Greg Landrum 01ec60a856 Fixes #7078 (#7155) ...

* add MolOps::expandAttachmentPoints, along with tests

* support expandAttachmentPoints in the mol file parser

* switch the v2 stuff in the guts of the reaction parser

* add collapseAttachmentPoints()
add addAsQueries option to expandAttachmentPoints()

lots of testing

* an edge case and some cleanup

* add python wrapper for those two functions

* Update Code/GraphMol/FileParsers/FileParsers.h

Co-authored-by: Ric <ricrogz@users.noreply.github.com>

* changes in response to review

- support addCoords in expandAttachmentPoints()
- support the new attachment point stuff to/from CXSMILES
- add MolOps::details::addExplicitAttachmentPoint() and MolOps::details::isAttachmentPoint() utility functions

---------

Co-authored-by: Ric <ricrogz@users.noreply.github.com>

2024-02-28 17:05:53 +01:00

..

Abbreviations

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Basement/FeatTrees

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

ChemReactions

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

ChemTransforms

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

CIPLabeler

Support atropisomers in the conformer generator (#7098)

2024-02-06 15:48:25 +01:00

Depictor

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Deprotect

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

Descriptors

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

DetermineBonds

Fixes #6961 (#6971)

2023-12-09 06:17:53 +01:00

DistGeomHelpers

fix a memory overwrite (#7147)

2024-02-07 17:40:41 +01:00

FileParsers

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

FilterCatalog

fix several warnings originating from the swig wrappers (#7063)

2024-01-30 04:44:43 +01:00

Fingerprints

fix GCC 13.2 warnings about redundant move in return statement (#7029)

2024-01-09 09:29:33 +01:00

FMCS

fix GCC 13.2 warnings about redundant move in return statement (#7029)

2024-01-09 09:29:33 +01:00

ForceFieldHelpers

fix GCC 13.2 warnings about redundant move in return statement (#7029)

2024-01-09 09:29:33 +01:00

FragCatalog

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

GeneralizedSubstruct

Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)

2023-12-19 04:44:06 +01:00

GenericGroups

New tests for specical query atoms and atropisomers (#7010)

2024-01-11 05:54:14 +01:00

libs

Unset executable flag

2019-10-10 20:18:43 +09:00

MarvinParse

[v2 API] MRV parsers (#7110)

2024-02-02 18:48:30 +01:00

MMPA

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

MolAlign

Add multithreading to getBestRMS and new getAllConformerBestRMS (#6896)

2023-11-22 17:35:06 +01:00

MolCatalog

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

MolChemicalFeatures

fix GCC 13.2 warnings about redundant move in return statement (#7029)

2024-01-09 09:29:33 +01:00

MolDraw2D

Fixes #7140 (#7150)

2024-02-12 15:50:02 +01:00

MolEnumerator

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

MolHash

Fixes #6472 - remove aromatic bond flags in Molhash anonymous graph (#7027)

2024-01-09 06:12:03 +01:00

MolInterchange

Fixes #5923 (#7039)

2024-01-19 18:43:30 +01:00

MolStandardize

Add a 'force' option to MolStandardizer::Uncharger (#7088)

2024-02-06 15:34:28 +01:00

MolTransforms

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

PartialCharges

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

RascalMCES

Extra rascal option (#7073)

2024-01-23 06:05:58 +01:00

ReducedGraphs

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

RGroupDecomposition

Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)

2024-01-23 17:13:53 +01:00

ScaffoldNetwork

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

ShapeHelpers

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

SLNParse

refactor(python): replace deprecated unittest methods (#6304)

2023-07-14 07:51:15 +02:00

SmilesParse

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

StructChecker

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Subgraphs

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

Substruct

Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)

2024-01-23 17:13:53 +01:00

SubstructLibrary

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

TautomerQuery

Add Python modules to generate stubs and automatically patch docstrings (#6919)

2023-11-30 04:54:18 +01:00

test_data

fix a problem with reading older pickles (#7180)

2024-02-22 14:03:45 +01:00

testExecs

Unset executable flag

2019-10-10 20:18:43 +09:00

Trajectory

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

Wrap

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

AddHs.cpp

Fixes #7123 (#7124)

2024-02-02 05:27:47 +01:00

AdjustQuery.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Aromaticity.cpp

Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)

2024-01-23 17:13:53 +01:00

Atom.cpp

Improve output of debugMol (#7172)

2024-02-25 17:46:21 +01:00

Atom.h

Improve output of debugMol (#7172)

2024-02-25 17:46:21 +01:00

atomic_data.cpp

Fixes #6961 (#6971)

2023-12-09 06:17:53 +01:00

atomic_data.h

Include element name in atomic data (#5524)

2022-09-06 14:35:29 +02:00

AtomIterators.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

AtomIterators.h

Run clang-format against header files (#4143)

2021-06-08 07:57:51 +02:00

Atropisomers.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Atropisomers.h

Support atropisomers in the conformer generator (#7098)

2024-02-06 15:48:25 +01:00

Bond.cpp

Improve output of debugMol (#7172)

2024-02-25 17:46:21 +01:00

Bond.h

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

BondIterators.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

BondIterators.h

Run clang-format against header files (#4143)

2021-06-08 07:57:51 +02:00

bulktest.cpp

Modernize deprecated header inclusion (#3137)

2020-05-04 10:40:57 +02:00

Canon.cpp

Fixes #7023 (#7136)

2024-02-06 15:57:21 +01:00

Canon.h

Add a "rootedAtAtom" to MolToSmarts (#6581)

2023-08-19 19:17:45 +02:00

catch_adjustquery.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

catch_canon.cpp

Fixes #7023 (#7136)

2024-02-06 15:57:21 +01:00

catch_chirality.cpp

Fixes #7140 (#7150)

2024-02-12 15:50:02 +01:00

catch_graphmol.cpp

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

catch_molbundle.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

catch_moliterators.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

catch_organometallics.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

catch_pickles.cpp

fix a problem with reading older pickles (#7180)

2024-02-22 14:03:45 +01:00

catch_queries.cpp

switch to catch2 v3 (#6898)

2023-11-15 06:45:42 +01:00

catch_sgroups.cpp

Fixes #5923 (#7039)

2024-01-19 18:43:30 +01:00

Chirality.cpp

Fixes #7140 (#7150)

2024-02-12 15:50:02 +01:00

Chirality.h

Fixes #7140 (#7150)

2024-02-12 15:50:02 +01:00

CMakeLists.txt

Fixes #7140 (#7150)

2024-02-12 15:50:02 +01:00

Conformer.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

Conformer.h

Allow some tolerance in flatness determination (#6696)

2023-09-07 16:50:56 +02:00

ConjugHybrid.cpp

Initial support for non-tetrahedral stereochemistry (#5084)

2022-05-20 09:07:16 +02:00

cptest.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

details.h

Change boost int types to std types (#2233)

2019-01-22 17:45:03 +01:00

FindRings.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

FindStereo.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

GraphMol.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

GraphMol.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

hanoitest.cpp

Fix a pathological slow case with the new getMolFrags() (#7121)

2024-02-06 04:23:48 +01:00

itertest.cpp

Modernize deprecated header inclusion (#3137)

2020-05-04 10:40:57 +02:00

Kekulize.cpp

Fixes #5505: problems when kekulizing molecules with query bonds (#5550)

2022-09-13 14:49:45 +02:00

Matrices.cpp

Improve test coverage and some bug fixes (#4536)

2021-09-26 07:45:06 +02:00

memtest1.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

MolBundle.h

Fix minimal build, allow building without boost::serialization (#6932)

2023-11-23 05:57:05 +01:00

MolOps.cpp

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

MolOps.h

Fixes #7078 (#7155)

2024-02-28 17:05:53 +01:00

molopstest.cpp

Fixes #7123 (#7124)

2024-02-02 05:27:47 +01:00

MolPickler.cpp

fix a problem with reading older pickles (#7180)

2024-02-22 14:03:45 +01:00

MolPickler.h

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

MonomerInfo.cpp

Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)

2021-09-28 13:40:43 -04:00

MonomerInfo.h

Fixes #4535: support operator<< for AtomPDBResidueInfo (#4564)

2021-09-28 13:40:43 -04:00

new_canon.cpp

Support atropisomers in the conformer generator (#7098)

2024-02-06 15:48:25 +01:00

new_canon.h

Fixes #6975 (#6972)

2023-12-11 17:40:30 +01:00

NontetrahedralStereo.cpp

Initial support for non-tetrahedral stereochemistry (#5084)

2022-05-20 09:07:16 +02:00

PeriodicTable.cpp

Fixes #5210 (#5408)

2022-07-11 11:20:03 +02:00

PeriodicTable.h

Include element name in atomic data (#5524)

2022-09-06 14:35:29 +02:00

QueryAtom.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

QueryAtom.h

Enable optional visualization of complex query atoms in a more compact form (#6056)

2023-02-16 12:34:05 +01:00

QueryBond.cpp

Fixes github #4311 (#4312)

2021-07-09 15:06:54 +02:00

QueryBond.h

Run clang-tidy (readability-braces-around-statements) (#4977)

2022-03-10 08:00:10 +01:00

QueryOps.cpp

fixing issue 5890 (#7152)

2024-02-09 13:24:59 +01:00

QueryOps.h

Fix Mol block parser by resetting atomic number to 0 for COMPOSITE_OR query atoms (#6349) (#6768)

2024-01-23 17:13:53 +01:00

querytest.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

RDKitBase.h

Enhanced stereo read/write support in SDF files. (#2022)

2018-09-26 15:44:23 +02:00

RDKitQueries.h

Fixes #1903 (#1971)

2018-07-25 09:14:17 +02:00

regress.txt

Unset executable flag

2019-10-10 20:18:43 +09:00

Renumber.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

resMolSupplierTest.cpp

Reformat C/C++ code ahead of 2023.03 release (#6295)

2023-04-28 04:42:35 +02:00

Resonance.cpp

run clang_format (#5676)

2022-11-01 04:14:26 +01:00

Resonance.h

- fixed #3349 (#3354)

2020-09-02 04:51:20 +02:00

RingInfo.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

RingInfo.h

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

Rings.h

Fix typo (#2862)

2019-12-31 06:43:27 +01:00

ROMol.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

ROMol.h

Issue 6411 ROMol hasquery (#6739)

2023-09-25 13:23:37 +02:00

RWMol.cpp

Fixes #7064 (#7141)

2024-02-22 06:46:39 +01:00

RWMol.h

Reformat C/C++ code ahead of 2023.03 release (#6295)

2023-04-28 04:42:35 +02:00

SanitException.h

Run clang-tidy (modernize-use-override) (#4251)

2021-07-01 05:18:56 +02:00

sanitTest.cpp

Modernize deprecated header inclusion (#3137)

2020-05-04 10:40:57 +02:00

StereoGroup.cpp

Improve output of debugMol (#7172)

2024-02-25 17:46:21 +01:00

StereoGroup.h

fragmentation of mol loses any sgroups (#7056)

2024-01-25 13:32:55 +01:00

SubstanceGroup.cpp

Fixes #5923 (#7039)

2024-01-19 18:43:30 +01:00

SubstanceGroup.h

Fixes #5923 (#7039)

2024-01-19 18:43:30 +01:00

test1.cpp

Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6842)

2024-01-23 06:21:26 +01:00

test_fixtures.h

Fixes #6944 (#6950)

2023-12-01 05:41:14 +01:00

test-valgrind.cpp

run clang-tidy with readability-braces-around-statements (#2899)

2020-01-25 14:19:32 +01:00

testChirality.cpp

Fixes #7115 (#7117)

2024-02-01 05:02:46 +01:00

testMolBundle.cpp

Improve test coverage and some bug fixes (#4536)

2021-09-26 07:45:06 +02:00

testPickler.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00

testPicklerGlobalSettings.cpp

Run clang-format against cpp (#4358)

2021-10-20 04:25:27 +02:00

testSGroup.cpp

Fixes #7064 (#7141)

2024-02-22 06:46:39 +01:00

UnitTestQueryMol.py

Reformat Python code for 2023.03 release (#6294)

2023-04-28 06:53:56 +02:00

WedgeBonds.cpp

atropisomer handling added (#6903)

2023-12-22 04:58:18 +01:00