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
b993f89afe
remove the bjam-based build system
2010-09-27 03:54:07 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
5cc9d6ddeb
fixes and tests for two isotope-related problems:
...
1) issue 3073163
2) incorrect calculation of AMW with isotopes present
2010-09-22 13:26:30 +00:00
Greg Landrum
60894f6e22
make assignRadicals visible to client code
2010-09-20 02:09:24 +00:00
Greg Landrum
116c036c07
doc updates for writers to indicate that "-" writes to stdout;
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rename computedProps property to __computedProps
2010-09-19 13:13:10 +00:00
Greg Landrum
ff7d14f692
include ring-membership by default in the morgan fps
2010-09-15 05:59:27 +00:00
Greg Landrum
4db8233db6
sync with trunk
2010-09-10 05:12:41 +00:00
Greg Landrum
f54a9cb385
removed AtomProps and BondProps
2010-09-10 04:32:20 +00:00
Greg Landrum
052ec66542
cleanups:
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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
1eacf5d26a
merge in a change from the trunk to allow this to build on windows more easily
2010-09-07 18:27:04 +00:00
Greg Landrum
514b59e12f
remove duped function
2010-09-07 05:02:37 +00:00
Greg Landrum
cb6cdb99b3
merge in a set of changes from Riccardo V. to install .h files as well;
...
this needs more testing.
2010-09-04 14:07:22 +00:00
Greg Landrum
6e31713dd9
correct handling of chirality and make it optional (now by default disabled);
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allow bond order to be ignored
2010-09-04 05:54:27 +00:00
Greg Landrum
bc78908f1f
update feature defns and make them more readable
2010-09-03 11:12:32 +00:00
Greg Landrum
a25f17a45c
add fcfp-like invariants for the morgan fingerprinter
2010-09-02 06:00:17 +00:00
Greg Landrum
e7eb09057d
fix a typo in the Crippen parameters (thanks to C. Kramer for pointing this out)
2010-08-31 14:59:36 +00:00
Greg Landrum
0b94555f88
fix (and test) potential crashing bug
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with use of close() in SDWriters
2010-08-30 05:00:58 +00:00
Greg Landrum
bcd141432f
generalize the tests
2010-08-28 14:16:26 +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
b988fb9669
support changing the bond length in depictions
2010-08-21 00:17:59 +00:00
Greg Landrum
0ce95829a5
cleanup deprecated args
2010-08-21 00:16:55 +00:00
Greg Landrum
18a8be8538
add isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() convenience functions
2010-08-21 00:16:02 +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
29c10590b4
change the ring-invariant computation scheme:
...
The original version using products of primes broke down for proteins (or things with
large numbers of atoms) since collisions were quite possible.
Switched to using a hashing scheme; collisions are also possible here, but are even
less likely.
2010-08-14 06:21:47 +00:00
Greg Landrum
688fd98e6a
fix an SSS fingerprint bug
2010-08-09 06:40:17 +00:00
Greg Landrum
e13bd027e3
make sure we use the dynamic version of regex on windows
2010-07-30 17:03:41 +00:00
Greg Landrum
3f08f58208
add close() method to writers
2010-07-28 04:29:58 +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
ce8cb4aa81
doc typo fixed
2010-07-26 05:15:24 +00:00
Greg Landrum
33121bd4f3
add FindAllSubgraphsofLengthMToN
2010-07-22 07:49:23 +00:00
Greg Landrum
9c4870ba63
tests for issue 3030388
2010-07-17 05:40:33 +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
930c8cd407
stop using static libs for boost regex; they seem to cause more problems than they solve
2010-07-09 04:15:09 +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
248e9c80b2
minor updates
2010-06-23 04:15:38 +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
5ef1a2c6eb
improve depiction quality by (optionally) doing a bit of chemistry perception
2010-06-23 04:07:23 +00:00
Greg Landrum
3e0d9a75d0
fix and test sf.net issue 3019283
2010-06-22 05:08:00 +00:00
Greg Landrum
7d690ef390
add a bit more morgan functionality
2010-06-21 04:29:28 +00:00
Greg Landrum
eba44a48fd
doc update
2010-06-20 14:04:12 +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
d23bdac363
fix and test sf.net issue 3018558
2010-06-20 03:46:58 +00:00
Greg Landrum
9bd1326ab0
get the windows build working
2010-06-19 03:55:19 +00:00
Greg Landrum
46bfbba903
make sure to convert atoms from rxn files into queries;
...
add reaction depiction;
add ChemicalReactionToRxnBlock();
This stuff needs more testing and so far has only been built on linux.
2010-06-17 05:57:18 +00:00
Greg Landrum
9edbb9909a
more extensive testing of pickler
2010-06-17 05:53:37 +00:00
Greg Landrum
f735138787
get this building on the mac again
2010-06-10 05:43:20 +00:00
