Brian Kelley f8fde2f7d8 ChemDraw Document and read/write support for the RDKit (#8539) ...

* ChemDraw Document and read/write support for the RDKit

* Add missing test file

* Rev chemdraw version

* Rev chemdraw version

* Rev chemdraw version for g++11

* Update CMakeLists.txt

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

* Build chemdraw from an external CMake file

* Remove unused platform bigendian check

* Revert changes to constants, remove unused ones

* Keep the original constant names

* Remove __main__ section

* Use as much of the ChemDraw CMakeList as possible

* Skip installing expat

* Rev chemdraw version to fix windows issue

* Don't install expat, set the appropriate CHEMDRAW_BUILD definition

* resolve windows builds

* Fix minimal lib builds

* Move ChemDraw document to private header

* Move utility functions to ChemDraw namespace

* Move ChemDraw to v2 unique ptr api namespace

* Make class enum

* Switch to camelCase

* Response to review

* Move ChemDrawToDocument to ChemDraw namespace

* Update External/ChemDraw/Wrap/rdChemDraw.cpp

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

* Fix typo

* Update External/ChemDraw/Wrap/rdChemDraw.cpp

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

* Add better documentation

---------

Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

2025-07-03 06:01:58 +02:00

..

Abbreviations

Improve doc string for ParseAbbreviations in python wrapper. (#8049)

2024-11-28 13:54:04 +01:00

Basement/FeatTrees

Run clang-format against cpp (#4358)

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

ChemReactions

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

ChemTransforms

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

CIPLabeler

Make assignCIPLabels Ctrl+c interruptable (#8589)

2025-06-27 08:27:44 +02:00

Depictor

rdkit-targets.cmake now uses cmake package names for external libraries instead of absolute paths (#8552)

2025-05-24 07:27:03 +02:00

Deprotect

Fixes #7989 Incorrect benzyl deprotection reaction (#7990)

2024-11-07 18:34:59 +01:00

Descriptors

Fixed out of bounds vector access in GetGeodesicMatrix (#8601)

2025-06-25 06:26:41 +02:00

DetermineBonds

Some cleanup of the xyz2mol code (#8567)

2025-06-05 08:43:22 -04:00

DistGeomHelpers

Fixes #8559 (#8560)

2025-06-06 15:30:07 +02:00

EnumerateStereoisomers

Fixes the problems with wiggly bonds and EnumerateStereoisomers from #8508 (#8598)

2025-06-25 09:25:11 +02:00

FileParsers

ChemDraw Document and read/write support for the RDKit (#8539)

2025-07-03 06:01:58 +02:00

FilterCatalog

Check for PAINS_C file existence in update_pains.py script (#8431)

2025-04-11 11:16:25 +02:00

Fingerprints

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

FMCS

style: apply modernize-use-override (#8137)

2025-04-25 12:24:58 +02:00

ForceFieldHelpers

Small cleanups of the MMFF94 code (#8593)

2025-06-24 08:07:51 +02:00

FragCatalog

remove no-op macros and dead code (pt 4) (#8037)

2025-01-26 07:49:50 +01:00

GeneralizedSubstruct

Run clang-format across everything (#7849)

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

GenericGroups

Modernization of some substructure code (#8450)

2025-05-12 06:33:25 +02:00

libs

Unset executable flag

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

MarvinParse

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

MMPA

Fix shifting of a potentially negative number (#8014)

2024-11-24 06:50:16 +01:00

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

remove no-op macros and dead code (pt 4) (#8037)

2025-01-26 07:49:50 +01:00

MolDraw2D

Fix irritating warning when DrawMolMCHLasso compiled. (#8540)

2025-05-27 04:56:35 +02:00

MolEnumerator

Implements #8222 adds react_idx (index of reactant) to product atoms (#8231)

2025-02-06 17:07:55 +01:00

MolHash

Fixes #8405 (#8406)

2025-04-04 15:13:39 +02:00

MolInteractionFields

style: apply modernize-use-override (#8137)

2025-04-25 12:24:58 +02:00

MolInterchange

Fixes #8460 (#8468)

2025-04-28 07:38:50 +02:00

MolProcessing

Fix some more mem errors in 2024.09.1 (#7899)

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

MolStandardize

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

MolTransforms

Fix inversion of stereo with canonicalizeConformer (#7878)

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

PartialCharges

Suppress large amounts of 'BOOST_NO_CXX98_FUNCTION_BASE macro redefined' warnings in clang/emcc builds (#7747)

2025-03-29 20:04:58 +01:00

RascalMCES

Rascal Fix 8360 (#8376)

2025-04-08 10:12:58 +02:00

ReducedGraphs

Fix off-by-one error in Reduced Graph fingerprint bitstring. (#8385)

2025-04-07 13:20:19 +02:00

RGroupDecomposition

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

ScaffoldNetwork

Allow inclusion of molecule names in ScaffoldNetwork (#7956)

2024-10-30 06:11:30 +01:00

ShapeHelpers

Fix inversion of stereo with canonicalizeConformer (#7878)

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

SLNParse

Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)

2025-01-28 21:09:03 +01:00

SmilesParse

Fixes #8471 (#8585)

2025-06-15 16:21:07 +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

Modernization of some substructure code (#8450)

2025-05-12 06:33:25 +02:00

SubstructLibrary

remove no-op macros and dead code (pt 1) (#8012)

2024-11-19 04:31:56 +01:00

SynthonSpaceSearch

Synthon space bad chiral count (#8550)

2025-06-03 13:09:09 +02:00

TautomerQuery

Modernization of some substructure code (#8450)

2025-05-12 06:33:25 +02:00

test_data

Fixes #7983 (#8342)

2025-03-20 07:40:33 +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

Update createStereoGroup to accept bond list (#8587)

2025-06-16 06:04:34 +02:00

AddHs.cpp

fix a logic error in needsHs (#8442)

2025-04-16 14:36:45 +02:00

AdjustQuery.cpp

apply query adjustments when makeAtomsGeneric is enabled (#8315)

2025-03-04 13:50:24 +01:00

Aromaticity.cpp

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

Atom.cpp

add clearPropertyCache() (#8533)

2025-05-18 08:14:05 +02:00

Atom.h

add clearPropertyCache() (#8533)

2025-05-18 08:14:05 +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

feed dummy perpendicular point for cross product to prevent zero error in normalization during atropisomer chirality, fixes #8602 (#8603)

2025-06-26 19:34:17 +02:00

Atropisomers.h

Fixes #7983 (#8342)

2025-03-20 07:40:33 +01:00

Bond.cpp

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

Bond.h

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +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

remove no-op macros and dead code (pt 4) (#8037)

2025-01-26 07:49:50 +01:00

Canon.cpp

Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)

2025-01-28 21:09:03 +01:00

Canon.h

Fix canonicalization of stereogroups (#7041)

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

catch_adjustquery.cpp

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

catch_canon.cpp

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

catch_chirality.cpp

A few mem fixes in tests (#8521)

2025-05-13 12:17:52 +02:00

catch_graphmol.cpp

add clearPropertyCache() (#8533)

2025-05-18 08:14:05 +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

Fix the way carbon is handed in cleanupOrganometallics() (#8301)

2025-03-03 17:30:41 +01:00

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

Fixes #8420 (#8428)

2025-04-10 19:15:34 +02:00

Chirality.h

style: apply modernize-use-override (#8137)

2025-04-25 12:24:58 +02:00

CMakeLists.txt

Cpp enumerate stereoisomers (#8563)

2025-06-05 08:29:54 +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

Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)

2025-01-28 21:09:03 +01:00

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

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

FindStereo.cpp

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +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 across everything (#7849)

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

itertest.cpp

remove no-op macros and dead code (pt 2) (#8035)

2025-01-11 14:10:00 +01:00

Kekulize.cpp

Synthon space bad chiral count (#8550)

2025-06-03 13:09:09 +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

fix a problem with stereogroups involving bonds and getMolFrags() (#8558)

2025-05-27 16:43:20 +02:00

MolOps.h

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

molopstest.cpp

fix a problem with stereogroups involving bonds and getMolFrags() (#8558)

2025-05-27 16:43:20 +02:00

MolPickler.cpp

GitHub 7865 haspropwithvaluequery leaks (#7872)

2024-10-30 06:12:40 +01:00

MolPickler.h

Expose propertyFlags to CFFI and MinimalLib (#7960)

2024-11-07 06:08:27 +01:00

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

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

NontetrahedralStereo.cpp

fix: apply modernize-use-nullptr (#8134)

2025-01-09 07:56:10 +01:00

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

Github8353 (#8354)

2025-03-17 19:54:15 +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

Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)

2025-03-29 07:26:03 +01:00

QueryOps.h

Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)

2025-03-29 07:26:03 +01:00

querytest.cpp

A few mem fixes in tests (#8521)

2025-05-13 12:17:52 +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

add clearPropertyCache() (#8533)

2025-05-18 08:14:05 +02:00

ROMol.h

add clearPropertyCache() (#8533)

2025-05-18 08:14:05 +02:00

RWMol.cpp

fix a problem with stereogroups involving bonds and getMolFrags() (#8558)

2025-05-27 16:43:20 +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 a problem with stereogroups involving bonds and getMolFrags() (#8558)

2025-05-27 16:43:20 +02:00

StereoGroup.h

fix a problem with stereogroups involving bonds and getMolFrags() (#8558)

2025-05-27 16:43:20 +02:00

SubstanceGroup.cpp

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

SubstanceGroup.h

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

test1.cpp

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +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

Moving towards getting all tests to pass when using the new stereo code (#8409)

2025-04-15 14:00:32 +02:00

testMolBundle.cpp

Improve test coverage and some bug fixes (#4536)

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

testPickler.cpp

Replace GetImplicitValence() and GetExplicitValence() with GetValence() (#7926)

2025-01-28 21:09:03 +01:00

testPicklerGlobalSettings.cpp

Run clang-format against cpp (#4358)

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

testSGroup.cpp

Add SCSR parsing to RDKit (#8147)

2025-05-14 13:37:59 +02:00

UnitTestQueryMol.py

Reformat Python code for 2023.03 release (#6294)

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

WedgeBonds.cpp

A couple optimizations to when the ring finding code is called (#8482)

2025-04-30 16:21:49 +02:00