Paolo Tosco f96787eede - added a check for non-NULLness of d_atom and d_bond pointers ...

in the AtomElectrons and BondElectrons constructors
- removed superfluous NULLness check in ConjElectrons destructor
- outer electrons are used instead of atomic number to
  determine formal charging behaviour
- better handling of electronegativity using Allen electronegativity
  instead of the number of outer electrons
- removed superfluous code in sanitizeMol() (I had missed the
  "If there is a failure in the sanitization, a SanitException will be thrown"
  note)
- used getOtherAtom() method whose existence I ignored (thanks Greg!)

2015-10-19 00:06:31 +01:00

..

Basement/FeatTrees

update copyright statements

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

ChemReactions

Major conversion of std::string API to const std::string &

2015-09-25 15:15:59 -04:00

ChemTransforms

Major conversion of std::string API to const std::string &

2015-09-25 15:15:59 -04:00

Depictor

merge with master

2015-01-22 06:30:51 -05:00

Descriptors

Fixes #623

2015-09-22 05:00:57 -04:00

DistGeomHelpers

chirality test added and flag for them introduced

2015-09-29 11:30:54 +02:00

FileParsers

Fix regressions occurring when building with msvc9

2015-10-14 09:43:16 +02:00

FilterCatalog

make this build safely on the mac

2015-09-27 02:27:53 -04:00

Fingerprints

Move the query information functions from Fingerprints to QueryOps.h

2015-08-18 16:41:24 +02:00

FMCS

fmcs: fixes #631 with chiralirty

2015-10-07 14:40:31 +03:00

ForceFieldHelpers

Change to const std::string & API

2015-09-25 15:15:21 -04:00

FragCatalog

Change to const std::string & API

2015-09-25 15:15:21 -04:00

libs

initial import

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

MolAlign

add a central method for calculating the number of threads that supports negative numbers

2015-09-04 13:48:52 +02:00

MolCatalog

Dictionary access is saniztized and optimized.

2015-01-15 12:23:29 -05:00

MolChemicalFeatures

Code/RDBoost/Exceptions.h moved to Code/RDGeneral

2015-03-16 22:31:48 +01:00

MolDraw2D

support not clearing the background in drawings or explicitly setting the color;

2015-09-17 05:15:59 +02:00

MolDrawing

Dictionary access is saniztized and optimized.

2015-01-15 12:23:29 -05:00

MolHash

get the MolHash code building on windows

2015-04-14 06:07:11 +02:00

MolTransforms

Code/RDBoost/Exceptions.h moved to Code/RDGeneral

2015-03-16 22:31:48 +01:00

PartialCharges

robustify the #577 tests

2015-08-24 20:38:04 +02:00

ReducedGraphs

tests don't actually need static libs

2015-09-18 04:52:10 +02:00

ShapeHelpers

initial set of changes introducing python3 support

2014-06-17 18:26:41 +02:00

SLNParse

Fixes trailing whitespace parsing issues.

2015-09-26 10:40:43 -04:00

SmilesParse

Fixes FLEX/BISON infinite loop error

2015-09-25 16:09:24 -04:00

Subgraphs

Code/RDBoost/Exceptions.h moved to Code/RDGeneral

2015-03-16 22:31:48 +01:00

Substruct

- added ResonanceMolSupplier

2015-10-04 23:21:28 +01:00

test_data

RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog

2015-07-14 10:31:31 -04:00

testExecs

initial import

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

Wrap

Merge branch 'master' of https://github.com/ptosco/rdkit

2015-10-18 22:05:19 +01:00

AddHs.cpp

fix the chiral volume flag

2015-08-14 16:07:21 +02:00

AdjustQuery.cpp

add support for converting dummies to queries

2015-08-22 05:43:42 +02:00

Aromaticity.cpp

- fixed indentation

2015-07-16 20:10:21 +01:00

Atom.cpp

Merge remote-tracking branch 'upstream/master'

2015-10-18 22:03:19 +01:00

Atom.h

Change to const std::string & API

2015-09-25 15:15:21 -04:00

atomic_data.cpp

Fixes #510

2015-05-20 05:19:40 +02:00

atomic_data.h

get this building with MSVC++

2012-04-25 03:11:07 +00:00

AtomIterators.cpp

added const qualifiers to methods that are actually const

2015-04-13 22:47:00 +02:00

AtomIterators.h

added const qualifiers to methods that are actually const

2015-04-13 22:47:00 +02:00

Bond.cpp

convert ringInfo to a pointer

2015-03-22 16:46:36 +01:00

Bond.h

convert ringInfo to a pointer

2015-03-22 16:46:36 +01:00

BondIterators.cpp

added const qualifiers to methods that are actually const

2015-04-13 22:47:00 +02:00

BondIterators.h

added const qualifiers to methods that are actually const

2015-04-13 22:47:00 +02:00

bulktest.cpp

update copyright statements

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

Canon.cpp

merge

2015-04-10 09:44:18 +02:00

Canon.h

Bugfix: consider doIsomericSmiles flag in canonicalizeFragment

2015-03-20 16:38:23 +01:00

Chirality.cpp

Reverts non-string API related optimization

2015-09-26 10:40:24 -04:00

Chirality.h

merge with master

2015-01-22 06:30:51 -05:00

CMakeLists.txt

- added ResonanceMolSupplier

2015-10-04 23:21:28 +01:00

Conformer.cpp

update copyright statements

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

Conformer.h

Major conversion of std::string API to const std::string &

2015-09-25 15:15:59 -04:00

ConjugHybrid.cpp

stop messing up aromaticity and hybridization;

2013-11-30 08:07:09 +01:00

cptest.cpp

Fixes #384

2015-03-30 07:20:24 +02:00

details.h

add a forgotten file

2014-11-11 08:35:12 +01:00

FindRings.cpp

Fixes #526

2015-06-20 04:54:54 +02:00

GraphMol.cpp

remove exe property from source files

2011-01-13 04:22:56 +00:00

GraphMol.h

update copyright statements

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

hanoitest.cpp

Bugfix in SmilesWrite and some additional tests for getMolFrags function

2015-04-16 10:53:20 +02:00

itertest.cpp

Progress towards #181

2013-12-14 15:45:45 +01:00

Kekulize.cpp

- fixed missed kekulization of aromatic carbocations such as cyclopropenyl

2015-07-17 01:00:34 +01:00

Matrices.cpp

fix a dumb typo

2015-08-04 04:29:27 +02:00

memtest1.cpp

more property testing

2014-11-02 11:31:06 +01:00

MolDiscriminators.cpp

Dictionary access is saniztized and optimized.

2015-01-15 12:23:29 -05:00

MolOps.cpp

Fix regressions occurring when building with msvc9

2015-10-14 09:43:16 +02:00

MolOps.h

fix typo in docs

2015-09-11 11:21:43 +02:00

molopstest.cpp

Fixes #584

2015-08-27 10:00:35 +02:00

MolPickler.cpp

remove Atom::setMass()

2015-03-22 17:57:04 +01:00

MolPickler.h

changes suggested by Roger S:

2013-10-08 05:49:54 +02:00

MonomerInfo.h

Major conversion of std::string API to const std::string &

2015-09-25 15:15:59 -04:00

new_canon.cpp

new canon: tune special graph invariant

2015-06-15 15:43:02 +02:00

new_canon.h

New canonicalization: two small fixes

2015-04-21 13:24:53 +02:00

PeriodicTable.cpp

start to take a swing at the locale problem; this still needs testing on non-linux

2012-12-12 03:24:54 +00:00

PeriodicTable.h

remove some compiler warnings; patch from Roger S

2012-12-08 03:48:41 +00:00

QueryAtom.cpp

switch to using references to smart pointers for the Match functions;

2014-05-10 06:21:27 +02:00

QueryAtom.h

switch to using references to smart pointers for the Match functions;

2014-05-10 06:21:27 +02:00

QueryBond.cpp

introduce QueryBond::QueryMatch, as with QueryAtoms;

2014-05-07 05:29:25 +02:00

QueryBond.h

introduce QueryBond::QueryMatch, as with QueryAtoms;

2014-05-07 05:29:25 +02:00

QueryOps.cpp

Move the query information functions from Fingerprints to QueryOps.h

2015-08-18 16:41:24 +02:00

QueryOps.h

first pass at #567

2015-08-21 16:45:00 +02:00

querytest.cpp

remove Atom::setMass()

2015-03-22 17:57:04 +01:00

RDKitBase.h

update copyright statements

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

RDKitQueries.h

update copyright statements

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

regress.txt

initial import

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

Renumber.cpp

Fixes #584

2015-08-27 10:00:35 +02:00

resMolSupplierTest.cpp

- made a SMARTS pattern smarter

2015-10-07 12:18:03 +01:00

Resonance.cpp

- added a check for non-NULLness of d_atom and d_bond pointers

2015-10-19 00:06:31 +01:00

Resonance.h

- added a check for non-NULLness of d_atom and d_bond pointers

2015-10-19 00:06:31 +01:00

RingInfo.cpp

remove more extraneous preconditions

2013-12-02 04:15:43 +01:00

RingInfo.h

update copyright statements

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

Rings.h

more changes connected to sf.net issue 249

2012-09-16 05:40:17 +00:00

ROMol.cpp

Fixes #384

2015-03-30 07:20:24 +02:00

ROMol.h

Fixes #384

2015-03-30 07:20:24 +02:00

RWMol.cpp

Fixes #610

2015-09-09 18:39:56 +02:00

RWMol.h

Fixes #384

2015-03-30 07:20:24 +02:00

SanitException.h

Major conversion of std::string API to const std::string &

2015-09-25 15:15:59 -04:00

sanitTest.cpp

Dictionary access is saniztized and optimized.

2015-01-15 12:23:29 -05:00

test1.cpp

Fixes #610

2015-09-09 18:39:56 +02:00

test_list.py

get the new lapack-free version working on windows

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

testCanon.cpp

remove exe property from source files

2011-01-13 04:22:56 +00:00

testChirality.cpp

Fixes #553

2015-08-09 07:19:46 +02:00

testPickler.cpp

Dictionary access is saniztized and optimized.

2015-01-15 12:23:29 -05:00

UnitTestQueryMol.py

python3 portability fixes for pandas and the ipython notebook

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