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40 Commits

Author SHA1 Message Date
Greg Landrum
f3d06ac331 refactor a bit to make this more logical 2012-03-26 03:08:02 +00:00
Greg Landrum
2bb34056dd first pass at adding support for atom invariants in the rdkit, atom-pairs, and topological torsions fingerprints 2012-03-25 12:58:42 +00:00
Greg Landrum
c0f07b6f10 change the semantics of the count-simulation in atom pair and topological torsion fps 2011-12-18 14:19:15 +00:00
Greg Landrum
6b78d8484a add an amide bond count calculator; add molecular formula calculator; add alternate method for converting torsion and atom-pair fps to bit vects 2011-12-16 04:17:28 +00:00
Greg Landrum
60c03f3725 fix and test sf.net issue 3441641 2011-11-24 03:37:22 +00:00
Greg Landrum
dac565e485 add the ability to ignore atoms in the TT and AP fingerprints 2011-06-15 03:20:10 +00:00
Greg Landrum
37c342046a add isotopic mass information; add molecular formula calculation; add isotopic mass calculator; expose additional descriptors to java 2011-04-18 10:11:09 +00:00
Greg Landrum
6fa65fbc68 move the _VSA descriptors into C++ 2011-03-21 05:02:12 +00:00
Greg Landrum
498eb1ef63 back out some of the changes from rev1663. 
we are no longer templating the descriptor functions and have moved the calculation
of the pattern matchers into statics inside the functions themselves.
This solves a crashing problem with the cartridge on the mac.
 2011-03-16 04:39:07 +00:00
Greg Landrum
aca2fc18f8 move the lipinski defns into the header file 2011-03-15 07:51:35 +00:00
Greg Landrum
4325789d25 move lipinski descriptors to C++. 
rename CalcCrippenDescriptors -> calcCrippenDescriptors
 2011-03-14 10:24:42 +00:00
Greg Landrum
456e68456b move PSA into C++ 2011-03-12 07:00:48 +00:00
Greg Landrum
28747ea745 checkin some fragment and fingerprint changes. these are not yet well tested 2011-01-14 06:24:03 +00:00
Greg Landrum
8b62f880d0 make getting the fcfp-like descriptors from python easier 2010-12-15 05:19:47 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
ff7d14f692 include ring-membership by default in the morgan fps 2010-09-15 05:59:27 +00:00
Greg Landrum
514b59e12f remove duped function 2010-09-07 05:02:37 +00:00
Greg Landrum
6e31713dd9 correct handling of chirality and make it optional (now by default disabled); 
allow bond order to be ignored
 2010-09-04 05:54:27 +00:00
Greg Landrum
a25f17a45c add fcfp-like invariants for the morgan fingerprinter 2010-09-02 06:00:17 +00:00
Greg Landrum
04dc23247e add additional forms of the morgan, atom-pair, and topological torsion fps 2010-07-02 04:17:21 +00:00
Greg Landrum
7d690ef390 add a bit more morgan functionality 2010-06-21 04:29:28 +00:00
Greg Landrum
7d5a9f75ff move the AtomPair and TopologicalTorsion fingerprint code into the Fingerprints directory 2010-06-20 06:15:37 +00:00
Greg Landrum
ec6841970a expose connectivity invariants to python 2010-05-12 04:19:21 +00:00
Greg Landrum
27bcbc105c rework the way version names are exposed to python to replace leading and trailing __s with a single leading _ 2010-01-27 05:01:58 +00:00
Greg Landrum
a70e794a5c fix required for python2.6 with msvc-8.0 2009-10-17 08:32:54 +00:00
Greg Landrum
9a2952373f modify hashed atom-pair fingerprints to return SparseIntVects instead of BitVects 
add minLength and maxLength option for atom pairs
add hashed topological torsions.
 2009-06-04 05:50:08 +00:00
Greg Landrum
812325431a error check max lengths in topological torsions 2009-06-03 13:26:14 +00:00
Greg Landrum
5f24388119 rename argument to "fromAtoms" 2009-03-20 05:59:16 +00:00
Greg Landrum
7f190d58b6 support doing Morgan fingerprints only from particular atoms 2009-03-05 12:52:34 +00:00
Greg Landrum
2485fa00f3 minor cleanup work 2009-03-05 10:16:16 +00:00
Greg Landrum
e9d1313e3e add includeAtoms option to atompairs and topological torsions 2009-03-05 10:04:32 +00:00
Greg Landrum
f7127675d9 add morgan fingerprints 2009-03-05 08:01:26 +00:00
Greg Landrum
c1f3e68afb this is just a test 2008-12-08 06:34:45 +00:00
Greg Landrum
79b8a77f93 get rid of those irritating POSIX_C_SOURCE warnings 2008-07-08 06:59:59 +00:00
Greg Landrum
15813775d6 no one knows how this managed to sneak through the cracks 2008-05-30 14:47:46 +00:00
Greg Landrum
88e9f47933 doc update 2007-11-30 05:15:38 +00:00
Greg Landrum
74069dc0a6 move the Labute ASA calculation into c++; expose crippen contributions to python. 
This stuff has not yet been built on windows and the python side is not
yet ready to be checked in. This is a backup commit.
 2007-10-13 09:31:23 +00:00
Greg Landrum
1d248607c1 GraphMol/Descriptors: 
- fix a boundary condition problem
 - clean up some compiler warnings
 - translate exceptions
 2007-10-11 16:49:55 +00:00
Greg Landrum
1a9bbfae0f move torsions into C++ too 
this still has not been tested on windows
NOTE: there is a known bug in the size of the topological torsion
fingerprints (they are 1 bit too small), this is to maintain
backwards compatibility with the python code, which also had this
bug.
 2007-10-08 06:16:50 +00:00
Greg Landrum
6a1637c053 A good start on getting the atom-pair stuff into C++; 
This has been tested on Linux only, Windows is not going to work until
(at least) the workspace has been updated.
 2007-10-07 15:40:32 +00:00