* SHARED-12256: Add test and change function.
* SHARED-12256: Update to only wrapping changes.
* SHARED-12256: Parameterize tests.
* SHARED-12256: GetPropIfPresent changes.
* Revert "SHARED-12256: GetPropIfPresent changes."
This reverts commit f598f8c161.
* SHARED-12256: Make default the keyword in the boost wrappings.
* SHARED-12256: Overload function instead of using a sentinel.
* SHARED-12256: Extend GetProp changes.
* SHARED-12256: Add entry point for tests and fix tests.
* Remove Dict::getData() for a strict abstraction boundary
Replace direct access to Dict's internal std::vector<Pair> with
encapsulated methods: size(), empty(), const iteration via
begin()/end(), appendPair(), markNonPOD(), and getRawVal().
This enables future changes to Dict's internal representation
without breaking callers.
Ref: rdkit/rdkit#9112
* Harden Dict::appendPair to take a populated Pair by move
appendPair(Pair&&) now auto-detects non-POD status via
RDValue::needsCleanup(), eliminating markNonPOD() and the
risk of dangling references or uninitialized entries.
needsCleanup() is placed next to destroy() on RDValue to
keep the POD/non-POD distinction in one place.
* Remove vestigial dictHasNonPOD param from streamReadProp
Both callers ignored the output. Non-POD detection is now handled
by Dict::appendPair via RDValue::needsCleanup().
* unbork java build
* Address PR review: bulk append, rename getRawVal, add custom data test
- Add Dict::append(vector<Pair>&&) for bulk insertion with reserve
- Use bulk append in streamReadProps to restore pre-allocation
- Rename getRawVal -> getRDValue per reviewer preference
- Add test verifying custom AnyTag data is destroyed through Dict lifecycle
* heed self-review
* don't manually implement vec.insert
* Add test: ExplicitBitVect round-trip through Dict serialization
Exercises the full streamWriteProps/streamReadProps path with an
ExplicitBitVect in an RDProps Dict, confirming the custom handler
is invoked and no memory is leaked (verified under valgrind).
* in anyTag test, assert destructors ran a specific number of times.
---------
Co-authored-by: bddap (Coding Agent) <andrew+bot@dirksen.com>
* Defer numpy initialization to first use in rdchem, rdmolops, cDataStructs
`from rdkit import Chem` unconditionally bootstrapped numpy (~120ms) via
import_array()/boost::python::numpy::initialize() in module init functions,
even when no numpy-dependent APIs were called. This is costly in cold-start
environments like AWS Lambda.
Move numpy initialization behind lazy guards (static bool + first-call init)
in rdchem.so, rdmolops.so, and cDataStructs.so. Numpy now loads only when
an API that actually needs it is invoked (GetDistanceMatrix, GetPositions,
SetPositions, GetAdjacencyMatrix, ConvertToNumpyArray, etc.).
Also change Conformer::SetPos to accept python::object instead of
np::ndarray to prevent Boost.Python from requiring numpy type conversion
before the lazy guard runs.
Adds test_lazy_numpy.py with subprocess-based tests verifying:
- `from rdkit import Chem` does not load numpy
- SmilesToMol/MolToSmiles work without numpy
- numpy loads on demand when array APIs are called
* skip inchi tests if not available
* switch to threadsafe once_flag, like elsewhere
* finish ifdef style
* switch to magic static style
* Revert "switch to magic static style"
This reverts commit 7300188db7.
* cleanup of stereogroups and wedges for non-chiral sites
* fixed testShapeHelpers for Arm64 build
* reorg the tests a bit
* rename and document option
* add to the python wrappers
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* add the _CIPNeighborRanks property
* store CIP-ranked chiral neighbors
* store CIP-ranked SP2 bond and atropisomer anchors
* add a test
* boost headers in test
* add Atom::NOATOM
* add NOATOM test
* amend and clarify implicit H in Tetrahedral
* rename property
* rename property to _CIPNeighborOrder
* deprecate Chirality::StereoInfo::NOATOM
* move molzip to its own file
* basics working
* more testing
* another test
* minor
* fix doxygen comment format
* fix alignment with co-directional exit vectors;
some modernization
* JSON parsing
python wrapper
* response to review
* response to review
* explicitly test that the first frag does not move
---------
Co-authored-by: = <=>
* extra SSS match functions for atoms/bonds
initial implementation and testing
* add baseline to test
* add a functor for matching atom coords
* support the extra checks in python
* refactor the way the python callbacks are handled
* test tolerances
* expose the AtomCoordsMatcher to python
* allow the extra checks to override the default matching
---------
Co-authored-by: = <=>
* Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742)
This adds a new api, `RDKit::MolOps::ExtractMolFragment`, to allow efficient
extractions of mol fragments from large mols. Compared to the approach where
we delete "unwanted" atoms/bonds from the input mol, this api is faster for
small mols (about 2x faster) and at least 3x faster for big mols
(was 10x faster for "CCC"*1000).
* clang-format
* review comments
* cleanup
* Consolidate copying subsets of molecules
* Readd missing tests
* Update comment to restart build
* Remove missing test
* Remove debugging comment, fix warnings
* Fix warnings on gcc11
* Add docs
* Make vector<bool> dynamic_bitset<>
* Update copyright
* Add swig wrappers
* Use new designated constructor API
* Fix windows builds
* Change enum values from unsigned int to integer
* Fix unsigned int variable
* Update Code/GraphMol/Wrap/test_subset.py
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Subset.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ChemTransformsTests.java
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Reponse to review
* Fix documentation
* Remove comments
* Remove unnecessary comments
* Fix one liners
* Change assertion to be clearer (and not one-liners)
* Run clang-format
---------
Co-authored-by: Your Name <you@example.com>
Co-authored-by: Hussein Faara <hussein.faara@schrodinger.com>
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* do not remove hydrides by default
* add a minimal test
* add release note about behavior change
* require Hydrides to have degree 1
* also allow hydrides with degree 0 (ionic bond)
* suggested changes
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Trim spaces from RDProp strings to simulate reading from SDFiles
* Update documentation
* Use the correct doc strings
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* backup
builds but no tests
* deprecate old form
* initial basic tests for bond property lists
* Tests pass
Fixes#8777
* add deprecations to release notes
* - avoid computing size of a constant at runtime
- replace multiple instances of a numeric constant with a literal constant
- avoid unnecessary copying of strings in iterations and function calls
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Fist pass at CDX support
* Enable CDX support for reading (also) in the CDXMLParser API
* Add cdxml test files
* Update swig wrappers for CDXMLFormat and Parameters
* Add constructor to ChemDrawParserParams
* Add Java SWIG support for ChemDraw
* Add chemdraw define to rdconfig
* Add missing chemdraw deps
* Remove direct expat link
* Fix Java linkages for ChemDraw
* Remove bad merge code
* Remove bad merge code
* Fix csharp builds
* Add sniffer for the ChemDraw DataStream
* Include filesystem
* Fix test on windows
* Add more CDX tests
* Ensure streams are open in binary mode to support CDX on windows
* Fix text to show that a Block is the text input, not a file
* Fix CSharp test
* Disable CDX tests when not building chemdraw
* Turn back on chemdraw
* Response to review
* Turn off chemdraw support for the limited external test
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* get SynthonSpace.cpp to build also when RDK_USE_BOOST_SERIALIZATION is
not defined
* test should not fail when RDK_USE_BOOST_SERIALIZATION is not defined
* - expose reading/writing PNG metadata to CFFI and MinimalLib
- add relevant CFFI and MinimalLib unit tests
- add RDK_USE_BOOST_PROGRAM_OPTIONS CMake option
- enable using standalone zlib in the absence of boost::iostreams for parsing PNG files
- enable linking against maeparser in the absence of boost::iostreams also on Windows
- enable building RDKit in the absence of boost::program_options
* add check for boost::program_options
* change size_t into std::uint64_t in SearchResults for consistency with doTheSearch() which uses std::uint64_t
* change size_t into std::uint64_t in SearchResults for consistency with
SynthonSpaceSearcher::doTheSearch()
* set CMake policy to allow YAeHMOP to require a version which is not
actually supported
* reverted External/YAeHMOP/CMakeLists.txt to master version
* check if Windows build will work
* fix build
* configure zlib install location
* build zlib dependency
* include zlib header directory
* explicitly set PropertyFlags.AllProps so the test does not fail on
static builds
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Adds a df_forceStop to stop readers and writers, clears out queues on destructor
* Propery implement close function, requires protected closeStreams
* changes from greg's version
* close() needs to be called in the derived destructors
* Close the writers before the reader to avoid deadlock
* Don't process trailing new lines
* Don't accept pushes if the queue is done
* Add mutex protecting d_threadCounter, remove unneeded forceStop checks
* Update Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add comment for the d_threadCounterMutex unlock
---------
Co-authored-by: = <=>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Parsing SCSR
* add scsrol to mol
* removed bad include file
* loosen distGeom test slightly
* add wrap test for SCSRMol
* Add test for scsr in python
* tests added for scsr and strict parsing removed
* remove extra stuff
* More fully specified use of SCSRMol for PR CI build
* Added flags for SCSR expansion to not include any leaving groups
* Added MolFromScsrParams to Wrap for python
* added SCSRMol destructor
* Added two tests for RNA macromols, and fixed a bug they revealed
* Added new tests abd expected files
* changes as per PR review
* SCSR Chnages for leaving groups
* fixed testScsr.py
* hydrogen bond treatment
* in SCSR expand, allow Hbond to be autoatically detected
* changes as per code review
* Adding new test file
* chages for SCSR contructors, destructors for CI build
* fixed pyton for SCSR hydrogen bond modes, and added tests
* Added new test files
* fixed edge case for SCSR
* fix checksum for inchi
* consistent capitalization of SCSR throughout
* switch to enum class
* make things shorter
* simplify
* get rid of the ATTCHORD class
* New section for SCSR in RDKit_book
* addeed section to RDKit_Book
* SCSRMol is no longer exposed in Python
* fix leak in MolFromSCSRFile()
light refactoring
* expose MolFromSCSRFile() to python
make the MolFromSCSR functions work with default args
a bit more testing
* removed C++ access to SCSRMol
* CXMsiles now ouputs hbonds, fix to template matching, and a few other things
* Addl fix for bad aromaticity in Hbond rings
* Test files needed
* Test files needed
* try to fix a CI build errors
* CI error fix
* Added missing test file
* CMake version - for CI build
* remove full file compoarison from macromol test file
* accidental change to debug restored to release
* Code review changes
* As per PR review
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* use std::span for substruct match callbacks
This removes a copy from every evaluation of potential matches
* some cleanup/modernization
* some modernization
* deprecate chiralAtomCompat
* small optimization
* remove naked pointers
* improve new_timings.py script
* changes suggested in review
* response to review
* response to review
