Greg Landrum
67eccc1620
fix and tests Issue3375684
2011-07-23 03:49:36 +00:00
Greg Landrum
951f4b7fd3
fix and tests sf.net issue3375647
2011-07-22 15:53:05 +00:00
Greg Landrum
f61d48cadf
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
Greg Landrum
10cb677b33
fix and test Issue3374639
2011-07-22 10:55:40 +00:00
Greg Landrum
92533d95d5
expose the Cleanup() function
2011-07-11 03:03:54 +00:00
Greg Landrum
c7a9903e41
fix and test issue 3359739
2011-07-09 04:46:55 +00:00
Greg Landrum
739a989617
improve error message
2011-07-09 03:22:24 +00:00
Greg Landrum
dad3885839
fix and test sf.net issue 3349243
2011-07-02 04:25:59 +00:00
Greg Landrum
d34f3dd6b2
do isotope work relative to the most common isotope
2011-07-01 04:34:14 +00:00
Greg Landrum
9316758cec
improved handling of isotope specifications (still definitely not optimal)
2011-07-01 03:42:35 +00:00
Greg Landrum
e92b467051
test cleanups
2011-07-01 03:12:18 +00:00
Greg Landrum
dd15020a0f
remove use of a static variable that was causing problems with thread safety while writing smiles
2011-06-29 02:21:01 +00:00
Greg Landrum
1df2618213
fix and test issue 3316600
2011-06-15 05:34:15 +00:00
Greg Landrum
dac565e485
add the ability to ignore atoms in the TT and AP fingerprints
2011-06-15 03:20:10 +00:00
Greg Landrum
f0c0a060a2
fix and test Issue 3313540
2011-06-10 03:27:46 +00:00
Greg Landrum
6568324650
better fix for sf.net issue 3313539
2011-06-09 05:31:46 +00:00
Greg Landrum
a7cbd1a818
better fix for sf.net issue 3313539
2011-06-09 05:30:45 +00:00
Greg Landrum
deae1affcb
provisional fix and test sf.net issue 3313539
2011-06-08 05:18:14 +00:00
Greg Landrum
c9161554b9
clean up some compiler warnings from clang
2011-05-26 02:36:23 +00:00
Greg Landrum
5f85129f22
initial support for clang
...
this is minor build-system variations and some code cleanup
the python wrapper still needs cleanup and
the sln stuff doesn't work at all under clang due to weirdness with boost::regex
2011-05-25 19:40:31 +00:00
Greg Landrum
faab610321
add string replacements to smiles and smarts parsers
2011-05-22 10:45:14 +00:00
Greg Landrum
cbd8928642
improve error reporting for smiles, smarts, and sln parsers
...
(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;
...
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.
...
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++.
...
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.
...
- 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)
...
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;
...
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
