Greg Landrum
cdaaed4d56
sync back to trunk
2013-01-13 10:15:55 +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
d0778ecb8c
sync with trunk
2012-12-22 03:42:58 +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
df3f6e9d39
backup commit; not actually working yet
2012-12-08 06:06:53 +00:00
Greg Landrum
96760b37de
fix and test sf.net issue 270
2012-12-04 07:13:08 +00:00
Greg Landrum
c9e55a65bf
add fromAtoms support for fingerprints
2012-09-14 16:17:30 +00:00
Greg Landrum
93f6445e01
minor cleanup to RWMol::insertMol; add combineMols to ChemTransforms
2012-07-10 04:00:46 +00:00
Greg Landrum
d895c2108a
the problem was actually on 32bit machines, not windows... update for that
2012-04-12 06:28:09 +00:00
Greg Landrum
40ecb362c1
get that working again on linux
2012-04-12 04:46:00 +00:00
Greg Landrum
6229f639a5
clean up some debugging printing; get the handling of the sanitization options more robust on windows; this needs testing back on mac and linux
2012-04-12 04:23:41 +00:00
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
35a01ad00c
doc updates
2012-02-26 18:53:19 +00:00
Greg Landrum
7ba9571e3c
further refinements
2012-02-26 08:47:14 +00:00
Greg Landrum
39e986b775
updates to docs and release notes
2012-01-07 06:53:11 +00:00
Greg Landrum
3eeb1bf30c
initial version of a DFS-based ring finder
2012-01-02 15:34:43 +00:00
Greg Landrum
ccbf50075b
add another experimental version of the layered fingerprint (backup commit, this is not yet done)
2011-12-08 06:03:03 +00:00
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
