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Release_2016_03
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2238 Commits

Author SHA1 Message Date
Greg Landrum
88e193269d Fixes github #1073 (#1074) 
* Fixes #1073

* add a tests for #1073
 2016-10-10 10:21:57 +02:00
Greg Landrum
b929e5f7e4 Fixes #1051 2016-10-10 10:21:08 +02:00
Greg Landrum
4716167dc0 Fixes #1044 (#1077) 2016-10-10 10:17:59 +02:00
Greg Landrum
4930ba4f16 fixes #1023 (#1027) 2016-10-10 10:17:25 +02:00
Paolo Tosco
4a675c631c FMCS fix for Windows DLLs (#1030) 
* - Fixed a bug which prevented FMCS to work correctly on Windows when
  linking to DLLs

* - removed spurious debugging info
- fixed function name

* - correct fix for the pyFMCS issue

* - the already existing macro RDKIT_WRAP_DECL is used in lieu of
  RDFMCS_DLLIMPORT
 2016-08-18 12:40:03 +02:00
Greg Landrum
52cb217795 Support ETKDG from within the SWIG wrappers (#1010) 
* add test files

* add seed to the mol name so that it is obvious

* add support (and tests) for ETKDG to Java
 2016-08-18 11:49:07 +02:00
Paolo Tosco
633c7f8807 Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams() (#1007) 
* - calcImplicitValence() and setNumExplicitHs() are now called after
  all aromaticity flags have been set

* - ChemicalForceFields.MMFFHasAllMoleculeParams() now operates on a copy of the molecule
  such that atom and bond aromaticity are not altered by the check
- test11 was added to GraphMol/ForceFieldHelpers/Wrap/testHelpers.py to check
  for the two bugs fixed by this PR

* - modified the prototype of MMFFHasAllMoleculeParams() to take a const ROMol&
  and make a copy of that within the function body
- removed unnecessary imports from testHelpers.py
- replaced EmbedMolecule() with a quicker test

* - WIP

* - now the issue seems to be properly fixed, as the implicit valence
  made explicit does not sum up anymore to the already explicit valence
 2016-08-18 11:48:47 +02:00
Greg Landrum
29b829f9b8 Fixes #962 (#1003) 2016-08-18 11:47:45 +02:00
Greg Landrum
3b2f5a5212 Fix github #908 2016-08-18 11:47:38 +02:00
Greg Landrum
d112cbb5e0 Fix github #868 2016-08-18 11:46:32 +02:00
Brian Kelley
9cbab232be Fixes middle-justified symbols in sd files, adds M_CHG tests (#1002) 
* Adds boost::trim, M  CHG tests

* stoi is a c++11 feature

* Actually test charges
 2016-08-18 11:41:08 +02:00
NadineSchneider
0b40ccae9f ChemReactions: Bugfix in copy constructor (#996) 2016-08-18 11:40:34 +02:00
Paolo Tosco
e73fde7130 - RCSB SDF files which feature right-justified element names can now be parsed (#994) 
- added a relevant test
 2016-08-18 11:40:03 +02:00
Greg Landrum
b29f463298 A variety of drawing-related changes (#986) 
* Fixes #982
also changes bond-wedging algorithm to favor lighter non-ring bonds

* prefer wedging bonds to lower-degree atoms

* Fixes #983

* small fixes
- Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom
- Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom.

* Fixes #985

This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
 2016-08-18 11:39:27 +02:00
Greg Landrum
608b69104a Fixes #975 (#976) 2016-07-22 06:31:31 +02:00
Greg Landrum
cf9e8248fe Fixes #953 (#954) 2016-07-22 06:31:05 +02:00
Greg Landrum
855cddcbea Fixes #932 (#950) 2016-06-23 04:28:20 +02:00
Greg Landrum
917d6421d9 Fix/github910 (#913) 
* A big step towards solving #910

1) Rank atoms by inverse atomic number (ensures Hs go last)
2) Use heavy-atom degree when doing layout (ensures Hs do not change gross geometry)

* basic testing

* take degree into account with ranks too

* further improvements of relative ranking.
definitely need some cleanup of this now

* some cleanup

* add an explicit test
 2016-05-20 06:24:37 +02:00
Greg Landrum
55131ca01d Fixes #906 2016-05-16 15:07:37 +02:00
Greg Landrum
8b99fd924f Fixes #904 (#905) 2016-05-16 15:07:13 +02:00
Greg Landrum
0bf0267417 Fixes depictor problem with empty fragments (#894) 
@rvianello caught that this one was causing intermittent problems on windows.
 2016-05-16 15:06:01 +02:00
Greg Landrum
a24de4c10c Merge pull request #870 from bp-kelley/fix/fixes-numrotatablebonds-python 
Fixes regression in python api CalcNumRotatableBonds
 2016-05-16 15:04:44 +02:00
Greg Landrum
4d4b5f6a28 Fix for github874 (#877) 
* Fixes #874

* minor cleanup

* test for 874
 2016-05-16 15:00:22 +02:00
Greg Landrum
c0f9be86c8 Get things building with gcc4.4 on centos6 
* Fixes exposing shared_ptr<const T> to python

* remove some of the pragmas for pre 4.5 versions of gcc

* get things working with centos6 and gcc4.4
 2016-04-17 11:48:35 -04:00
Greg Landrum
21cbc23783 remove debugging output 2016-04-15 15:10:42 +01:00
Greg Landrum
0ff9a758aa width is now right (at least much closer to it) 
height also looks good, but we still need a vertical shift if there is a subscript
 2016-04-15 15:09:19 +01:00
Greg Landrum
e2dca37212 another test case 2016-04-14 15:56:44 +02:00
Greg Landrum
8c3d28da67 Fixes #860 2016-04-14 15:50:36 +02:00
Greg Landrum
369adf58b5 Fix a typo in smiles.ll 
The problem would only show up when RDK_USE_FLEXBISON is enabled.
 2016-04-13 12:27:00 +02:00
Greg Landrum
3215014aa6 Merge pull request #857 from DoliathGavid/mcs_bugfix 
Fix out of range dereference in MCS code.
 2016-04-13 09:59:11 +02:00
Doliath Gavid
1729c90748 Fix crazy out of range dereference 2016-04-12 19:42:24 -04:00
Greg Landrum
b9751b687c post-pull cleanup on #853 
Suggested in the comments post-merge
 2016-04-12 02:58:23 +02:00
Greg Landrum
33489e70e3 Fixes #852 
* Fixes #852

The test added is the usual thing for the drawing code: produce some files for visual inspection.

* limit the number of lines in a short wedge
 2016-04-11 13:40:44 -04:00
Brian Kelley
373708c4c8 Merge pull request #851 from greglandrum/fix/use_of_isotopes_in_ReduceProductToSideChains 
stop including isotope labels in reduceProductToSideChains()
 2016-04-08 14:13:51 -04:00
Greg Landrum
bb4df7c082 stop including isotope labels on dummies from reduceProductToSideChains() 
The atom-map info is there and is sufficient, adding the redundant isotope info does not help
 2016-04-08 03:38:06 +02:00
Paolo Tosco
e4a9df4c89 - fixed a bug in getUFFAngleBendParams() 2016-04-08 00:07:00 +01:00
Paolo Tosco
f80a736468 - further improvement to avoid exception on Linux with Python 3.x 
- extension of the fix to all other flush() and close() methods
 2016-04-02 23:19:11 +01:00
Paolo Tosco
7b5c41b734 - fixed the crash in testGithub497() on Windows with Python 3.x and MSVC 2015 2016-04-02 14:50:12 +01:00
Paolo Tosco
fee571a392 - attempt to fix a crash on Windows with Python 3.x when running 
testGithub497()
 2016-04-02 01:22:55 +01:00
Brian Kelley
bd8bdb09d4 Fixes exception when using gcc 4.1 or earlier (RHEL5 default compiler) 2016-04-01 11:02:35 -04:00
Greg Landrum
ccc723040c Merge pull request #840 from NadineSchneider/master 
Add some utils functions to ChemReactions
 2016-04-01 16:12:47 +02:00
Greg Landrum
7ca16e6d54 Merge pull request #828 from greglandrum/fix/github188 
Fixes #188
 2016-04-01 16:11:48 +02:00
Brian Kelley
b872fb823e Merge pull request #839 from greglandrum/feat/additional_cleanups 
Additional "hypervalent" halogen cleanups
 2016-04-01 08:42:07 -04:00
Nadine Schneider
7a109aea89 Add some utils functions to ChemReactions 
Chemical reactions: provide function to re/move agents
Chem Reactions: Add utils function to remove atom-mapping numbers
 2016-04-01 10:14:21 +02:00
Nadine Schneider
d3f9d7c6e1 RDKFingerprint: add an unfolded count-based version of the RDKFingerprint 
- add a bitinfo map to the RDKFingerprint
- refactor some code to largely avoid code duplicates
 2016-04-01 09:10:47 +02:00
Greg Landrum
f762346ced make the perchlorate cleanup pattern more generic to cover all halogenates; 
Fixes #115
 2016-04-01 07:54:32 +02:00
Brian Kelley
80f38ecce9 Merge pull request #832 from greglandrum/feat/github831 
feat/github831: Add getSDText() static method.
 2016-03-30 23:51:35 -04:00
Greg Landrum
2e961be508 rename method to getText() 2016-03-31 05:17:41 +02:00
Brian Kelley
5b91ced93d Merge pull request #830 from greglandrum/dev/suppress_unused 
Fix a bunch of compiler warnings
 2016-03-30 14:55:53 -04:00
Greg Landrum
a54596d820 Merge pull request #821 from DoliathGavid/alignTransformFix 
Fix alignMols so that it takes into account of QueryAtoms and QueryBonds
 2016-03-30 17:23:05 +02:00