Maciej Wójcikowski 50299cbbf2 Improve AddHs for molecules read from PDB (#1647) ...

* Add AtomPDBResidueInfo during molops::addhs

* Test addhs and AtomPDBResidueInfo

* Little cleanup

* Fix serial

* Refactor code, add unique Hs labels

* Move code to separate function + bugfix.

* Make function optional (AddHs residueInfo param)

* Rename argument

2018-01-18 17:10:19 +01:00

..

Basement/FeatTrees

first pass, using google style

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

ChemReactions

backport the fix for #1695

2018-01-13 04:39:17 +01:00

ChemTransforms

Partial support for reading CXSMILES (#1237)

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

Depictor

get this compiling

2018-01-14 05:37:36 +01:00

Descriptors

Fixes github #1702 (#1706)

2018-01-04 11:34:47 -05:00

DistGeomHelpers

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

2017-11-14 03:58:35 +01:00

FileParsers

Improve AddHs for molecules read from PDB (#1647)

2018-01-18 17:10:19 +01:00

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

Version 2 of ETKDG (#1597)

2017-10-31 06:43:28 -05:00

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

Use numpy not numeric for boost 1.65+ - fixes #1581 (#1664)

2017-11-18 06:30:32 +01:00

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)

2017-10-29 11:51:51 +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

There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral (#1673)

2017-12-01 12:37:57 +00:00

PartialCharges

Issue1071/yapf (#1078)

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

ReducedGraphs

Use numpy not numeric for boost 1.65+ - fixes #1581 (#1664)

2017-11-18 06:30:32 +01:00

RGroupDecomposition

backport the fix for #1695

2018-01-13 04:39:17 +01:00

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

Issue 1652 (#1654)

2017-11-27 20:22:27 +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

Dev/substructlibrary docs (#1620)

2017-11-22 09:05:28 +01:00

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

Improve AddHs for molecules read from PDB (#1647)

2018-01-18 17:10:19 +01:00

AddHs.cpp

Improve AddHs for molecules read from PDB (#1647)

2018-01-18 17:10:19 +01:00

AdjustQuery.cpp

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

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

Aromaticity.cpp

Fixes #1703 (#1714)

2018-01-13 04:39:17 +01:00

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

Fixes #1668 (#1669)

2017-11-29 10:58:41 -05:00

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

part of fix for #1703

2018-01-13 04:39:17 +01:00

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)

2017-10-06 11:07:10 -04:00

MolOps.h

Improve AddHs for molecules read from PDB (#1647)

2018-01-18 17:10:19 +01:00

molopstest.cpp

Fixes #1703 (#1714)

2018-01-13 04:39:17 +01:00

MolPickler.cpp

Allows CIS/TRANS double bonds to be de-pickled (#1710) (#1711)

2018-01-07 14:54:01 -05:00

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

Allows CIS/TRANS double bonds to be de-pickled (#1710) (#1711)

2018-01-07 14:54:01 -05:00

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