Justin Gullingsrud bda9ffbeec Incremental synthon search (#8855) ...

* Iterated interface to substructure search

* Add a test

* Add python unit test

* Expose the toTryChunkSize parameter to python

* Respect the maxHits parameter; sort the hitset

* Treat maxHits=-1 as infinite

* Add callback versions of fp and rascal search; conform to C++ style

* Add fp and rascal C++ tests

* maxHits=-1 tripped me up again

* Add fp and rascal python wrappers.

Changed the name of the callback-based method to have "Incremental"
in the name because the overloaded versions with default arguments
can't be reliably selected by the boost python runtime.  Probably
better to have a different method name anyway since the return type
is None instead of a results object.

* Delete stray printf.

* Run clang-format

* Use std::int64_t instead of ssize_t for portability

* Make docstrings on callback-based methods more descriptive

* Stop incremental search if the callback returns true.

* Add an example of incremental synthon search to the getting started docs

* trivial commit to force CI rerun

* Reformat single line if statements.

* Make SearchResultsCallback take const ref input

* Fix another one-liner

* Oops - another one-liner

2025-11-08 04:27:16 +01:00

..

Abbreviations

Allow abbreviations without XBonds (#8933)

2025-11-06 16:33:25 +01:00

Basement/FeatTrees

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

ChemReactions

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +01:00

ChemTransforms

propagate string_view (#8858)

2025-10-14 19:15:37 +02:00

CIPLabeler

Make assignCIPLabels Ctrl+c interruptable (#8589)

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

Depictor

Fixes #8776 (#8875)

2025-10-17 05:52:27 +02:00

Deprotect

Fixes #7989 Incorrect benzyl deprotection reaction (#7990)

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

Descriptors

add conditional logic for GETAWAY test (#8923)

2025-11-04 16:05:56 +01:00

DetermineBonds

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

DistGeomHelpers

Change docs in Python EmbedMultipleConfs. (#8900)

2025-10-28 02:09:14 +01:00

EnumerateStereoisomers

Mem fixes (#8640)

2025-07-21 05:57:50 +02:00

FileParsers

added new attributes for scsr template as per BIOVIA doc 2023 (#8911)

2025-11-06 12:24:45 +01:00

FilterCatalog

Use std::string_view for property keys (#8844)

2025-10-09 16:14:48 +02:00

Fingerprints

Allow using generators for similarity maps (#8912)

2025-11-06 19:12:29 +01:00

FMCS

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

ForceFieldHelpers

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

FragCatalog

propagate string_view (#8858)

2025-10-14 19:15:37 +02:00

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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MMPA

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MolAlign

Fix some more mem errors in 2024.09.1 (#7899)

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

MolCatalog

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MolChemicalFeatures

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MolDraw2D

Use properties in the MolDrawOptions python wrappers to make setting/getting colours easier (#8857)

2025-10-09 14:14:19 +02:00

MolEnumerator

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

MolHash

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MolInteractionFields

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MolInterchange

ignore whitespace in patch (#8927)

2025-11-04 16:04:39 +01:00

MolProcessing

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

MolStandardize

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

MolTransforms

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

PartialCharges

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

RascalMCES

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

ReducedGraphs

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

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

RGroupDecomposition

Allow Multiple Core Hits in the Same Molecule in RGroupDecomposition (#8813)

2025-10-29 21:50:19 +01:00

ScaffoldNetwork

Add safeSetattr to more params / options objects (#8842)

2025-10-08 16:15:20 +02:00

ShapeHelpers

Minor refactor of the python wrappers (#8847)

2025-10-05 09:42:31 +02:00

SLNParse

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

SmilesParse

Change extern types to static consts (#8765)

2025-11-07 05:15:22 +01:00

StructChecker

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

Subgraphs

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

Substruct

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

SubstructLibrary

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

SynthonSpaceSearch

Incremental synthon search (#8855)

2025-11-08 04:27:16 +01:00

TautomerQuery

Modernization of some substructure code (#8450)

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

test_data

Fixes #8689 (#8738)

2025-09-03 12:15:09 +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

Partial fix to a problem with implicit Hs being written to SMARTS (#8893)

2025-10-24 07:50:06 +02:00

AddHs.cpp

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +01:00

AdjustQuery.cpp

apply query adjustments when makeAtomsGeneric is enabled (#8315)

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

Aromaticity.cpp

fixes #5078 (#8795)

2025-09-22 11:06:42 +02:00

Atom.cpp

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +02:00

Atom.h

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +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 for Issue 8602 (#8668)

2025-08-20 10:10:47 +02:00

Atropisomers.h

Fixes #7983 (#8342)

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

Bond.cpp

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +02:00

Bond.h

Merge simple AND queries onto atoms. (#8830)

2025-10-09 04:38:42 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

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

Partial fix to a problem with implicit Hs being written to SMARTS (#8893)

2025-10-24 07:50:06 +02:00

catch_canon.cpp

Fixes #8689 (#8738)

2025-09-03 12:15:09 +02:00

catch_chirality.cpp

Fixes #8712 (#8736)

2025-09-11 05:01:08 +02:00

catch_graphmol.cpp

Implements #8873 (#8904)

2025-11-04 16:10:56 +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

Fixes #8726 (#8874)

2025-10-17 16:51:22 +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

remove (#8872)

2025-10-23 11:21:36 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

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

Fixes #8712 (#8736)

2025-09-11 05:01:08 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

itertest.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MolBundle.h

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

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

MolOps.cpp

propagate string_view (#8858)

2025-10-14 19:15:37 +02:00

MolOps.h

Fixes #8726 (#8874)

2025-10-17 16:51:22 +02:00

molopstest.cpp

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +01:00

MolPickler.cpp

Change extern types to static consts (#8765)

2025-11-07 05:15:22 +01:00

MolPickler.h

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

MonomerInfo.h

Some modernization of core GraphMol classes (#7228)

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

new_canon.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

new_canon.h

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +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

Fix a couple issues related to atom list handling in V3000 mol blocks (#8824)

2025-10-09 05:26:01 +02:00

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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

Resonance.cpp

Fix #8638 (#8639)

2025-07-25 14:33:32 +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

Implements #8873 (#8904)

2025-11-04 16:10:56 +01:00

ROMol.h

add clearPropertyCache() (#8533)

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

RWMol.cpp

Do not reset the ringInfo information when adding bonds to RWMol (#8934)

2025-11-07 14:41:01 +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

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

StereoGroup.cpp

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

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

StereoGroup.h

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

SubstanceGroup.cpp

Add SCSR parsing to RDKit (#8147)

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

SubstanceGroup.h

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

test1.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

test_fixtures.h

Fixes #6944 (#6950)

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

test-valgrind.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

testChirality.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

testMolBundle.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

testPickler.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +02:00

testPicklerGlobalSettings.cpp

Refactor iostreams includes (#8846)

2025-10-08 16:08:01 +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