Greg Landrum
329bf48b77
fix a pathological symmetry case by modifying the atom invariants
2014-08-24 10:51:35 +02:00
Greg Landrum
5d6b636b07
Merge branch 'master' into NewCanonicalization_24July2014
2014-08-24 10:46:22 +02:00
Greg Landrum
0480778575
add some docs
2014-08-24 07:01:41 +02:00
Greg Landrum
23c56924fc
Merge branch 'master' into fmcs_port_21Feb2014
2014-08-24 06:27:59 +02:00
Greg Landrum
16083f4665
Merge pull request #316 from jandom/Feature_ColorHighlightAtoms
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Custom color to highlight atoms in Mol2Image
2014-08-24 06:23:36 +02:00
Jan Domanski
18b790a0a9
Custom color to highlight atoms in Mol2Image
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Tiny usability improvement, with docs and example
2014-08-23 11:27:52 +01:00
Greg Landrum
88ce84aa9c
certainly should not be including the chiral tag itself in the comparison
2014-08-23 09:46:35 +02:00
Greg Landrum
4a4d724466
hanoi tests passing again
2014-08-23 03:22:09 +02:00
Greg Landrum
06478b7779
Merge remote-tracking branch 'origin/NewCanonicalization_24July2014'
2014-08-23 02:03:52 +02:00
Greg Landrum
f9906e055b
add in a few more tests with ring stereo. These currently fail.
2014-08-23 02:02:51 +02:00
Greg Landrum
3a9169d642
bug fix from Roger
2014-08-23 02:01:28 +02:00
Greg Landrum
bcfa4714e6
Merge branch 'NewCanonicalization_24July2014' of https://github.com/rdkit/rdkit into NewCanonicalization_24July2014
2014-08-22 07:33:23 +02:00
Greg Landrum
2d8500b407
Fixes #314
2014-08-21 07:29:09 +02:00
Greg Landrum
326fdc0463
Merge remote-tracking branch 'origin/master' into NewCanonicalization_24July2014
2014-08-21 05:08:56 +02:00
Greg Landrum
ae70d43b33
cleanup cartridge makefile and document command-line options
2014-08-21 05:07:51 +02:00
Greg Landrum
c0c7451568
Merge pull request #312 from ptosco/master
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Herschbach-Laurie fallback implemented to fix GitHub 308
2014-08-20 04:57:20 +02:00
Greg Landrum
3d824d72bd
Merge pull request #315 from NadineSchneider/master
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Extended chemical reaction functionality and add chemical reactions to cartridge
2014-08-19 14:47:02 +02:00
Schneider
5f9a241b8b
PGSQL cartridge: Add new reaction functionalities to cartridge
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- Supports reaction type
- Input reaction as SMILES, SMARTS or ctab
- Supports GiST-index substucture/superstructure scans
- Supports reaction fingerprints
2014-08-19 13:13:57 +02:00
Schneider
8aac978f1b
ChemReactions: Extented functionality of chemical reactions
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- Module to generate reaction fingerprints: structural FP for screening,
difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now
2014-08-19 13:08:11 +02:00
Schneider
5774337c89
MolOps: Add function to get the number of atoms with a distinct property
2014-08-19 13:01:10 +02:00
Schneider
3af5ba223c
ExplicitBitVect: Add +operator to concatenate two ExplicitBitVects
2014-08-19 12:59:50 +02:00
Greg Landrum
6d9d74daff
complete the fix for #313 by checking in a missed .cmake file and output using older versions of flex and bison (just to be sure)
2014-08-19 07:40:01 +02:00
Greg Landrum
8959e07798
Fixes #313
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NOTE: this still needs testing on machines with older versions of flex/bison
2014-08-19 07:20:04 +02:00
Greg Landrum
1169fd2b26
cleanup some old debug printing
2014-08-19 03:46:36 +02:00
Paolo Tosco
1c3a03961d
- fixed a bug which caused the MMFF parameterization code
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to segfault when a system not listed in the MMFFBndk
table was found. THe Herschbach-Laurie fallback according
to MMFF.V was implemented and a relevant test was added
in testMMFFHelpers.cpp
2014-08-18 16:11:03 +01:00
Greg Landrum
dad92c50e1
that did not work at all; try again another day
2014-08-16 15:37:13 +02:00
Greg Landrum
418fcd0466
that was not particularly successful; add boost as well
2014-08-16 15:31:07 +02:00
Greg Landrum
fe03fb6459
try adding cartridge to the travis build
2014-08-16 14:58:05 +02:00
Greg Landrum
9ebe94ab83
Fixes #311
2014-08-16 14:24:28 +02:00
Greg Landrum
4c8cbb8611
do not default to building inchi and avalon code
2014-08-16 06:31:53 +02:00
Greg Landrum
d4fe3825b1
initial pass at adding avalon fps to cartridge. needs more testing
2014-08-16 06:31:01 +02:00
Greg Landrum
43c143ec24
Merge remote-tracking branch 'origin/master'
2014-08-16 05:22:17 +02:00
Greg Landrum
e1f0e91619
Fixes : #240
2014-08-16 05:20:39 +02:00
Greg Landrum
efc009fa40
Merge branch 'AlexanderSavelyev-fmcs_port_21Feb2014' into fmcs_port_21Feb2014
2014-08-15 04:46:17 +02:00
Greg Landrum
ec4980a14a
disable two very long running tests
2014-08-15 04:45:41 +02:00
Alexander Savelyev
51e886d89d
fmcs cosmetic changes. code clean-up. unit tests
2014-08-14 22:11:44 +04:00
Greg Landrum
3074ddbcaa
fix a deprecation warning
2014-08-14 09:25:27 +02:00
Greg Landrum
170205afe5
Fixes #296
2014-08-14 05:38:17 +02:00
Greg Landrum
a202e07737
Merge pull request #309 from rvianello/travis-ci-2
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travis-ci script update
2014-08-12 03:35:35 +02:00
Riccardo Vianello
a0b78d0899
upgrade the py27 build to boost 1_55 + add java wrappers to py34
2014-08-11 21:02:02 +02:00
Greg Landrum
7fdac1f3a4
Fixes #295
2014-08-11 15:34:02 +02:00
Greg Landrum
55ad544dde
first pass at FMCS in the java wrappers, including a basic test. this is nowhere near done
2014-08-10 08:00:37 +02:00
Greg Landrum
c8582645b2
Merge branch 'master' into fmcs_port_21Feb2014
2014-08-10 07:29:09 +02:00
Greg Landrum
4fc6a95ae9
"Fix" a problem with modern versions of boost and old versions of SWIG
2014-08-10 07:28:37 +02:00
Greg Landrum
c37ddd908e
first pass at adding fmcs to the swig wrapper (untested)
2014-08-10 07:08:58 +02:00
Greg Landrum
cfffaf7a70
update docs for rdFMCS
2014-08-09 07:26:21 +02:00
Greg Landrum
a02b7227f3
support the matchValences argument from python
2014-08-09 07:12:46 +02:00
Greg Landrum
4c1c5498f9
remove some compiler warnings; possible minor optimization
2014-08-09 07:12:24 +02:00
Greg Landrum
1a75b51fcd
Merge branch 'master' into fmcs_port_21Feb2014
2014-08-09 06:16:08 +02:00
Greg Landrum
101a5879d7
focus the tests being run
2014-08-08 09:16:01 +02:00
