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
Greg Landrum
b36e6a911f
fix a drawing bug
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update release notes and docs
implement the new dummy atom stuff in ChemTransforms
expose lists of atom rings and bond rings from RingInfo
2008-05-14 20:20:52 +00:00
Greg Landrum
26a4124ad9
remove files for old build system
2008-02-20 17:06:59 +00:00
Greg Landrum
1d40302dcb
This builds and tests correctly with msvc8. Linux and msvc7 tests are still required.
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The primary changes consist of cleaning up edge cases that lead to memory errors (under VC8 with debugging turned out)
2008-02-16 05:25:53 +00:00
Greg Landrum
59fef17517
mostly working under linux... iterate back to windows
2008-02-13 05:36:48 +00:00
Greg Landrum
d44f340db1
This setup now builds on windows, but almost certainly won't on linux... for that another iteration or so is going to be required. Checkin now to get that iteration started
2008-02-08 05:01:56 +00:00
Greg Landrum
5b550374cb
fix problems with chirality and replaceCore
2008-01-30 15:39:46 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
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The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
430a83bd96
merge in the jamfiles from the bjam branch;
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various and sundry minor code cleanups;
this probably does not yet build on windows... that is next
2007-11-23 15:55:30 +00:00
Greg Landrum
3e6cb74075
cleanup and documentation changes
2007-11-14 06:09:52 +00:00
Greg Landrum
5da5c9f7a6
add support for not removing dummies out from the core
2007-10-24 16:36:17 +00:00
