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2331 Commits

Author SHA1 Message Date
Nadine Schneider
0cf0dd37ce Bugfix in SmilesWrite and some additional tests for getMolFrags function 2015-04-16 10:53:20 +02:00
Greg Landrum
37841d7e78 update library ordering for cartridge makefile 2015-04-16 05:11:15 +02:00
Nadine Schneider
0b8b6a3690 Some performance fixes for the new canonicalization 
- handling molecules/proteins with multiple fragments
- add criteria for using special symmetry invariant
 2015-04-15 18:42:29 +02:00
Greg Landrum
895668e610 changes to the SWIG wrappers to get them working on windows 2015-04-15 05:32:06 +01:00
Greg Landrum
b1b5a535d5 get the MolHash code building on windows 2015-04-14 06:07:11 +02:00
Greg Landrum
781d205863 Merge pull request #479 from rvianello/atomiterator_bonditerator_const 
added const qualifiers to some methods of Atom/Bond iterator classes
 2015-04-14 05:27:19 +02:00
Greg Landrum
87da7cd81d Merge pull request #478 from rvianello/install_FMCS_Graph_header 
install missing FMCS/Graph.h header file
 2015-04-14 05:07:07 +02:00
Riccardo Vianello
d1c515b26a added const qualifiers to methods that are actually const 2015-04-13 22:47:00 +02:00
Greg Landrum
bbdea57838 clean some comments out of the sql input 2015-04-13 07:27:46 +02:00
Riccardo Vianello
72576ba4e1 install missing Graph.h header file 2015-04-12 17:43:42 +02:00
Greg Landrum
3077ea75dc an optimization for when molecules have no stereochemistry indicated 2015-04-12 06:44:45 +02:00
Greg Landrum
68a8cf4ce8 do not kekulize if there are neither aromatic bonds nor aromatic atoms 2015-04-12 05:59:35 +02:00
Greg Landrum
f196784218 update expected cartridge reaction-test results 2015-04-11 07:22:10 +02:00
Greg Landrum
d778060bcf Merge branch 'master' into mol_hash_and_fmcs_Feb2015 2015-04-11 06:44:22 +02:00
Greg Landrum
c19628be5f Merge branch 'mol_hash_and_fmcs_Feb2015' of github.com:rdkit/rdkit into mol_hash_and_fmcs_Feb2015 2015-04-11 03:31:13 +02:00
Greg Landrum
80f7ac4515 Merge branch 'master' of github.com:rdkit/rdkit 2015-04-11 03:06:13 +02:00
Greg Landrum
0e56ca1dc0 default to 400 iterations for the dgeom force field 2015-04-11 03:06:08 +02:00
Alexander Savelyev
b0177a4ea1 restore java and python wrappers. New parameter (matchChiralTag) was added. New function findFMCS_P() receives json parameters 2015-04-10 16:24:58 +03:00
Nadine Schneider
0132cc72e9 Merge branch 'newCanon' into master3 
Conflicts:
	Code/GraphMol/SmilesParse/test.cpp
 2015-04-10 10:25:47 +02:00
Nadine Schneider
f1babca032 some clean-up in new_canon.h 2015-04-10 09:47:18 +02:00
Nadine Schneider
b4c230c7d0 new_canon: move hanoiSort to a seperate file 2015-04-10 09:47:17 +02:00
Greg Landrum
97d70dd306 add compile-time option to use new sterochem 2015-04-10 09:47:17 +02:00
Greg Landrum
a66662b2a2 switch back to using the previous stereochemistry code for now 2015-04-10 09:47:17 +02:00
Greg Landrum
97c0bcc202 safety first 2015-04-10 09:47:17 +02:00
Nadine Schneider
ca4bcca6ae Include atom-mapping numbers if present in the canonicalization 2015-04-10 09:47:16 +02:00
Nadine Schneider
6ae384a34a Fix for canonicalization of chem reactions 2015-04-10 09:47:16 +02:00
Nadine Schneider
33f9906572 Chemical reactions: allow canonical order in reaction smiles 2015-04-10 09:47:15 +02:00
Nadine Schneider
267e4b9f0e Fix in SmilesWrite 2015-04-10 09:47:15 +02:00
Nadine Schneider
69ceace885 Bugfix in SpecialChiralityAtomCompareFunctor and additional tests 
Conflicts:

	Code/GraphMol/hanoitest.cpp
 2015-04-10 09:47:09 +02:00
Greg Landrum
fba1bf24ee update expected results 2015-04-10 09:44:32 +02:00
Nadine Schneider
5d963846b8 merge 2015-04-10 09:44:18 +02:00
Greg Landrum
7b0d494dc3 update expected results from cartridge tests 2015-04-10 09:29:26 +02:00
Greg Landrum
2cad2e05aa update expected results in java 2015-04-10 09:29:26 +02:00
Greg Landrum
b50260fa85 update README.md to include fingerprints 2015-04-09 04:21:38 +01:00
Paolo Tosco
0fc9499c81 - modified Code/GraphMol/CMakeLists.txt to make it build under Windows 
- modified Code/GraphMol/FileParsers/testMolSupplier.cpp in order
  to avoid testSetStreamIndices() failure on Windows due to CR+LF
  issues
 2015-04-08 16:23:19 +01:00
Alexander Savelyev
ec6ecdd3bc request notes were fixed. chirality algorithm was slighlty improved 2015-04-06 19:53:19 +03:00
Brian Kelley
48a7549773 Travis Tests could not find the mol file 2015-04-06 10:07:11 -04:00
Brian Kelley
bf8821f60f Added test file for atom list round tripping 2015-04-05 22:41:23 -04:00
Brian Kelley
85e2e94d20 Fix MolFile Atom Line List Writer 
Only the first element in the atom one was being
written correctly, the remainder were not being
padded correctly and could not be round tripped.
 2015-04-05 20:47:02 -04:00
Greg Landrum
d3d362a702 merge master 2015-04-03 07:23:23 +02:00
Greg Landrum
d7474cd621 Merge branch 'Issue469' 2015-04-03 07:14:39 +02:00
Greg Landrum
a0b9b94f34 check empty string handling in the cartridge too 2015-04-02 11:15:33 +02:00
Greg Landrum
c134974d3a support empty SMILES and SMARTS strings 2015-04-02 11:11:09 +02:00
Greg Landrum
f0d4cf1ec6 first pass at a solution for #469 2015-04-02 10:10:22 +02:00
Jan Holst Jensen
d0b3f9e84e Add code to accept blank SMILES input. 
No-Structures are saved to database dumps as blank strings ''.
This patch allows dumps with No-Structures to be read back in.
 2015-04-01 16:54:12 +02:00
Greg Landrum
2b107bd886 Fixes #467 2015-04-01 02:37:02 +02:00
Alexander Savelyev
c6be709dad fix fmcs comparator functions 2015-03-30 18:26:48 +03:00
Alexander Savelyev
dc208b0829 chirality flag was implemented for fmcs() function 2015-03-30 18:17:57 +03:00
Greg Landrum
b78bb40ca5 Fixes #384 2015-03-30 07:20:24 +02:00
Greg Landrum
5264919ccc update version of the Chi descriptors 2015-03-26 08:42:54 -04:00