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50 Commits

Author SHA1 Message Date
Greg Landrum
92533d95d5 expose the Cleanup() function 2011-07-11 03:03:54 +00:00
Greg Landrum
f87a54950d documentation update 2011-04-02 04:58:48 +00:00
Greg Landrum
3ba11316b2 initial pass at requiring core-dummy matches in replaceCore; remove an extra header import from MolOps.cpp 2011-03-28 06:13:48 +00:00
Greg Landrum
d6741adc22 make some types more explicit in MolOps.h (easier SWIG wrapping) 
support finding non-specfied chiral centers
remove vestigial GetFragmentSmiles() function
additional flexibility in AllChem.TransformMol()
 2011-02-24 08:00:39 +00:00
Greg Landrum
e2521dccbc add murcko decomposition; 
be sure pathToSubmol copies over coordinates
 2011-02-21 06:43:53 +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
3b3d44db16 remove exe property from source files 2011-01-13 04:22:56 +00:00
Greg Landrum
90787f08ad fix a core leak 2011-01-05 08:45:35 +00:00
Greg Landrum
7baa1769fd switch to having the RDKit fingerprinter default to 2 bits per path instead of 4 2011-01-02 11:17:15 +00:00
Greg Landrum
c25a2dde0f improve docstrings 2010-12-28 05:24:36 +00:00
Greg Landrum
c07c7220c7 more tuning of the substruct fingerprint 2010-11-22 04:12:00 +00:00
Greg Landrum
f3fbef45c5 update copyright statements 2010-09-26 17:04:37 +00:00
Greg Landrum
60894f6e22 make assignRadicals visible to client code 2010-09-20 02:09:24 +00:00
Greg Landrum
4b78f97572 add findAllPathsOfLengthsMtoN(), corresponds to findAllSubgraphsOfLengthsMtoN() 
support path-based (i.e. non-branched fingerprints)
 2010-08-21 00:20:18 +00:00
Greg Landrum
33121bd4f3 add FindAllSubgraphsofLengthMToN 2010-07-22 07:49:23 +00:00
Greg Landrum
7065810cfd - add describeQuery() method to atoms (this is primarily for debugging) 
- add SetConjugation() and SetHybridization() methods for molecules.
 2010-06-23 04:14:25 +00:00
Greg Landrum
c164209877 doc updates 2010-04-10 01:01:57 +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
22e60f20aa update versioning information 2010-01-26 05:29:25 +00:00
Greg Landrum
96adbc11ea remove the deprecated assign{Atom,Bond}ChiralCodes functions 2009-08-02 15:33:08 +00:00
Greg Landrum
bd738367e3 remove the function DaylightFingerprintMol() 2009-07-02 04:32:36 +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
7db437c88c docstring fix 2009-04-16 03:19:49 +00:00
Greg Landrum
9685e9992b add an include 2009-04-15 13:23:16 +00:00
Greg Landrum
498dccf417 support more control over layered fps 2009-04-15 09:47:46 +00:00
Greg Landrum
8712b86f33 add experimental warning 2009-03-20 06:10:09 +00:00
Greg Landrum
6042af28b9 add removeStereochemistry function to MolOps 2009-03-06 09:55:53 +00:00
Greg Landrum
c276cd0fe7 indicate that DaylightFingerprintMol() is deprecated 2009-02-09 06:26:07 +00:00
Greg Landrum
dc87df759a merge in layered fingerprints branch (https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/LayeredFingerprints_22Nov2008), revs 889:922 2008-12-11 04:55:08 +00:00
Greg Landrum
a74e024dc3 make mergeQueryHs work when there is no query to start with 2008-12-10 16:43:14 +00:00
Greg Landrum
54730482c5 push AssignStereochemistry() into python wrapper; should have been done a while ago 2008-12-05 14:33:45 +00:00
Greg Landrum
8b321cc5b4 fix 2318431: deprecation warnings from numpy 2008-11-21 05:55:08 +00:00
Greg Landrum
57cd641e50 in replaceCore: support labelling dummies with the index of the corresponding atom in the core 2008-11-06 09:10:38 +00:00
Greg Landrum
0a99a0155e merge revs 840:846 of Release_Q32008_1RC1 branch back to trunk 2008-09-30 16:29:53 +00:00
Greg Landrum
023f7b4f0f Merge changes from the iterative chirality branch: 
https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/IterativeChirality_20Aug2008
into the trunk.
This covers revs 798-828.

Dependent chirality should now be correctly handled, but the
handling of ring stereochemistry, i.e. things like:
C[C@H]1CC[C@H](C)CC1
is still not 100% correct.
 2008-09-19 09:40:15 +00:00
Greg Landrum
6e05e3c7c2 update the chirality from 3d stuff a bit and expose it to python; fix a reporting error in SDMolSupplier 2008-07-09 15:43:04 +00:00
Greg Landrum
c9eb4e91e1 merge revs 736:741 from branch http://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/NumPyPort_27June2008 
This removes the numeric python dependency and switches to relying on numpy.
current status of tests from branch: pass on lin32 and 64 and win32.
 2008-07-05 07:42:38 +00:00
Greg Landrum
76f32244aa - support splitting a molecule into fragments (in MolOps) 
- expose the calculation of atom CIP ranks
 2008-06-27 03:43:42 +00:00
Greg Landrum
f71a301574 rename the new fingerprint to RDKFingerprint instead of RDKFingerprint2 2008-05-08 18:44:45 +00:00
Greg Landrum
a1ed48bccb add an alternate approach for hashing fingerprints 2008-04-08 16:06:25 +00:00
Greg Landrum
3e6cb74075 cleanup and documentation changes 2007-11-14 06:09:52 +00:00
Greg Landrum
5da5c9f7a6 add support for not removing dummies out from the core 2007-10-24 16:36:17 +00:00
Greg Landrum
560239d7c0 move fingerprint folding stuff into C++. This implementation should break no existing code 2007-09-27 05:27:16 +00:00
Greg Landrum
37d96faca8 expose RingInfo structure 2007-08-03 04:49:52 +00:00
Greg Landrum
4e7d182fcc Support editable molecules in Python. 
This is Feature Request #1764162
http://sourceforge.net/tracker/index.php?func=detail&aid=1764162&group_id=160139&atid=814653

This implementation has been tested on Windows
 2007-07-31 05:30:11 +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
6615ae5a01 SDMolSupplier: don't throw on errors parsing molecules. This allows the parsing of further mols to continue. 
Conformer.cpp: make sure we don't ask for space for zero atoms.

Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.

molopstest.cpp: bad smiles corrected in one test.exe

ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)

Wrap/MolOps.cpp: docs for replacesubstructs.
 2006-09-18 05:21:39 +00:00
Greg Landrum
81f341882e try to get ChemTransforms checked in 2006-07-18 05:33:58 +00:00
Greg Landrum
5d03333c22 setup svn keywords (should have done this before import... grn) 2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00