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1723 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
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
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
Riccardo Vianello
d1c515b26a added const qualifiers to methods that are actually const 2015-04-13 22:47:00 +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
d778060bcf Merge branch 'master' into mol_hash_and_fmcs_Feb2015 2015-04-11 06:44:22 +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
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
c134974d3a support empty SMILES and SMARTS strings 2015-04-02 11:11:09 +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
Greg Landrum
ea7f446369 and fix ChiNn too (#463) 2015-03-26 08:41:09 -04:00
Greg Landrum
61eba20423 add another test for #463 2015-03-26 08:38:02 -04:00
Greg Landrum
9208936bbb Fixes #463 2015-03-26 07:10:02 -04:00
Greg Landrum
8c3d698472 remove some compiler warnings 2015-03-22 18:13:58 +01:00
Greg Landrum
797db2fa82 remove Atom::setMass() 2015-03-22 17:57:04 +01:00
Greg Landrum
37673af15a remove dativeFlag from atoms 2015-03-22 17:48:06 +01:00
Greg Landrum
577f5fb4c8 convert ringInfo to a pointer 2015-03-22 16:46:36 +01:00
Greg Landrum
12d2ffb6b2 Merge branch 'master' of https://github.com/rdkit/rdkit 2015-03-22 04:39:19 +01:00
Greg Landrum
ebaf3aff89 additional test related to #432 2015-03-21 07:17:09 +01:00
Nadine Schneider
7ddff9c71c Some performance fixes 2015-03-20 18:19:08 +01:00
Nadine Schneider
7e59908121 SmilesWrite: introduce new function for fragments 2015-03-20 16:38:23 +01:00
Nadine Schneider
95dae49968 Some bugfixes in new_canon 
- Order of comparison in SpecialChiralityAtomCompareFunctor
- Handling of Bond::STEREOANY in the bondholder vector
 2015-03-20 16:38:23 +01:00
Nadine Schneider
140dc2d938 Bugfix: consider doIsomericSmiles flag in canonicalizeFragment 2015-03-20 16:38:23 +01:00
Nadine Schneider
b8492cb698 Bugfix in canonicalisation of fragments 2015-03-20 16:38:23 +01:00