniker)
 2013-01-08 15:10:51 +00:00
Greg Landrum
72efd4a58b support a somewhat more consistent API for size/value info across the data types; 
add DataStructs.ConvertToNumpyArray function;
 2012-12-03 08:41:53 +00:00
Greg Landrum
dc60eb0c47 add another test 2012-01-10 04:08:58 +00:00
Greg Landrum
0086f88100 additional consistency checking 2012-01-10 04:04:07 +00:00
Greg Landrum
b6300a86fe support bit vects <-> byte strings 2012-01-08 06:12:47 +00:00
Greg Landrum
29312e73e1 minor updates 2012-01-03 07:50:53 +00:00
Greg Landrum
05bc49c452 support initializing from FPS text as well as creating it; add some tests 2011-12-20 05:24:06 +00:00
Greg Landrum
a574c1f017 add support for generating FPS-style hex strings 2011-12-18 14:20:00 +00:00
Greg Landrum
cc45e65939 further clang cleanups 2011-05-27 03:29:56 +00:00
Greg Landrum
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
b993f89afe remove the bjam-based build system 2010-09-27 03:54:07 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
052ec66542 cleanups: 
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
 2010-09-08 04:25:57 +00:00
Greg Landrum
20096c76a9 refactoring of the BitVect interface to make capitalization consistent 
w/ the rest of the RDKit. i.e.: SetNumBits -> setNumBits
 2010-05-30 15:15:46 +00:00
Greg Landrum
f49a9dbe66 documentation update 2010-01-25 07:00:16 +00:00
Greg Landrum
9727cffa61 make python wrappers and tests optional 2010-01-22 11:22:58 +00:00
Greg Landrum
c346a41951 get the tests working on windows. 2010-01-19 06:34:58 +00:00
Greg Landrum
76297b0fff builds and passes tests on linux 2009-09-28 11:02:18 +00:00
Greg Landrum
9cabf87374 remove vflib from Jamfiles 
remove const specifiers from return values in DataStructs
add initial pass at query-query matching for Atoms and Bonds
fix and test for sf.net issu 2738320
add Mol.AddRecursiveQuery() method to Mol
 2009-06-29 11:47:38 +00:00
Greg Landrum
1480eccb87 expose tanimoto similarity on SparseIntVects 2009-06-19 04:19:45 +00:00
Greg Landrum
423433a3e4 support Tversky similarity for SparseIntVects 2009-06-18 14:37:03 +00:00
Greg Landrum
f0b288cfed big changes again (repeat the 979, 980 disaster on the correct branch) 2009-02-04 20:13:44 +00:00
Greg Landrum
8bf7a4c187 now all tests pass here as well 2009-02-03 05:26:10 +00:00
Greg Landrum
b50e69b171 bad argument removed 2009-01-05 05:02:21 +00:00
Greg Landrum
2580fbaaa2 this is probably a ways from done, but now at least we can run bjam under mingw without it immediately erroring out 2008-11-15 17:14:13 +00:00
Greg Landrum
299689095a operator== and operator!= should be const; support unsigned SparseIntVects as well 2008-07-28 03:40:30 +00:00
Greg Landrum
ba8454586b initial version of Tversky similarity (feature request 2015633) along with a bit of refactoring 
http://sourceforge.net/tracker/index.php?func=detail&aid=2015633&group_id=160139&atid=814653
 2008-07-11 11:13:03 +00:00
Greg Landrum
887cab543e not done with this change yet, but need to change machines 2008-07-09 05:59:47 +00:00
Greg Landrum
79b8a77f93 get rid of those irritating POSIX_C_SOURCE warnings 2008-07-08 06:59:59 +00:00
Greg Landrum
a3e6cb057e this is a mass of cleanup stuff; mostly line endings 2008-07-07 13:21:24 +00:00
Greg Landrum
ac5a7d72c7 these are no longer needed 2008-07-07 06:36:34 +00:00
Greg Landrum
940a9733b9 add operator== and operator!= to BitVects 2008-06-16 07:09:13 +00:00
Greg Landrum
029e08d6b4 merge in the changes from the 64 bit port branch r703:717 2008-06-11 05:01:17 +00:00
Greg Landrum
a6c1a64d1a remove some compiler warnings 
rearrange the argument ordering for the Dice similarity stuff so 
that it can be invoked the same as the other similarity metrics.
 2008-04-24 19:03:34 +00:00
Greg Landrum
213c2323bd add returnDistances support to the SparseIntVects too 2008-04-24 12:06:29 +00:00
Greg Landrum
10faff5964 add "distance" support; some code cleanup 2008-04-24 09:04:50 +00:00
Greg Landrum
2fdfc3b9e4 - speed up Dice similarity between SparseIntVects (a lot) 
- add bulk Dice similarity for SIVs to wrapper
- speed up bulk Dice similarity for bit vects
- test a bit more
 2008-04-15 05:19:48 +00:00
Greg Landrum
9bb88cb2cf - speed up Dice similarity between SparseIntVects (a lot) 
- add bulk Dice similarity for SIVs to wrapper
- speed up bulk Dice similarity for bit vects
- test a bit more
 2008-04-15 05:18:52 +00:00
Greg Landrum
26a4124ad9 remove files for old build system 2008-02-20 17:06:59 +00:00
Greg Landrum
430a83bd96 merge in the jamfiles from the bjam branch; 
various and sundry minor code cleanups;
this probably does not yet build on windows... that is next
 2007-11-23 15:55:30 +00:00
Greg Landrum
3299bb7eaa move the SimilarityWrapper func out of the python wrapper and into the main c++ interface... it is of general interest 2007-10-25 04:25:18 +00:00
Greg Landrum
93834a90bd remove support for the useAbs function; 
add bounds support on the dice metric
 2007-10-05 15:35:11 +00:00
Greg Landrum
0ab0653c18 move DiceSimilarity code into c++ 2007-10-04 03:34:06 +00:00
Greg Landrum
67f7dab587 fix a problem with __len__ in python (can't do it if we return a Long); 
wrap GetLength() instead;
add getNonzeroElements()
 2007-09-28 03:45:03 +00:00
Greg Landrum
7726cb9d8a getting close to right here; still needs windows testing 2007-09-23 06:54:37 +00:00
Greg Landrum
1fa8cd321b add SparseIntVect in both c++ and Python 
This still needs windows testing.
 2007-09-22 18:49:37 +00:00
Greg Landrum
47d47a49d3 remove vestiges of old windows build system 2007-07-31 17:09:53 +00:00
Greg Landrum
8b3de2e02e Fix and test sf.net bug 1719831 (http://sourceforge.net/tracker/index.php?func=detail&aid=1719831&group_id=160139&atid=814650) 
Cleanup similar issues in UniformGrid3D

MolOps.cpp: docs patch
 2007-05-16 08:14:44 +00:00
Greg Landrum
0951bb0a87 acceleration for bulk fingerprint comparisons; 
this should have been checked in a while ago
 2007-05-16 03:30:28 +00:00
Greg Landrum
e9e865d33f some rather embarassing typos preventing a linux build were fixed 2007-04-24 17:50:18 +00:00