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24bbcec6fda00a787d7c0671d27f4995bcee151b
Commit Graph

904 Commits

Author SHA1 Message Date
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
0d160c48f8 additional functionality required by the knime nodes 2011-04-12 10:09:41 +00:00
Greg Landrum
800a4c2149 additional functionality required by the knime nodes 2011-04-12 10:07:52 +00:00
Greg Landrum
9ebc0a67d3 add 2011-04-08 02:48:25 +00:00
Greg Landrum
7e3c70f71a missed some files on the commit 2011-04-08 02:46:35 +00:00
Greg Landrum
c7ef21088b add initial version of new swig wrappers 2011-04-07 05:22:00 +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
f598ac672c version bump 2011-03-21 05:00:02 +00:00
Greg Landrum
403a669ac8 add some additional descriptors to the cartridge 2011-03-19 04:25:48 +00:00
Greg Landrum
4e27c74652 test TPSA 2011-03-16 06:40:58 +00:00
Greg Landrum
3510396ad0 expose and test descriptor calculators. 2011-03-16 06:33:04 +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
b419b0d1ae switch to the "real" calculators where possible 2011-03-15 11:05:56 +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
f619c0bbe1 add rotatable bonds function 2011-03-10 05:14:32 +00:00
Greg Landrum
14f8e228db allow serialization of qmols too 2011-03-10 04:57:18 +00:00
Greg Landrum
80e5f1f38a remove leak 2011-03-09 05:10:14 +00:00
Greg Landrum
9a9ad4a534 expand atom and bond api 2011-03-09 05:07:00 +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
4f713e4e37 code reformatting : 
- tabs->spaces
  - fix indentation
 2011-02-28 06:40:43 +00:00
Greg Landrum
ca7c7173ee add support for blob I/O of molecules; fps still need to be added 2011-02-28 06:39:48 +00:00
Greg Landrum
9fe5a57aec support MolSuppliers and ROMol.{set,get}Prop 2011-02-26 05:53:03 +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
f7165fac1a minor wrapper cleanups 2011-02-24 07:34:26 +00:00
Greg Landrum
ae19a9d54b add bitvect morgan fps; rename morgan fp functions 2011-02-24 04:23:51 +00:00
Greg Landrum
4ca59a1987 clean up conformer handling in ChemTransforms 2011-02-22 06:16:23 +00:00
Greg Landrum
6191520012 updated std::list and std::vector support for java 2011-02-21 18:31:47 +00:00
Greg Landrum
0bc15ead9d additions to drawing code and SWIG wrappers 2011-02-21 06:45:34 +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
Greg Landrum
5a217746fb drop the qmol type when we uninstall 2011-02-14 19:12:53 +00:00
Greg Landrum
d7fa651e94 again, be more explicit with types 2011-02-12 05:51:43 +00:00