Brian Cole 360421e2a8 Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0 (#1635) ...

* Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0.

Fixing two distinct bugs:

- A randomSeed of 0 didn't use '0' as the seed even though the
  documentation said that it should.

- Very large seeds could overflow the 'int' representation during
  calculation of a new internal seed. This would make
  EmbedMultipleConfs non-deterministic even though the user provided a
  valid seed.

* Adding a C++ test for case pull request #1635.

2017-11-15 06:53:42 +01:00

..

Basement/FeatTrees

first pass, using google style

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

ChemReactions

send a string, not a stringstream, to the log message

2017-11-15 06:47:49 +01:00

ChemTransforms

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

Depictor

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

Descriptors

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

DistGeomHelpers

Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0 (#1635)

2017-11-15 06:53:42 +01:00

FileParsers

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

FilterCatalog

Further cmake improvements (#1515)

2017-08-07 15:49:08 +02:00

Fingerprints

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

FMCS

another pass of clang modernize

2017-10-12 06:35:51 +02:00

ForceFieldHelpers

Version 2 of ETKDG (#1597)

2017-11-15 06:50:39 +01:00

FragCatalog

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

libs

initial import

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

MMPA

another clang-format run

2017-10-12 06:42:15 +02:00

MolAlign

another clang-format run

2017-10-12 06:42:15 +02:00

MolCatalog

clang-tidy output

2017-04-22 17:09:24 +02:00

MolChemicalFeatures

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

MolDraw2D

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

MolDrawing

Partial support for reading CXSMILES (#1237)

2017-01-31 13:50:36 -05:00

MolHash

another pass of clang modernize

2017-10-12 06:35:51 +02:00

MolTransforms

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

PartialCharges

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +02:00

ReducedGraphs

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

RGroupDecomposition

another clang-format run

2017-10-12 06:42:15 +02:00

ShapeHelpers

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

SLNParse

Further cmake improvements (#1515)

2017-08-07 15:49:08 +02:00

SmilesParse

Add support for %(NNN) notation for ring closures (#1624)

2017-11-15 06:48:11 +01:00

StructChecker

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

Subgraphs

merge to master

2017-07-21 04:50:35 +02:00

Substruct

another clang-format run

2017-10-12 06:42:15 +02:00

SubstructLibrary

another clang-format run

2017-10-12 06:42:15 +02:00

test_data

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

testExecs

initial import

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

Trajectory

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

Wrap

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

AddHs.cpp

merge on master; modernization needs to be repeated

2017-09-05 17:09:50 +02:00

AdjustQuery.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

Aromaticity.cpp

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

Atom.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Atom.h

Fixes #1041 (#1070)

2016-09-22 14:38:13 +02:00

atomic_data.cpp

SMILES lexer optimization/enhancement (#1575)

2017-09-17 09:12:53 -04:00

atomic_data.h

Fixes #694

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

AtomIterators.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

AtomIterators.h

Fix/github1366 (#1382)

2017-03-28 16:01:36 -04:00

blah

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

blah.hpp

[MRG] Fix PDB reader + add argument to toggle proximity bonding (#1629)

2017-11-15 06:53:31 +01:00

Bond.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

Bond.h

Add cis/trans tags to double bonds (#1316)

2017-02-26 08:15:44 -05:00

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

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Canon.h

Partial support for reading CXSMILES (#1237)

2017-01-31 13:50:36 -05:00

Chirality.cpp

another clang-format run

2017-10-12 06:42:15 +02:00

Chirality.h

first pass, using google style

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

CMakeLists.txt

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

Conformer.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

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

clang-tidy output

2017-04-22 17:09:24 +02:00

details.h

first pass, using google style

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

FindRings.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

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

another clang-format run

2017-10-12 06:42:15 +02:00

itertest.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

Kekulize.cpp

Fix for #1478 (#1486)

2017-07-02 11:31:14 +02:00

Matrices.cpp

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

memtest1.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

MolBundle.h

another clang-format run

2017-10-12 06:42:15 +02:00

MolDiscriminators.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

MolOps.cpp

another pass of clang modernize

2017-10-12 06:35:51 +02:00

MolOps.h

handle the heavy-atom degree queries differently (#1560)

2017-09-12 16:10:15 -04:00

molopstest.cpp

another clang-format run

2017-10-12 06:42:15 +02:00

MolPickler.cpp

another clang-format run

2017-10-12 06:42:15 +02:00

MolPickler.h

another clang-format run

2017-10-12 06:42:15 +02:00

MonomerInfo.h

first pass, using google style

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

new_canon.cpp

another pass of clang modernize

2017-10-12 06:35:51 +02:00

new_canon.h

Fixes github1567 (#1576)

2017-09-19 08:04:18 -04:00

PeriodicTable.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

PeriodicTable.h

Fixes #381 (#924)

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

QueryAtom.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

QueryAtom.h

set atom->setQuery() to delete old query (#1604)

2017-10-03 17:46:06 -04:00

QueryBond.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

QueryBond.h

set atom->setQuery() to delete old query (#1604)

2017-10-03 17:46:06 -04:00

QueryOps.cpp

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

QueryOps.h

handle the heavy-atom degree queries differently (#1560)

2017-09-12 16:10:15 -04:00

querytest.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

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

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

resMolSupplierTest.cpp

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

Resonance.cpp

run clang-format with c++-11 style over that

2017-04-22 17:19:10 +02:00

Resonance.h

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

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

RingInfo.cpp

a number of other small changes from manually reviewing the PR

2017-04-22 17:24:57 +02:00

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

Merge branch 'master' into modern_cxx

2017-10-05 05:58:38 +02:00

ROMol.h

Add a MolBundle class (#1537)

2017-09-11 13:04:58 -04:00

RWMol.cpp

another clang-format run

2017-10-12 06:42:15 +02:00

RWMol.h

another clang-format run

2017-10-12 06:42:15 +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

Fix/github1453 (#1463)

2017-07-02 11:29:39 +02:00

test_list.py

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +02:00

testCanon.cpp

clang-tidy output

2017-04-22 17:09:24 +02:00

testChirality.cpp

Fixes github1497 (#1555)

2017-09-11 08:37:32 -04:00

testMolBundle.cpp

Add a MolBundle class (#1537)

2017-09-11 13:04:58 -04:00

testPickler.cpp

another pass of clang modernize

2017-10-12 06:35:51 +02:00

testPicklerGlobalSettings.cpp

Dev/pickle properties (#1277)

2017-02-09 16:06:01 +01:00

UnitTestQueryMol.py

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +02:00