Greg Landrum
357f41cc5f
somewhat optimized version from Roger.
...
get the return vector the right size.
note: this still is not thread safe.
2013-02-10 04:18:19 +00:00
Greg Landrum
a597e0ac0a
add C++ implementation of MACCS keys
...
(contribution from Roger Sayle)
2013-02-09 16:01:07 +00:00
Greg Landrum
2936cec6ff
add fromAtoms support for RDKit and layered fingerprints
2012-09-13 04:34:43 +00:00
Greg Landrum
d84d5218a9
further layeredfp2 improvements
2012-07-09 05:19:33 +00:00
Greg Landrum
11c42cf1b2
fix an oversight: add getHashedMorganFingerprint
2012-07-02 07:03:55 +00:00
Greg Landrum
1c95a978dd
fix a typo
2012-04-06 05:42:53 +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
6dcbdb246b
at this point I think all descriptors and fingerprints work
2012-02-25 07:14:29 +00:00
Greg Landrum
a99ad44859
clean up some compiler warnings
2011-12-31 15:58:57 +00:00
Greg Landrum
561b41522a
fix issue 3415636
2011-09-30 05:53:00 +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
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
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
9301733e6c
another round of query fingerprint improvement
2010-11-20 15:23:42 +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
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
4b78f97572
add findAllPathsOfLengthsMtoN(), corresponds to findAllSubgraphsOfLengthsMtoN()
...
support path-based (i.e. non-branched fingerprints)
2010-08-21 00:20:18 +00:00
Greg Landrum
c78be3f5ee
another change to the hashing mechanism; version bump; query miss cleared up
2010-08-14 11:35:00 +00:00
Greg Landrum
8800620677
fix a problem with layered fingerprint hashing; switch back to using the RNG to generate bits
2010-07-27 19:56:54 +00:00
Greg Landrum
9c4870ba63
tests for issue 3030388
2010-07-17 05:40:33 +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
7d5a9f75ff
move the AtomPair and TopologicalTorsion fingerprint code into the Fingerprints directory
2010-06-20 06:15:37 +00:00
Greg Landrum
3951d47b5f
add option to get fingerprint as bit vector
2010-06-20 05:12:33 +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
655ec54b16
fix and test issue 2875658
2009-10-10 06:05:24 +00:00
Greg Landrum
db4b9aaab4
handle sf.net issue 2848863
2009-09-02 03:50:34 +00:00
Greg Landrum
bd738367e3
remove the function DaylightFingerprintMol()
2009-07-02 04:32:36 +00:00
Greg Landrum
cde962ad6e
support queries better in the layered fingerprinting
2009-05-07 13:29:54 +00:00
Greg Landrum
498dccf417
support more control over layered fps
2009-04-15 09:47:46 +00:00
Greg Landrum
c0759d094c
fix a fromAtoms problem with the morgan fps
2009-03-06 09:17:12 +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
f7127675d9
add morgan fingerprints
2009-03-05 08:01:26 +00:00
Greg Landrum
e94b0090ae
make the layered fingerprints more suited for substructure filtering
2009-02-10 10:17:22 +00:00
Greg Landrum
f98527e572
minor reorg
2008-12-11 07:29:23 +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
06736b4446
this now passes with boost 1.35 instead of 1.34.1; edit to get 1.34.1 compatibility back
2008-05-26 17:05:22 +00:00
Greg Landrum
830e96a231
remove a compiler warning
2008-05-20 06:51:47 +00:00
Greg Landrum
2f91b59836
do an explicit backwards compatibility check with fingerprints
2008-05-17 05:57:41 +00:00
Greg Landrum
f71a301574
rename the new fingerprint to RDKFingerprint instead of RDKFingerprint2
2008-05-08 18:44:45 +00:00
Greg Landrum
8f8a885b50
test required fp trends;some optimization work
2008-04-09 07:10:30 +00:00
Greg Landrum
61b05af6fc
Modify suppliers and parsers so that they don't throw
...
exceptions into python when reading a bad molecule. (Feature
request 1932875)
Modify constructors for both suppliers and parsers so that
throw BadFileExceptions if they cannot open the file. (Feature
request 1938303)
2008-04-09 03:33:49 +00:00
Greg Landrum
a1ed48bccb
add an alternate approach for hashing fingerprints
2008-04-08 16:06:25 +00:00
Greg Landrum
e93d67efab
fix a problem with the folding and test that folding is doing something reasonable
2007-10-04 05:15:33 +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
