Brian Kelley a02f2b0bb1 Fix/sanitizerxn merge hs (#1367) ...

* Fixes exceptions to use correct functionName

* Deprecates ChemDrawAdjustParams name sciquest integration/eln searching
 doesn’t map to this behavior.  renamed  MatchOnlyAtRgroupAdjustParams

* Python wrapper for deprecated API

* fixHs now is more intelligent about merging hs.

The only cases where hs can’t be merged is if they are mapped
to a non hydrogen in the product.

* Updates deprecated ChemDrawAdjustParams

2017-03-20 14:30:36 +00:00

..

Basement/FeatTrees

first pass, using google style

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

ChemReactions

Fix/sanitizerxn merge hs (#1367)

2017-03-20 14:30:36 +00:00

ChemTransforms

Partial support for reading CXSMILES (#1237)

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

Depictor

Fix/github1286 (#1307)

2017-03-04 12:35:26 -05:00

Descriptors

Fix/github1262 (#1265)

2017-01-22 05:49:52 +01:00

DistGeomHelpers

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

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

FileParsers

Fix two problems with the PDB parsing (#1341)

2017-03-04 12:34:27 -05:00

FilterCatalog

Exposes normalize option to GetFlattenedFunctionalGroupHierarchy (#1165)

2016-11-12 16:02:28 +01:00

Fingerprints

Fix/github879 (#1354)

2017-03-08 23:17:04 -05:00

FMCS

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

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

ForceFieldHelpers

- Optimization of UFF and MMFF forcefields (#1218)

2017-01-04 08:33:34 +01:00

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

Dev/rdmmpa api update (#1291)

2017-02-27 17:08:01 +01:00

MolAlign

Issue1071/yapf (#1078)

2016-09-23 04:58:46 +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

the functionality was already there, this just shows how to use it (#1355)

2017-03-12 09:57:43 -04:00

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/github1262 (#1265)

2017-01-22 05:49:52 +01:00

PartialCharges

Issue1071/yapf (#1078)

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

ReducedGraphs

Issue1071/yapf (#1078)

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

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

Fix handling of Hs in SMARTS queries (#1339)

2017-03-08 23:17:50 -05:00

StructChecker

replace std::map::at with std::map::find

2016-11-14 16:17:38 +00:00

Subgraphs

Issue1071/yapf (#1078)

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

Substruct

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

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

test_data

Fixes #607 (#1075)

2016-09-23 04:57:07 +02:00

testExecs

initial import

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

Trajectory

Fix trajectory tests

2016-11-15 13:47:52 +00:00

Wrap

Fixes #1352 (#1353)

2017-03-06 11:22:54 -05:00

AddHs.cpp

Merge fix/github908 branch

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

AdjustQuery.cpp

replaceBond and generic atoms and bonds in adjustQueryProperties() (#1141)

2016-11-04 12:41:06 +01:00

Aromaticity.cpp

Partial support for reading CXSMILES (#1237)

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

Atom.cpp

Adds Atom atom map and rlabel apis (#1004)

2016-08-11 04:46:41 +02:00

Atom.h

Fixes #1041 (#1070)

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

atomic_data.cpp

Fixes #1204 (#1212)

2016-12-19 12:50:28 -05:00

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

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

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

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 #1294 (#1302)

2017-02-10 08:50:28 -05:00

Chirality.h

first pass, using google style

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

CMakeLists.txt

Dev/pickle properties (#1277)

2017-02-09 16:06:01 +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

SSSR performance improvements to support larger systems (#1131)

2016-10-29 04:38:14 +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

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

Partial support for reading CXSMILES (#1237)

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

molopstest.cpp

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

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

MolPickler.cpp

Dev/pickle properties (#1277)

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

MolPickler.h

Small change to enum to prevent overflowing in boost when the compiler chooses int type (#1351)

2017-03-06 05:31:37 +01:00

MonomerInfo.h

first pass, using google style

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

new_canon.cpp

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

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

new_canon.h

Partial support for reading CXSMILES (#1237)

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

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

Partial support for reading CXSMILES (#1237)

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

QueryOps.h

Partial support for reading CXSMILES (#1237)

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

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

Removes exponetial numBonds behavior (#1154)

2016-11-12 16:05:06 +01:00

ROMol.h

Removes exponetial numBonds behavior (#1154)

2016-11-12 16:05:06 +01:00

RWMol.cpp

stop using getBondWithIdx() in removeBond() (#1363)

2017-03-12 10:07:17 -04:00

RWMol.h

replaceBond and generic atoms and bonds in adjustQueryProperties() (#1141)

2016-11-04 12:41:06 +01:00

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

replaceBond and generic atoms and bonds in adjustQueryProperties() (#1141)

2016-11-04 12:41:06 +01:00

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 #1294 (#1302)

2017-02-10 08:50:28 -05:00

testPickler.cpp

Dev/pickle properties (#1277)

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

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