Greg Landrum
2187437649
fix a couple typos
2014-07-07 15:57:27 +02:00
Greg Landrum
288feb7a8a
support partial fragmentation on bonds;
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Fixes #288
2014-07-02 05:47:02 +02:00
Greg Landrum
f5cf3322fe
code cleanup: removing compiler warnings
2014-05-08 06:06:07 +02:00
Greg Landrum
302b84960b
improve docs;
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cleanup some compiler warnings;
add parseQueryDefText()
2014-05-03 06:45:35 +02:00
Greg Landrum
d7971cc40c
Fixes #171
2013-12-06 06:54:31 +01:00
Greg Landrum
4ace62f019
remove more clang warnings
2013-12-02 05:10:23 +01:00
Greg Landrum
6c354852d1
small cleanups
2013-11-07 10:57:18 +01:00
Greg Landrum
6d936e9d31
Merge branch 'master' of https://github.com/rdkit/rdkit
2013-11-02 07:23:31 +01:00
Greg Landrum
95c6c7f261
fragmentOnBonds() fix
2013-11-02 07:17:42 +01:00
Greg Landrum
afb9f1ddfa
add fragmentOnBonds() to python API
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Fixes #142
2013-10-30 04:59:29 +01:00
Greg Landrum
70f2829524
do not include _static versions for test links. This breaks on windows
2013-03-22 05:18:35 +00:00
Greg Landrum
5a340dd454
Fix a typo
2013-03-01 06:53:17 +00:00
Greg Landrum
c595c29cb2
add missing headers for "make install"
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fixes github issue 2
2013-02-05 04:57:59 +00:00
Greg Landrum
ea42bf5465
BRICS-related bug fixes
2013-02-05 04:56:10 +00:00
Greg Landrum
89398a10c2
make sure computed props get cleared
2013-01-31 04:54:28 +00:00
Greg Landrum
84d6ddb3f3
add fragmentOnBRICSBonds()
2013-01-30 06:31:06 +00:00
Greg Landrum
fa2b82b606
breaking all BRICS bonds now works
2013-01-29 16:22:27 +00:00
Greg Landrum
00655e7bd6
backup commit; may not build
2013-01-29 06:28:31 +00:00
Greg Landrum
052b87564c
add one more test for issue 275
2013-01-09 13:12:27 +00:00
Greg Landrum
03ef0e6f1b
Add support for merging recursive queries on the C++ side
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(contribution from Sereina Riniker)
A pure Python version of this was in the tutorial material from the RDKit UGM.
2013-01-08 15:13:01 +00:00
Greg Landrum
68e370d581
initial pass at a fix for sf.net issu275
2012-12-18 17:16:06 +00:00
Greg Landrum
bef74c1c81
initial support for reading query files. Python wrapper still needs to be done.
2012-12-17 10:28:35 +00:00
Greg Landrum
57572918de
add initial support for addRecursiveQueries to ChemTransforms.
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active and tested in C++ and python, in the SWIG wrapper but untested.
still needs linux and windows builds.
2012-12-17 09:06:02 +00:00
Greg Landrum
cfaea83d7d
optimizations for molecule construction
2012-08-27 04:52:27 +00:00
Greg Landrum
93f6445e01
minor cleanup to RWMol::insertMol; add combineMols to ChemTransforms
2012-07-10 04:00:46 +00:00
Greg Landrum
2e5b33e2fd
fix and test issue 3537675
2012-07-02 03:07:02 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
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there are still some problems with double bonds
2012-06-11 03:21:30 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
a99ad44859
clean up some compiler warnings
2011-12-31 15:58:57 +00:00
Greg Landrum
3b751bad46
fix and test issue 3453144
2011-12-13 04:56:56 +00:00
Greg Landrum
3ba11316b2
initial pass at requiring core-dummy matches in replaceCore; remove an extra header import from MolOps.cpp
2011-03-28 06:13:48 +00:00
Greg Landrum
633be739b0
- fix an edge case with disconnected molecules in the MurckoDecompose code.
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- test that empty results are handled properly in MurckoDecompose.
2011-03-04 06:37:26 +00:00
Greg Landrum
f3a570fe29
add the test file
2011-03-04 05:23:13 +00:00
Greg Landrum
e1e1e5929d
fix assignment of dummy positions in replaceCore
2011-03-03 05:02:13 +00:00
Greg Landrum
d6741adc22
make some types more explicit in MolOps.h (easier SWIG wrapping)
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support finding non-specfied chiral centers
remove vestigial GetFragmentSmiles() function
additional flexibility in AllChem.TransformMol()
2011-02-24 08:00:39 +00:00
Greg Landrum
4ca59a1987
clean up conformer handling in ChemTransforms
2011-02-22 06:16:23 +00:00
Greg Landrum
e2521dccbc
add murcko decomposition;
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be sure pathToSubmol copies over coordinates
2011-02-21 06:43:53 +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
cb6cdb99b3
merge in a set of changes from Riccardo V. to install .h files as well;
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this needs more testing.
2010-09-04 14:07:22 +00:00
Greg Landrum
2805355f34
First pass at the rewrite:
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this gets rid of all the "preceding atom" code and passes all tests on linux
builds on other OS's and more extensive regression testing is required
2010-05-31 14:08:11 +00:00
Greg Landrum
53485592ca
builds on windows with visual studio; need to pass back to linux now
2009-10-01 13:35:48 +00:00
Greg Landrum
76297b0fff
builds and passes tests on linux
2009-09-28 11:02:18 +00:00
Greg Landrum
9cabf87374
remove vflib from Jamfiles
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remove const specifiers from return values in DataStructs
add initial pass at query-query matching for Atoms and Bonds
fix and test for sf.net issu 2738320
add Mol.AddRecursiveQuery() method to Mol
2009-06-29 11:47:38 +00:00
Greg Landrum
8e731f9e70
move the MolDiscriminators calculations into Subgraphs in order to remove the lapack dependency from the core molecule code;
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At some point the BalabanJ calculation, still in MolDiscriminators.cpp, should be
moved to MolDescriptors.
2009-04-10 04:09:49 +00:00
Greg Landrum
8bf7a4c187
now all tests pass here as well
2009-02-03 05:26:10 +00:00
Greg Landrum
2580fbaaa2
this is probably a ways from done, but now at least we can run bjam under mingw without it immediately erroring out
2008-11-15 17:14:13 +00:00
Greg Landrum
57cd641e50
in replaceCore: support labelling dummies with the index of the corresponding atom in the core
2008-11-06 09:10:38 +00:00
Greg Landrum
21bb475b61
further jamfile mods for macosx
2008-10-19 05:36:09 +00:00
Greg Landrum
89a34d1a39
get this building on Darwin; NOTE: this may not work on win or linux yet
2008-09-03 19:24:35 +00:00
