Paolo Tosco 7aa42e3fd9 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

2016-08-06 05:21:48 +02:00

..

Catalogs

first pass, using google style

2015-11-14 14:58:11 +01:00

ChemicalFeatures

first pass, using google style

2015-11-14 14:58:11 +01:00

cmake/Modules

Made DistGeomHelpers test robust against small 3D coordinate variations (#961)

2016-06-28 20:11:31 +02:00

DataManip

Remove extra calls to python::register_exception_translator

2016-03-01 06:36:54 +01:00

DataStructs

Add a MultiFPBReader class (#909)

2016-05-29 09:38:14 -04:00

Demos

compiles without numpy warnings, all tests pass on ubuntu 15.04 with numpy 1.10

2015-11-28 06:49:34 +01:00

DistGeom

Improved planarity for ETKDG (#967)

2016-06-29 05:00:30 +02:00

doxygen

update doxygen files and add new logo without text

2013-07-11 07:19:33 +02:00

Features

first pass, using google style

2015-11-14 14:58:11 +01:00

ForceField

Dev/cleanup bad confs (#973)

2016-07-25 14:26:19 -04:00

Geometry

- removed the dependency on Trajectory from ROMol and ForceField

2016-05-11 19:37:09 +01:00

GraphMol

Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams() (#1007)

2016-08-06 05:21:48 +02:00

JavaWrappers

try and resolve intermittent travis build problems

2016-08-02 17:19:03 +02:00

ML

Remove extra calls to python::register_exception_translator

2016-03-01 06:36:54 +01:00

Numerics

- put SnapshotVect in the RDKit namespace

2016-05-11 23:41:31 +01:00

PgSQL/rdkit

- fixes typo which breaks the PostgreSQL cartridge build on Windows (#1008)

2016-08-05 05:02:52 +02:00

Query

Adds rdcasts where appropriate

2015-11-29 17:52:27 -05:00

RDBoost

Made DistGeomHelpers test robust against small 3D coordinate variations (#961)

2016-06-28 20:11:31 +02:00

RDGeneral

Fixes includes for older boost/gcc (#966)

2016-06-29 05:05:00 +02:00

SimDivPickers

Merge pull request #797 from greglandrum/fix/cleanup_register_execption

2016-03-12 08:03:45 -05:00

CMakeLists.txt

- added support for building the rdkit PostgreSQL cartridge within CMake

2016-02-21 22:00:10 +00:00

notes.txt

initial import

2006-05-06 22:20:08 +00:00

test_list.py

get geometry tests working on mac and include them in the default build

2009-10-02 10:12:46 +00:00