John Mayfield 2553cfce73 Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777) ...

* Improved handling of SP/TB/OH reording in SMILES/SMARTS.

- add a getMaxNbors(tag) utility function to avoid repeated logic in multiple places
- tweak getChiralPermutation() for handling implicit/missing ligands (uses -1), allow inverse lookup
- use the tweaked chiral ordering in the reading/writing from SMILES

* clang-format run

* Reviewer requested changes.
- curly braces on all if conditions
- null check raw pointers with precondition.

* Correct additional test case introduced in the last year

2024-10-21 04:55:08 +02:00

..

Abbreviations

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Basement/FeatTrees

Run clang-format against cpp (#4358)

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

ChemReactions

Fixes #7699 (#7904)

2024-10-16 16:21:52 +02:00

ChemTransforms

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

CIPLabeler

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

Depictor

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

Deprotect

Remove Descriptors as a dependency of many other RDKit libraries (#7700)

2024-08-13 13:22:43 +02:00

Descriptors

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

DetermineBonds

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

DistGeomHelpers

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

FileParsers

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

FilterCatalog

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Fingerprints

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

FMCS

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

ForceFieldHelpers

Do the announced deprecations (#7910)

2024-10-11 06:42:18 +02:00

FragCatalog

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

GeneralizedSubstruct

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

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

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

MMPA

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MolAlign

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

MolCatalog

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

MolChemicalFeatures

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

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

MolDraw2D

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

MolEnumerator

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

MolHash

Remove Descriptors as a dependency of many other RDKit libraries (#7700)

2024-08-13 13:22:43 +02:00

MolInterchange

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

MolProcessing

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

MolStandardize

Fixes #7044 (#7137)

2024-10-18 05:32:20 +02:00

MolTransforms

Fix inversion of stereo with canonicalizeConformer (#7878)

2024-10-10 09:57:39 -04:00

PartialCharges

Reformat Python code for 2023.03 release (#6294)

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

RascalMCES

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

ReducedGraphs

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

RGroupDecomposition

Restore "oops, exponential is a pain" code snippet in the RGD algorithm (#7898)

2024-10-07 09:08:50 -04:00

ScaffoldNetwork

Fix some more mem errors in 2024.09.1 (#7899)

2024-10-10 16:08:50 +02:00

ShapeHelpers

Fix inversion of stereo with canonicalizeConformer (#7878)

2024-10-10 09:57:39 -04:00

SLNParse

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

SmilesParse

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

StructChecker

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

Subgraphs

switch to catch2 v3 (#6898)

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

Substruct

Fixes #7685 (#7864)

2024-09-29 05:23:24 +02:00

SubstructLibrary

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

TautomerQuery

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

test_data

Fixes #7501 dative bonds in cdxml (#7757)

2024-08-28 05:59:43 +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 canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

AddHs.cpp

Postpone clearing computed properties until after all Hs removed (#7241)

2024-03-16 06:14:24 +01:00

AdjustQuery.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Aromaticity.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Atom.cpp

Fixes #7873 (#7885)

2024-10-11 06:42:52 +02:00

Atom.h

Fixes #7873 (#7885)

2024-10-11 06:42:52 +02:00

atomic_data.cpp

Switch to isoelectronic valence model (#7491)

2024-06-25 15:38:49 +02:00

atomic_data.h

Switch to isoelectronic valence model (#7491)

2024-06-25 15:38:49 +02:00

AtomIterators.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

AtomIterators.h

Run clang-format against header files (#4143)

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

Atropisomers.cpp

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

Atropisomers.h

Support atropisomers in the conformer generator (#7098)

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

Bond.cpp

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

Bond.h

A collection of small improvements from Roger S (#7566)

2024-06-26 08:29:57 +02:00

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

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

Canon.h

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

catch_adjustquery.cpp

switch to catch2 v3 (#6898)

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

catch_canon.cpp

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

catch_chirality.cpp

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

catch_graphmol.cpp

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

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_molops.cpp

Remove Descriptors as a dependency of many other RDKit libraries (#7700)

2024-08-13 13:22:43 +02:00

catch_organometallics.cpp

switch to catch2 v3 (#6898)

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

catch_periodictable.cpp

Add missing GetRow method and fix Python parameter names (#7575)

2024-06-28 12:47:34 +02:00

catch_pickles.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

catch_queries.cpp

switch to catch2 v3 (#6898)

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

catch_sgroups.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

Chirality.cpp

Only save the most recent CIP rank for sorting (#7932)

2024-10-19 07:17:54 +02:00

Chirality.h

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

CMakeLists.txt

add mol processing API (#7773)

2024-09-19 18:42:25 +02:00

Conformer.cpp

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

Conformer.h

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

ConjugHybrid.cpp

Fixes #7556 (#7646)

2024-07-22 16:34:08 +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

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

FindStereo.cpp

Fixes #7598 (#7604)

2024-07-15 14:15:32 -04:00

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 across everything (#7849)

2024-09-26 13:39:02 +02:00

itertest.cpp

Modernize deprecated header inclusion (#3137)

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

Kekulize.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +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

Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823)

2024-09-20 09:48:08 +02:00

MolOps.h

Documentation updates (#7933)

2024-10-19 17:19:59 +02:00

molopstest.cpp

Add overloads of MolOps::getMolFrags and MolOps::getMolFragsWithQuery (#7823)

2024-09-20 09:48:08 +02:00

MolPickler.cpp

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

MolPickler.h

Adds HasPropWithValue Pickler (#7692)

2024-08-26 16:27:58 +02:00

MolProps.cpp

Remove Descriptors as a dependency of many other RDKit libraries (#7700)

2024-08-13 13:22:43 +02:00

MonomerInfo.cpp

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

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

MonomerInfo.h

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

new_canon.cpp

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

new_canon.h

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

NontetrahedralStereo.cpp

Improved handling of SP/TB/OH reording in SMILES/SMARTS. (#6777)

2024-10-21 04:55:08 +02:00

PeriodicTable.cpp

Fixes #5210 (#5408)

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

PeriodicTable.h

Add missing GetRow method and fix Python parameter names (#7575)

2024-06-28 12:47:34 +02:00

QueryAtom.cpp

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

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

QueryAtom.h

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

QueryBond.cpp

Fixes github #4311 (#4312)

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

QueryBond.h

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

QueryOps.cpp

Adds HasPropWithValue Pickler (#7692)

2024-08-26 16:27:58 +02:00

QueryOps.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +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 canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

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 across everything (#7849)

2024-09-26 13:39:02 +02:00

Resonance.h

- fixed #3349 (#3354)

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

RingInfo.cpp

make sure outdated ring fusion information is recomputed before attempting to use it (#7274)

2024-03-20 09:37:10 +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

Some modernization of core GraphMol classes (#7228)

2024-03-17 06:04:04 +01:00

ROMol.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +02:00

RWMol.cpp

fix #7782 (#7783)

2024-10-03 06:52:34 +02:00

RWMol.h

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +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

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

StereoGroup.h

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00

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

Fix some mem errors in 2024.09.1 (#7867)

2024-10-03 16:05:43 +02:00

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

Switch to isoelectronic valence model (#7491)

2024-06-25 15:38:49 +02:00

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

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +02:00