Dan Nealschneider 3facd882d6 Speed up GetProp Python keyerrors (#8372) ...

* Speed up GetProp Python keyerrors

A common pattern _in Python_ for checking for the presence or
absence of a key is:

    try:
       return mol.GetProp('mykey')
    except KeyError:
       return None

Shockingly, this is really slow with boost python objects! I was
recently profiling a workflow and 90% of the time or more was
spent in failed GetProp calls (mostly on bonds, some on atoms
or mols).

I sped up the workflow by protecting the calls using HasProp. But
I think this is a silly trap we've set for our users.

The problem comes because boost::python uses a C++ exception to
indicate that there is already a Python exception set. In C++,
exceptions are slow - they require unrolling a stack. In Python,
exceptions are about the same speed as any other control flow!

This commit speeds up GetProp failures by circumventing the
boost throw_exception_already_set() mechanism.

In my testing, this speeds up failed GetProp substantially:

* Factor of 1000x on Mac
* Factor of 40x on Linux

* Update typed GetXXXProp to bypass boost exceptions

Based on PR #8372

Updates the typed GetIntProp, GetDoubleProp, etc to bypass C++
exceptions in access. This speeds up missing key errors
significantly - for instance, calling mol. GetIntProp with a
missing prop 100,000 times:

Before: 28s
After:  0.05s

2025-04-07 13:55:22 +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

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

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

ChemTransforms

Adds linker style zipping (#8289)

2025-03-06 05:44:25 +01:00

CIPLabeler

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

Depictor

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

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

Deprotect

Fixes #7989 Incorrect benzyl deprotection reaction (#7990)

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

Descriptors

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

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

DetermineBonds

Fix canonicalization of stereogroups (#7041)

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

DistGeomHelpers

Expose basinThresh to the python layer (#8283)

2025-02-20 10:12:17 +01:00

FileParsers

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

FilterCatalog

Fixes #8351 (#8363)

2025-03-20 07:03:45 -04:00

Fingerprints

mem fixes (#8276)

2025-02-20 05:59:30 +01:00

FMCS

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

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

ForceFieldHelpers

Fixes Github #7901 (#8264)

2025-02-13 12:46:56 +01:00

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

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

Fixes #7983 (#8342)

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

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

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

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

fix (#8144)

2025-01-09 07:52:46 +01:00

MolInterchange

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

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

MolProcessing

Fix some more mem errors in 2024.09.1 (#7899)

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

MolStandardize

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

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

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

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

ReducedGraphs

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

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

RGroupDecomposition

Fix memory leaks (#8298)

2025-02-25 16:58:19 +01:00

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 github #8364 and #8365 (#8366)

2025-03-31 15:58:47 +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

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

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

SubstructLibrary

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

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

SynthonSpaceSearch

add a missed RDKIT_SYNTHONSPACESEARCH_EXPORT (#8399)

2025-04-01 12:54:55 +02:00

TautomerQuery

Run clang-format across everything (#7849)

2024-09-26 13:39:02 +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

Speed up GetProp Python keyerrors (#8372)

2025-04-07 13:55:22 +02:00

AddHs.cpp

Fixes #8304 (#8316)

2025-03-04 14:56:08 +01:00

AdjustQuery.cpp

apply query adjustments when makeAtomsGeneric is enabled (#8315)

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

Aromaticity.cpp

Revert "Fixes #5134 (#5136)" (#8319)

2025-03-05 18:11:24 +01:00

Atom.cpp

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

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

Atom.h

amend declaration (#8302)

2025-03-04 14:03:13 +01:00

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

Fixes #7983 (#8342)

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

Atropisomers.h

Fixes #7983 (#8342)

2025-03-20 07:40:33 +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

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

apply query adjustments when makeAtomsGeneric is enabled (#8315)

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

catch_canon.cpp

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

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

catch_chirality.cpp

Fixes #7983 (#8342)

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

catch_graphmol.cpp

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

2025-03-29 07:26:03 +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_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 github #8364 and #8365 (#8366)

2025-03-31 15:58:47 +02:00

Chirality.h

Fixes github #8364 and #8365 (#8366)

2025-03-31 15:58:47 +02:00

CMakeLists.txt

Add Molecular Interaction Fields (#7993)

2024-12-14 17:08:43 +01:00

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

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

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

FindStereo.cpp

trimethylcyclohexane chirality error (#8272)

2025-02-24 17:41:54 +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

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

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

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

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

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

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

MolOps.h

Fixes #7983 (#8342)

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

molopstest.cpp

Revert "Fixes #5134 (#5136)" (#8319)

2025-03-05 18:11:24 +01:00

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

Fix canonicalization of stereogroups (#7041)

2024-10-11 17:09:18 +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

Github8353 (#8354)

2025-03-17 19:54:15 +01:00

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

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

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

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

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

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

2025-01-28 21:09:03 +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

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

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

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

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

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

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