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

..

Basement/FeatTrees

first pass, using google style

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

ChemReactions

ChemReactions: Bugfix in copy constructor (#996)

2016-07-27 10:22:13 -04:00

ChemTransforms

Fixes #511

2016-03-29 16:56:15 +02:00

Depictor

Fix/github910 (#913)

2016-05-20 05:23:12 +01:00

Descriptors

Get this building with RDK_THREADSAFE_SSS OFF

2016-06-22 16:50:22 +02:00

DistGeomHelpers

Fixes rounding errors in test (#1001)

2016-08-02 06:07:47 +02:00

FileParsers

Fixes middle-justified symbols in sd files, adds M_CHG tests (#1002)

2016-08-02 14:41:08 +02:00

FilterCatalog

Fix github #868 (#925)

2016-05-31 13:23:21 -04:00

Fingerprints

Fix for github874 (#877)

2016-04-23 11:53:13 -04:00

FMCS

Modifications to enable building with MinGW compilers (#960)

2016-06-25 09:12:40 +02:00

ForceFieldHelpers

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

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

FragCatalog

Remove extra calls to python::register_exception_translator

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

libs

initial import

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

MMPA

Modifications to enable building with MinGW compilers (#960)

2016-06-25 09:12:40 +02:00

MolAlign

Merge pull request #830 from greglandrum/dev/suppress_unused

2016-03-30 14:55:53 -04:00

MolCatalog

Remove extra calls to python::register_exception_translator

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

MolChemicalFeatures

Remove extra calls to python::register_exception_translator

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

MolDraw2D

A variety of drawing-related changes (#986)

2016-07-25 17:28:41 -04:00

MolDrawing

first pass, using google style

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

MolHash

rename rdk_unique_ptr to rdk_auto_ptr

2016-02-13 14:58:35 +01:00

MolTransforms

- fixed a few missing "const" declarations on "get" functions

2016-02-21 21:24:56 +00:00

PartialCharges

Remove extra calls to python::register_exception_translator

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

ReducedGraphs

Remove extra calls to python::register_exception_translator

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

ShapeHelpers

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

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

SLNParse

another batch of warnings squashed

2016-03-30 13:44:21 +02:00

SmilesParse

Fixes #893 (#958)

2016-06-24 14:20:47 +02:00

Subgraphs

first pass, using google style

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

Substruct

passes all tests except FMCS

2015-12-13 17:18:36 +01:00

test_data

- initial work to put the Trajectory code into a separate object

2016-05-09 19:05:15 +01:00

testExecs

initial import

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

Trajectory

Java wrappers for Trajectory/Snapshot objects (#977)

2016-07-20 22:51:01 -04:00

Wrap

Expose the aromatizeIfPossible parameter to python (#991)

2016-07-26 13:17:41 -04:00

AddHs.cpp

Merge fix/github908 branch

2016-07-27 04:49:55 +02:00

AdjustQuery.cpp

Adds aromatization and reaction options to AdjustQuery (#965)

2016-06-29 05:09:30 +02:00

Aromaticity.cpp

Add support for a simplified aromaticity model. (#942)

2016-06-17 17:48:20 -04:00

Atom.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

Atom.h

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

atomic_data.cpp

Fixes #694

2016-02-16 15:38:02 +01:00

atomic_data.h

Fixes #694

2016-02-16 15:38:02 +01:00

AtomIterators.cpp

first pass, using google style

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

AtomIterators.h

first pass, using google style

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

Bond.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

Bond.h

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

BondIterators.cpp

first pass, using google style

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

BondIterators.h

first pass, using google style

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

bulktest.cpp

first pass, using google style

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

Canon.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

Canon.h

first pass, using google style

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

Chirality.cpp

an alternate approach to fixing #805

2016-03-13 04:21:36 -07:00

Chirality.h

first pass, using google style

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

CMakeLists.txt

- removed the dependency on Trajectory from ROMol and ForceField

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

Conformer.cpp

first pass, using google style

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

Conformer.h

Fixes missing rdcast (caused infinite recursion)

2015-11-29 20:33:09 -05:00

ConjugHybrid.cpp

first pass, using google style

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

cptest.cpp

first pass, using google style

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

details.h

first pass, using google style

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

FindRings.cpp

Adds rdcasts where appropriate

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

GraphMol.cpp

first pass, using google style

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

GraphMol.h

first pass, using google style

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

hanoitest.cpp

first pass, using google style

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

itertest.cpp

first pass, using google style

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

Kekulize.cpp

Fixes #962 (#1003)

2016-08-05 07:57:20 -04:00

Matrices.cpp

Addressed code review suggestions

2016-02-09 09:21:48 +02:00

memtest1.cpp

first pass, using google style

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

MolDiscriminators.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

MolOps.cpp

make the perchlorate cleanup pattern more generic to cover all halogenates;

2016-04-01 07:54:32 +02:00

MolOps.h

Adds aromatization and reaction options to AdjustQuery (#965)

2016-06-29 05:09:30 +02:00

molopstest.cpp

Fixes #962 (#1003)

2016-08-05 07:57:20 -04:00

MolPickler.cpp

Fixes #713

2015-12-22 07:18:35 +01:00

MolPickler.h

first pass, using google style

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

MonomerInfo.h

first pass, using google style

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

new_canon.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

new_canon.h

remove wave of warnings

2016-03-30 13:09:59 +02:00

PeriodicTable.cpp

Fixes #381 (#924)

2016-05-30 19:58:39 -04:00

PeriodicTable.h

Fixes #381 (#924)

2016-05-30 19:58:39 -04:00

QueryAtom.cpp

first pass, using google style

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

QueryAtom.h

first pass, using google style

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

QueryBond.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

QueryBond.h

first pass, using google style

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

QueryOps.cpp

first pass, using google style

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

QueryOps.h

Dev/cleanup warnings (#948)

2016-06-22 13:49:15 -04:00

querytest.cpp

first pass, using google style

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

RDKitBase.h

update copyright statements

2010-09-26 17:04:37 +00:00

RDKitQueries.h

first pass, using google style

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

regress.txt

initial import

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

Renumber.cpp

first pass, using google style

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

resMolSupplierTest.cpp

first pass, using google style

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

Resonance.cpp

- fixed a couple of compilation warnings in Resonance.cpp/Resonance.h

2015-12-16 17:33:22 +00:00

Resonance.h

- fixed a couple of compilation warnings in Resonance.cpp/Resonance.h

2015-12-16 17:33:22 +00:00

RingInfo.cpp

Adds rdcasts where appropriate

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

RingInfo.h

first pass, using google style

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

Rings.h

first pass, using google style

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

ROMol.cpp

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

ROMol.h

Adds RDAny (smaller generic holder) Updates all used dictionaries (#896)

2016-05-29 17:04:21 +01:00

RWMol.cpp

Bug when removing stereo info?

2016-06-20 16:40:33 +01:00

RWMol.h

Fixes #940 (#941)

2016-06-14 07:47:15 +02:00

SanitException.h

first pass, using google style

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

sanitTest.cpp

first pass, using google style

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

test1.cpp

Fixes #381 (#924)

2016-05-30 19:58:39 -04:00

test_list.py

get the new lapack-free version working on windows

2009-10-31 05:24:15 +00:00

testCanon.cpp

first pass, using google style

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

testChirality.cpp

Fixes #803

2016-03-09 05:05:33 +01:00

testPickler.cpp

add a test for #713

2015-12-23 05:31:37 +01:00

UnitTestQueryMol.py

python3 portability fixes for pandas and the ipython notebook

2014-09-11 23:49:45 +02:00