rdkit

mirror of https://github.com/rdkit/rdkit.git synced 2026-06-05 22:04:27 +08:00

Files

Brian Cole e2fe6d8429 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.

2017-12-02 05:50:57 +01:00

Basement/FeatTrees

first pass, using google style

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

ChemReactions

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

ChemTransforms

Partial support for reading CXSMILES (#1237 )

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

Depictor

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

Descriptors

get the new code building with the old compiler (#1601 )

2017-10-02 09:37:18 +02:00

DistGeomHelpers

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

2017-12-02 05:50:57 +01:00

FileParsers

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

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

FilterCatalog

fixes #1435 (#1437 )

2017-05-31 08:29:32 +02:00

Fingerprints

Fix #1496 (#1517 )

2017-08-15 13:00:30 -04:00

FMCS

Add the option to match formal charges to FMCS (#1311 )

2017-02-28 08:49:28 -05:00

ForceFieldHelpers

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

FragCatalog

clear up a bunch of windows warnings (#1086 )

2016-10-04 06:46:07 -04:00

libs

initial import

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

MMPA

Adds canonicalization of atom maps (#1521 )

2017-08-12 05:36:09 +02:00

MolAlign

Added C++ version of getBestRMS() (#1568 )

2017-09-16 04:44:06 +02:00

MolCatalog

Issue1071/yapf (#1078 )

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

MolChemicalFeatures

Issue1071/yapf (#1078 )

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

MolDraw2D

Enable windows build that uses cairo (#1628 )

2017-12-02 05:46:18 +01:00

MolDrawing

Partial support for reading CXSMILES (#1237 )

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

MolHash

Issue1071/yapf (#1078 )

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

MolTransforms

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

PartialCharges

Issue1071/yapf (#1078 )

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

ReducedGraphs

Issue1071/yapf (#1078 )

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

RGroupDecomposition

get the new code building with the old compiler (#1601 )

2017-10-02 09:37:18 +02:00

ShapeHelpers

Issue1071/yapf (#1078 )

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

SLNParse

Partial support for reading CXSMILES (#1237 )

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

SmilesParse

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

2017-12-02 05:44:23 +01:00

StructChecker

Fixes github1497 (#1555 )

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

Subgraphs

Issue1071/yapf (#1078 )

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

Substruct

Add a MolBundle class (#1537 )

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

SubstructLibrary

Removes trailing spaces after \ to fix windows compilation errors (#1516 )

2017-08-06 16:38:15 -04:00

test_data

Fixes github1497 (#1555 )

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

testExecs

initial import

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

Trajectory

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

Wrap

add substructure searches of Mols using MolBundles from Python (#1603 )

2017-10-03 17:46:44 -04:00

AddHs.cpp

Fixes #1439 (#1530 )

2017-08-23 17:24:47 -04:00

AdjustQuery.cpp

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

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

Aromaticity.cpp

Partial support for reading CXSMILES (#1237 )

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

Atom.cpp

Fixes #1387 (#1392 )

2017-04-07 11:57:43 -04:00

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

Fix/github1366 (#1382 )

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

AtomIterators.h

Fix/github1366 (#1382 )

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

Bond.cpp

Fix/urange check (#1506 )

2017-09-11 21:17:33 +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

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

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

Canon.h

Partial support for reading CXSMILES (#1237 )

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

Chirality.cpp

Fixes github1497 (#1555 )

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

Chirality.h

first pass, using google style

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

CMakeLists.txt

Add a MolBundle class (#1537 )

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

Conformer.cpp

Fix/urange check (#1506 )

2017-09-11 21:17:33 +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

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

Fixes #1281 in a way (#1553 )

2017-09-08 12:10:07 -04:00

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

Fixes github1567 (#1576 )

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

itertest.cpp

Fix/github1366 (#1382 )

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

Kekulize.cpp

Fix for #1478 (#1486 )

2017-07-01 09:03:26 -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

MolBundle.h

Add a MolBundle class (#1537 )

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

MolDiscriminators.cpp

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

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

MolOps.cpp

Fixes #1605 (#1606 )

2017-10-07 07:08:56 +02:00

MolOps.h

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

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

molopstest.cpp

Fixes #1605 (#1606 )

2017-10-07 07:08:56 +02:00

MolPickler.cpp

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

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

MolPickler.h

Fixes blanking of non-query atom data when QueryAtomData was being pi… (#1541 )

2017-09-07 20:43:08 +02:00

MonomerInfo.h

first pass, using google style

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

new_canon.cpp

Fixes github1567 (#1576 )

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

new_canon.h

Fixes github1567 (#1576 )

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

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

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

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

QueryBond.cpp

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

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

QueryBond.h

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

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

QueryOps.cpp

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

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

QueryOps.h

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

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

querytest.cpp

Adds some additional canned atom and bond query definitions (#1047 )

2016-09-09 10:31:02 -04:00

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

Fixes #1162 (resMolSupplierTest failing with boost 1.62) (#1166 )

2016-11-30 14:15:22 +01:00

Resonance.cpp

Fixes #1162 (resMolSupplierTest failing with boost 1.62) (#1166 )

2016-11-30 14:15:22 +01:00

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

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

ROMol.h

Add a MolBundle class (#1537 )

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

RWMol.cpp

Fix/urange check (#1506 )

2017-09-11 21:17:33 +02:00

RWMol.h

Fixes atom documentation (#1505 )

2017-07-22 06:42:03 +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 )

2017-06-28 09:31:58 -04:00

test_list.py

Issue1071/yapf (#1078 )

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

testCanon.cpp

first pass, using google style

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

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

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

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

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