Greg Landrum
0d7bb5796f
Fixes #1793 ( #1795 )
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A bit of reformatting too.
2018-04-02 05:02:15 +02:00
Greg Landrum
ba12d98ad0
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers ( #1713 )
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* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
2018-01-07 14:19:47 -05:00
Greg Landrum
915cf08faa
run clang-format with c++-11 style over that
2017-04-22 17:19:10 +02:00
Greg Landrum
7c0bb0b743
clang-tidy output
2017-04-22 17:09:24 +02:00
Greg Landrum
7fa3cae4cd
clear up a bunch of windows warnings ( #1086 )
2016-10-04 06:46:07 -04:00
Nadine Schneider
d3f9d7c6e1
RDKFingerprint: add an unfolded count-based version of the RDKFingerprint
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- add a bitinfo map to the RDKFingerprint
- refactor some code to largely avoid code duplicates
2016-04-01 09:10:47 +02:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Brian Kelley
e1b92efeee
Adds more boost header file ignores
2015-10-18 22:23:58 -04:00
Brian Kelley
a146c3826a
Remove unused variables/functions and register keyword
2015-10-18 10:01:00 -04:00
Greg Landrum
00146b2cd7
Move the query information functions from Fingerprints to QueryOps.h
2015-08-18 16:41:24 +02:00
Greg Landrum
f89f65e16d
fix a typo causing problems with older vc++ versions
2014-02-06 04:58:54 +01:00
Greg Landrum
60a68669da
remove more clang warnings
2013-12-02 04:46:46 +01:00
Greg Landrum
cabb7f80a5
improved isComplexQuery() logic
2013-11-15 06:49:08 +01:00
Greg Landrum
5b67e9c3e0
rename layered fingerprint2 -> pattern fingerprint
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rearrange fingerprint code a bit
2013-03-28 09:44:33 +00:00
Greg Landrum
11e09f7d8b
further fingerprint improvements;
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remove unused arguments for the layered fingerprint
2013-03-28 03:54:13 +00:00
Greg Landrum
fbc0a7896e
further optimization; switch back to the original hashing scheme
2013-03-25 15:13:14 +00:00
Greg Landrum
29e36be8b4
back to the original fp hashing scheme + atom degrees
2013-03-25 14:39:52 +00:00
Greg Landrum
e4798fa498
another pass at getting the path canonicalization working
2013-03-25 09:13:58 +00:00
Greg Landrum
2ead7f14a4
change bond hash for the original algorithm;
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add optional (compile time) collision reporting
2013-03-19 05:19:42 +00:00
Greg Landrum
74555fcb25
rearrange bits in bond invars
2013-03-19 02:37:21 +00:00
Greg Landrum
242e662575
version number bump and some optimization work
2013-03-17 16:06:17 +00:00
Greg Landrum
b3aa7e0a4e
new hashing algorithm for path-based fingerprints pass 1;
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definitely some optimization work left to do, but this works and passes tests
2013-03-17 11:29:59 +00:00
Greg Landrum
d1cae9346f
an initial version of the "atomBits" feature for RDKit fingerprints
2013-03-12 04:39:43 +00:00
Greg Landrum
0c635ea239
add a couple extra rings and fix a typo
2012-12-04 10:54:44 +00:00
Greg Landrum
57a63be899
back to the earlier behavior
2012-09-26 02:34:12 +00:00
Greg Landrum
f191b965a8
optimization
2012-09-21 05:33:13 +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
fccea24ff1
efficiency improvements and added (crude) support for query structures to the LayeredFingerprint 2
2012-07-07 12:52:36 +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
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
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
c07c7220c7
more tuning of the substruct fingerprint
2010-11-22 04:12:00 +00:00
Greg Landrum
9301733e6c
another round of query fingerprint improvement
2010-11-20 15:23:42 +00:00
Greg Landrum
7fcea91f8b
be more permissive about including bits in the fp
2010-11-16 05:30:11 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
4b78f97572
add findAllPathsOfLengthsMtoN(), corresponds to findAllSubgraphsOfLengthsMtoN()
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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
688fd98e6a
fix an SSS fingerprint bug
2010-08-09 06:40:17 +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
f23262a823
working towards fix for sf.net issue 3030388; note: this still needs testing
2010-07-17 03:53:46 +00:00
Greg Landrum
20096c76a9
refactoring of the BitVect interface to make capitalization consistent
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w/ the rest of the RDKit. i.e.: SetNumBits -> setNumBits
2010-05-30 15:15:46 +00:00
Greg Landrum
bdc4f497db
optimization
2010-02-08 06:13:28 +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
621b99f225
some optimization work
2009-05-10 04:10:29 +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
e94b0090ae
make the layered fingerprints more suited for substructure filtering
2009-02-10 10:17:22 +00:00
