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41 Commits

Author SHA1 Message Date
Greg Landrum
da6cd73168 Run clang-format across everything (#7849) 
* run clang-format-18 across Code/*.cpp and Code/*.h

* run clang-format-18 across External
 2024-09-26 13:39:02 +02:00
Greg Landrum
6805789c71 add support for generating pattern fps for MolBundles (#3665) 
* add support for generating pattern fps for MolBundles

* get python wrappers building
 2020-12-29 07:33:09 +01:00
Greg Landrum
336c3a5103 add a version for the pattern fingerprint (#3496) 2020-10-15 15:33:19 +02:00
jones-gareth
21a8a263bd Tautomer search (#3205) 
* TautomerQuery class

* working test

* Comment header

* Merge with master. Greg's suggestions. More tests. Python wrapper

* Updated Pattern Fingerprints to merge with master. Reset email

* Java/C# wrappers. Java test

* Java/C# wrappers. Java test

* Java/C# wrappers. Java test

* Greg suggestions of 6_2_2020

* Explicit types in Java TautomerQueryTests class

* Update Code/GraphMol/QueryOps.h

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* get windows dll builds working

* Removed tautomer query wrappers from RDKit namespace

* Fixes from evaluation

* Template molecule identification fix. Greg's suggestion

* Final check search functor for evaluating template matches as they are found

Co-authored-by: Gareth Jones <gjones@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2020-06-24 17:27:40 +02:00
Eisuke Kawashima
e86e2c1d5d Modernization: use nullptr (#3143) 2020-05-25 09:40:01 +02:00
Greg Landrum
ec31bea97b clang-tidy-7 pass (#2408) 2019-04-16 12:05:47 -04:00
Brian Kelley
373a89021e Change boost int types to std types (#2233) 2019-01-22 17:45:03 +01:00
Greg Landrum
2738c35178 Fixes #1903 (#1971) 
* Fixes #1903

* update SWIG bindings too
 2018-07-25 09:14:17 +02:00
Paolo Tosco
c08ea49bda - enable building DLLs on Windows (#1861) 
* - enable building DLLs on Windows

* - export.h and test.h are now auto-generated by CMake
 2018-05-16 08:42:41 +02:00
Nadine Schneider
d3f9d7c6e1 RDKFingerprint: add an unfolded count-based version of the RDKFingerprint 
- 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
Greg Landrum
00146b2cd7 Move the query information functions from Fingerprints to QueryOps.h 2015-08-18 16:41:24 +02:00
Greg Landrum
5b67e9c3e0 rename layered fingerprint2 -> pattern fingerprint 
rearrange fingerprint code a bit
 2013-03-28 09:44:33 +00:00
Greg Landrum
11e09f7d8b further fingerprint improvements; 
remove unused arguments for the layered fingerprint
 2013-03-28 03:54:13 +00:00
Greg Landrum
242e662575 version number bump and some optimization work 2013-03-17 16:06:17 +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
2936cec6ff add fromAtoms support for RDKit and layered fingerprints 2012-09-13 04:34:43 +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
bf2416032e docstring cleanup 2012-01-07 15:10:42 +00:00
Greg Landrum
39e986b775 updates to docs and release notes 2012-01-07 06:53:11 +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
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
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
4db8233db6 sync with trunk 2010-09-10 05:12:41 +00:00
Greg Landrum
052ec66542 cleanups: 
remove x bit from headers and sources;
remove a couple empty files from Code/GraphMol
 2010-09-08 04:25:57 +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
f23262a823 working towards fix for sf.net issue 3030388; note: this still needs testing 2010-07-17 03:53:46 +00:00
Greg Landrum
c164209877 doc updates 2010-04-10 01:01:57 +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
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
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
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
560239d7c0 move fingerprint folding stuff into C++. This implementation should break no existing code 2007-09-27 05:27:16 +00:00
Greg Landrum
75a79b6327 initial import 2006-05-06 22:20:08 +00:00