Greg Landrum
cbd8928642
improve error reporting for smiles, smarts, and sln parsers
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(sf.net issue 3302363)
2011-05-15 10:10:56 +00:00
Greg Landrum
cbebed9e0d
fix and test sf.net issue 3299878
2011-05-11 05:31:39 +00:00
Greg Landrum
24bbcec6fd
typo
2011-04-18 11:27:41 +00:00
Greg Landrum
37c342046a
add isotopic mass information; add molecular formula calculation; add isotopic mass calculator; expose additional descriptors to java
2011-04-18 10:11:09 +00:00
Greg Landrum
f87a54950d
documentation update
2011-04-02 04:58:48 +00:00
Greg Landrum
b98fd417e6
make sure all confs get copied
2011-03-30 05:43:55 +00:00
Greg Landrum
8734dc86c8
cleanup
2011-03-30 03:28:35 +00:00
Greg Landrum
37e9a09b77
fix and tests issue 3238580
2011-03-30 02:33:18 +00:00
Greg Landrum
a7a145f3d9
modifications to the pickle binary format to make serialized molecules smaller
2011-03-29 04:35:43 +00:00
Greg Landrum
38f0e7ccbc
update a couple build files
2011-03-28 11:08:04 +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
2ffaa92cf7
fix and test issue3228150;
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note that as part of these changes MolToSmiles and MolToSmarts no longer have
side effects on the original molecule.
2011-03-26 06:51:50 +00:00
Greg Landrum
5c14f36de7
partial fix for Issue3228150
2011-03-25 03:26:03 +00:00
Greg Landrum
6fa65fbc68
move the _VSA descriptors into C++
2011-03-21 05:02:12 +00:00
Greg Landrum
498eb1ef63
back out some of the changes from rev1663.
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we are no longer templating the descriptor functions and have moved the calculation
of the pattern matchers into statics inside the functions themselves.
This solves a crashing problem with the cartridge on the mac.
2011-03-16 04:39:07 +00:00
Greg Landrum
aca2fc18f8
move the lipinski defns into the header file
2011-03-15 07:51:35 +00:00
Greg Landrum
4325789d25
move lipinski descriptors to C++.
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rename CalcCrippenDescriptors -> calcCrippenDescriptors
2011-03-14 10:24:42 +00:00
Greg Landrum
cb419d71ff
additional TPSA testing
2011-03-13 05:30:10 +00:00
Greg Landrum
456e68456b
move PSA into C++
2011-03-12 07:00:48 +00:00
Greg Landrum
c3c929f02d
fix and test sf.net issue 3202580
2011-03-08 05:00:01 +00:00
Greg Landrum
e953f540c8
remove a compiler warning
2011-03-08 03:59:32 +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
044fda398b
further ring-finding algorithmic changes to fix issue 3185548
2011-02-19 04:35:53 +00:00
Greg Landrum
aa1610797e
initial fix for Issue3184458, more work should still be done here.
2011-02-18 06:31:31 +00:00
Greg Landrum
28747ea745
checkin some fragment and fingerprint changes. these are not yet well tested
2011-01-14 06:24:03 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
e703428743
canonicalization test connected with issue 3154208
2011-01-11 05:12:19 +00:00
Greg Landrum
5592e31464
initial fix and tests for issue 3154208
2011-01-10 07:11:44 +00:00
Greg Landrum
c6c7af1e6a
fix and test issue 3152751
2011-01-07 05:04:26 +00:00
Greg Landrum
90787f08ad
fix a core leak
2011-01-05 08:45:35 +00:00
Greg Landrum
e269703e0e
some more natural product tests for issue 3139534
2011-01-05 06:30:56 +00:00
Greg Landrum
e784881358
stop calls to exit() from the flex code
2011-01-05 05:00:53 +00:00
Greg Landrum
f4a0012bc6
fix a residual problem with ring stereochem
2011-01-04 04:45:42 +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
4f0321acc7
cleanup
2010-12-29 07:10:10 +00:00
Greg Landrum
c20376ad15
typo
2010-12-28 17:57:54 +00:00
Greg Landrum
5891b5edc8
further work on bug 3139534
2010-12-28 15:43:20 +00:00
Greg Landrum
006c696067
an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534);
...
this needs a ton more testing, but it is worth getting a "working" version in
2010-12-28 10:38:14 +00:00
Greg Landrum
c25a2dde0f
improve docstrings
2010-12-28 05:24:36 +00:00
Greg Landrum
67dadac26e
fix and test bug 3145697
2010-12-27 07:20:34 +00:00
Greg Landrum
2cea8b58b4
fix for issue 3140490
2010-12-20 05:00:23 +00:00
Greg Landrum
e977a642f6
add support for writing non-canonical SMILES;
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add support for atom-mapping information in plain SMILES
2010-12-20 03:59:56 +00:00
Greg Landrum
aa7029bbc0
add onlyNonzeroInvariants experimental option
2010-12-15 05:20:17 +00:00
Greg Landrum
8b62f880d0
make getting the fcfp-like descriptors from python easier
2010-12-15 05:19:47 +00:00
Greg Landrum
681a30bd61
provisional fix for issue 3135833
2010-12-12 12:05:59 +00:00
