Paolo Tosco 7f71c7033d - made the ResonanceMolSupplier really lazy, i.e. resonance structure ...

enumeration is only carried out when the user asks for a structure
  or when the user explicitly request that calling the enumerate()
  member function. This makes object creation fast and enables
  calling getNumConjGrps(), getBondConjGrpIdx() and getAtomConjGrpIdx()
  member function without incurring in the cost of necessarily
  enumerating resonance structures
- fixed some int/unsigned int inconsistencies
- now bonds and atoms with do not belong to conjugated groups
  get a -1 index
- added a few Python wrappers
- added a few tests
- removed unused variables from Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp
- fixed ResonanceMolSupplier Java wrappers which were really broken

2015-11-03 14:57:56 +00:00

..

Basement/FeatTrees

update copyright statements

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

ChemReactions

Fixes bug in precondition & -> &&

2015-10-22 16:15:27 -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

fixes based on code review

2015-10-21 14:51:53 +02:00

FileParsers

Fix regressions occurring when building with msvc9

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

FilterCatalog

- Fixed a few glitches which caused the build to fail on Windows

2015-10-24 01:18:10 +01:00

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

- made the ResonanceMolSupplier really lazy, i.e. resonance structure

2015-11-03 14:57:56 +00:00

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

MMPA

Fixes #655

2015-11-02 04:36:50 +01:00

MolAlign

- added threading support to ResonanceMolSupplier and relevant tests

2015-11-01 23:01:34 +00:00

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

removed bare except statements

2015-09-07 13:27:14 +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

- made the ResonanceMolSupplier really lazy, i.e. resonance structure

2015-11-03 14:57:56 +00:00

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

- made the ResonanceMolSupplier really lazy, i.e. resonance structure

2015-11-03 14:57:56 +00:00

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 threading support to ResonanceMolSupplier and relevant tests

2015-11-01 23:01:34 +00:00

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

- fixed a problem with thiocarboxylates/thiolates not being perceived

2015-10-21 20:06:53 +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

fix undefined behavior for Windows x64 platform (for MMPA code)

2015-08-04 14:52:56 +03:00

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 the ResonanceMolSupplier really lazy, i.e. resonance structure

2015-11-03 14:57:56 +00:00

Resonance.cpp

- made the ResonanceMolSupplier really lazy, i.e. resonance structure

2015-11-03 14:57:56 +00:00

Resonance.h

- made the ResonanceMolSupplier really lazy, i.e. resonance structure

2015-11-03 14:57:56 +00:00

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