rdkit

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Files

Gareth Jones afd6586bcf Allow RGD to decompose 2 sidechains on unlabelled core atoms to separate R groups (#5618 )

* Initial work preparing the core

* Simple test case working

* Check for labels

* Fix for labels

* Development for core wildcard issue

* Fixed core wildcard issue

* First working test

* Updated tests

* All tests working

* Reorder tests

* Fix failing tests

* Remove uint type

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupDecomp.h

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* AddCore method for RGroupCore

* Revert addCore refactoring (thanks Clion)

* Fixed typo in tests

* Minor fixes

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupDecomp.h

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupDecompData.h

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/GraphMol/RGroupDecomposition/RGroupCore.cpp

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

2022-10-19 04:36:56 +02:00

Abbreviations

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

Basement/FeatTrees

Run clang-format against cpp (#4358 )

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

ChemReactions

Revert "Support ring-bond stereo flags in CXSMILES (#5595 )" (#5629 )

2022-10-08 17:33:23 +02:00

ChemTransforms

cdxml parser (#5273 )

2022-09-28 05:49:27 +02:00

CIPLabeler

make the catch tests build faster (#5284 )

2022-05-17 04:39:33 +02:00

Depictor

avoid incurring into division by zero (#5619 )

2022-10-06 05:51:01 +02:00

Deprotect

make the catch tests build faster (#5284 )

2022-05-17 04:39:33 +02:00

Descriptors

Fixes #5210 (#5408 )

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

DetermineBonds

Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557 )

2022-10-06 05:46:08 +02:00

DistGeomHelpers

Fix a problem when generating conformers for molecules with larger heteroatoms in conjugated 5-rings (#5586 )

2022-10-03 10:26:33 +02:00

FileParsers

Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557 )

2022-10-06 05:46:08 +02:00

FilterCatalog

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

Fingerprints

make the catch tests build faster (#5284 )

2022-05-17 04:39:33 +02:00

FMCS

fix potential bug (#5205 )

2022-04-17 05:22:50 +02:00

ForceFieldHelpers

Fixes #5210 (#5408 )

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

FragCatalog

Fix typo: quarternary --> quaternary (#5243 )

2022-04-29 08:09:34 +02:00

GenericGroups

make the catch tests build faster (#5284 )

2022-05-17 04:39:33 +02:00

libs

Unset executable flag

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

MMPA

Fix a number of crashing bugs in the python wrappers (#4810 )

2021-12-27 16:09:06 -05:00

MolAlign

Expose additional functionality to SWIG wrappers (#5614 )

2022-10-04 05:04:28 +02:00

MolCatalog

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

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

MolChemicalFeatures

Run clang-format against cpp (#4358 )

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

MolDraw2D

Add updateMolDrawOptionsFromJSON() (#5630 )

2022-10-10 04:41:35 +02:00

MolEnumerator

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

MolHash

Drop usage of CIP information from the canonicalization code (#5385 )

2022-07-13 05:40:23 +02:00

MolInterchange

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

MolStandardize

Fixes #5402 (#5542 )

2022-09-09 05:06:42 +02:00

MolTransforms

Fix Flake8 erorrs (#4252 )

2022-03-10 06:55:18 +01:00

PartialCharges

Run clang-format against cpp (#4358 )

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

ReducedGraphs

Run clang-format against cpp (#4358 )

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

RGroupDecomposition

Allow RGD to decompose 2 sidechains on unlabelled core atoms to separate R groups (#5618 )

2022-10-19 04:36:56 +02:00

ScaffoldNetwork

Drop usage of CIP information from the canonicalization code (#5385 )

2022-07-13 05:40:23 +02:00

ShapeHelpers

Run clang-format against cpp (#4358 )

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

SLNParse

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

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

SmilesParse

Revert "Support ring-bond stereo flags in CXSMILES (#5595 )" (#5629 )

2022-10-08 17:33:23 +02:00

StructChecker

Run clang-format against cpp (#4358 )

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

Subgraphs

[ENH]: Support greater use of findAtomEnvironmentOfRadiusN() (#4970 )

2022-03-09 14:01:24 +01:00

Substruct

Fixes #5210 (#5408 )

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

SubstructLibrary

Fixes #5210 (#5408 )

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

TautomerQuery

fix warnings (#5561 )

2022-09-14 06:36:42 +02:00

test_data

cdxml parser (#5273 )

2022-09-28 05:49:27 +02:00

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

Fix bad interaction between the useLegacyStereo options in the SMILES parser (#5576 )

2022-10-07 16:53:59 +02:00

AddHs.cpp

By default mergeQueryHs now will not remove isotopes (#5563 )

2022-09-16 17:29:32 +02:00

AdjustQuery.cpp

Fixes #4789 (#4790 )

2021-12-13 14:15:26 +01:00

Aromaticity.cpp

add condition for arom calc of large ringysystems (#5648 )

2022-10-16 08:10:22 +02:00

Atom.cpp

Initial support for non-tetrahedral stereochemistry (#5084 )

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

Atom.h

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

atomic_data.cpp

Include element name in atomic data (#5524 )

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

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

Bond.cpp

Improve test coverage and some bug fixes (#4536 )

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

Bond.h

add #include <utility> (#5060 )

2022-03-17 04:56:34 +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

Initial support for non-tetrahedral stereochemistry (#5084 )

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

Canon.h

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

catch_adjustquery.cpp

Fixes #4789 (#4790 )

2021-12-13 14:15:26 +01:00

catch_canon.cpp

Drop usage of CIP information from the canonicalization code (#5385 )

2022-07-13 05:40:23 +02:00

catch_chirality.cpp

Fixes #5659 (#5660 )

2022-10-18 15:16:26 +02:00

catch_graphmol.cpp

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

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

catch_moliterators.cpp

add ROMol::atomNeighbors() and ROMol::atomBonds() (#4573 )

2021-10-02 07:28:24 +02:00

catch_sgroups.cpp

Addresses #4434 (#4435 )

2021-08-24 05:10:06 +02:00

Chirality.cpp

Expose additional functionality to SWIG wrappers (#5614 )

2022-10-04 05:04:28 +02:00

Chirality.h

New version of AssignStereochemistry (#5442 )

2022-09-06 12:53:02 +02:00

CMakeLists.txt

Integrating xyz2mol Into The RDKit Core (GSoC 2022) (#5557 )

2022-10-06 05:46:08 +02:00

Conformer.cpp

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

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

Conformer.h

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

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

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

Speed up ring detection by reducing count() calls (#5663 )

2022-10-18 15:13:46 +02:00

FindStereo.cpp

Fixes #5659 (#5660 )

2022-10-18 15:16:26 +02:00

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

Run clang-format against cpp (#4358 )

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

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

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

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

MolOps.cpp

Fixes #5462 (#5463 )

2022-08-03 04:46:17 +02:00

MolOps.h

Add CXSMILES support for bond wedging and wiggly bonds (#5575 )

2022-09-24 05:44:01 +02:00

molopstest.cpp

fix + test (#5100 )

2022-03-17 04:53:17 +01:00

MolPickler.cpp

Fixes #5210 (#5408 )

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

MolPickler.h

Fixes https://github.com/rdkit/rdkit/issues/4621 (#5623 )

2022-10-06 16:45:14 +02:00

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

New version of AssignStereochemistry (#5442 )

2022-09-06 12:53:02 +02:00

new_canon.h

New version of AssignStereochemistry (#5442 )

2022-09-06 12:53:02 +02:00

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

add #include <utility> (#5060 )

2022-03-17 04:56:34 +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

Fixes #5152 (#5153 )

2022-04-04 06:07:57 +02:00

QueryOps.h

Fixes #5210 (#5408 )

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

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

Fix #4071 (#4080 )

2021-04-23 16:45:54 -04:00

resMolSupplierTest.cpp

Run clang-format against cpp (#4358 )

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

Resonance.cpp

Fixes #5210 (#5408 )

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

Resonance.h

- fixed #3349 (#3354 )

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

RingInfo.cpp

Fixes #4721 (#4722 )

2022-01-28 16:38:46 +01:00

RingInfo.h

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

Rings.h

Fix typo (#2862 )

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

ROMol.cpp

add info to debug (#5526 )

2022-09-06 13:03:08 +02:00

ROMol.h

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +02:00

RWMol.cpp

Fix memory safety issues found by OSS-Fuzz (#4983 )

2022-02-06 05:06:38 +01:00

RWMol.h

fix doxygen comments (#5254 )

2022-07-11 13:55:35 +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

add info to debug (#5526 )

2022-09-06 13:03:08 +02:00

StereoGroup.h

add info to debug (#5526 )

2022-09-06 13:03:08 +02:00

SubstanceGroup.cpp

add info to debug (#5526 )

2022-09-06 13:03:08 +02:00

SubstanceGroup.h

add info to debug (#5526 )

2022-09-06 13:03:08 +02:00

test1.cpp

Fixes a couple of query-related bugs (#3398 )

2020-09-17 08:16:43 +02:00

test-valgrind.cpp

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

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

testChirality.cpp

Drop usage of CIP information from the canonicalization code (#5385 )

2022-07-13 05:40:23 +02:00

testMolBundle.cpp

Improve test coverage and some bug fixes (#4536 )

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

testPickler.cpp

add boost::serialization support to ROMol (#5249 )

2022-05-07 11:11:53 +02:00

testPicklerGlobalSettings.cpp

Run clang-format against cpp (#4358 )

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

testSGroup.cpp

Allow removal of non-special H atoms in SGroups (#5399 )

2022-07-07 11:05:18 +02:00

UnitTestQueryMol.py

Remove a bunch of Python2-related warts (#2315 )

2019-03-06 20:43:49 -05:00