* 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>
* implement consistency check
* add more consistency checks
* check direction consistency accross double bond
* clean up directions for non-stereo bonds
* fix counts for second from atom dirs; add check
* handle inconconsistent bond dirs
* add more tests, pubchem cases, and update existing
* drop statics
* fix typo
* make sourceBond arg const
* fix consistency check
* switch the Query infrastructure to use std::function
* add releasenotes mention
* refactor makeAtomInRingOfSizeQuery() to use lambdas and support range queries
* add 'k' atom query to SMARTS
* changes in response to review
V3000 parsing sets aromatic flags on bonds but not atoms. When removeHs
strips an explicit H from nitrogen in an aromatic ring, molRemoveH
checked heavyAtom->getIsAromatic() to decide whether to increment
numExplicitHs — but that flag was always false for V3000-parsed atoms.
Without the explicit H count, the kekulizer cannot distinguish pyrrole N from pyridine N,
causing
"Can't kekulize mol" errors on valid ChemDraw-exported molblocks.
Fix: use isAromaticAtom(), which checks both atom and bond aromatic
flags
* switch the Query infrastructure to use std::function
* add releasenotes mention
* response to review
Removed commented-out function pointer declarations for match and data functions.
* Add RDLog::CaptureLog for capturing log messages
Adds an RAII `CaptureLog` class to `namespace RDLog` (alongside the
existing `LogStateSetter`) that redirects an RDKit logger's output to an
internal `std::stringstream` for the duration of its lifetime. On
destruction the original stream destination and enabled state are fully
restored. Nesting is supported: an inner capture shadows the outer one
and each collects its own messages independently.
The default constructor captures `rdErrorLog`; an explicit constructor
accepts any `RDLogger`. Both enable the logger if it was previously
disabled and restore that state on destruction.
Python bindings expose `rdBase.CaptureLog` as a context manager with a
`messages` read-only property, mirroring the existing `rdBase.BlockLogs`
pattern. Messages remain accessible after the `with` block exits.
C++ tests are added to `catch_logs.cpp` (6 Catch2 sections covering
basic capture, empty state, enable/restore, stream restore, explicit
logger, and nested captures). Python tests are added to
`UnitTestLogging.py` (6 unittest cases covering the same scenarios).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* CaptureLog: add per-level properties (error_messages, warning_messages, etc.)
The Python CaptureLog wrapper now captures all four log levels
simultaneously. Per-level properties (error_messages, warning_messages,
info_messages, debug_messages) give access to messages from each logger
independently; the existing messages property returns them all combined.
The C++ RDLog::CaptureLog class is unchanged — it remains a clean
single-logger RAII type. The Python wrapper composes four instances of
it, one per log level.
Suggested by bp-kelley in PR review.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Refactor CaptureLog: add named per-level subclasses
Add CaptureErrorLog, CaptureWarningLog, CaptureInfoLog, and CaptureDebugLog
as named convenience subclasses of CaptureLog, each capturing a specific
logger. Update Python bindings to expose the four named classes directly
(dropping the combined multi-capture approach), and update tests accordingly.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Simplify CaptureLog: no argument, captures rdErrorLog only
Remove the RDLogger argument overload, the four named subclasses, and the
PyCaptureLog template in favor of a single no-argument CaptureLog that
mirrors the Schrödinger CaptureRDErrorLog from which it was inspired.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* CaptureLog tests: add dp_dest restoration and LogStateSetter interaction
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Rename CaptureLog to CaptureErrorLog
The name CaptureLog was ambiguous; CaptureErrorLog is explicit about which
logger it captures and avoids redundancy within namespace RDLog.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Generalize CaptureErrorLog into CaptureLog with logger parameter
Replace CaptureErrorLog with CaptureLog, which accepts any RDLogger in
its constructor (e.g. rdErrorLog, rdWarningLog). Add CaptureErrorLog as
a convenience subclass that pre-fills rdErrorLog, preserving backward
compatibility for existing callers.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---------
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
* Fix Qt 6.5.8 link failure on macOS due to removed AGL framework
Qt 6.5.8 injects the AGL (Apple Graphics Layer) framework into the
WrapOpenGL::WrapOpenGL imported target's INTERFACE_LINK_LIBRARIES. AGL
was removed from macOS 14+ SDKs, causing a link error when building
MolDraw2DQt on modern macOS:
ld: framework not found AGL
This workaround filters AGL out of WrapOpenGL::WrapOpenGL's link
libraries after find_package(Qt6) populates them. The guard conditions
(APPLE and TARGET WrapOpenGL::WrapOpenGL) make it a no-op on other
platforms and Qt versions that do not create that target.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
* Broaden AGL workaround comment to not pin Qt 6.5.8 specifically
The issue may affect other Qt versions, not just 6.5.8.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---------
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
* add a test
* change stereo bond canonicalization
* update canonicalization watch test with fixed cases
* make canonicalization test stricter (compare CIP codes)
* add reverse symmetry condition
* rewrite double bond canonicalization code
* update tests
* fix multiline comment
* update java tests
* update python test
* nix switchBondDir (unused)
* fix and rename flipBondDir
* refactor comment
* fix shadowed var name, casting
* fix neighbor sorting
* make seen_bonds a vector
* abstract setDirectionFromNeighboringBond
* handle both sides of the bond have directions
* move getNeighboringStereoBond
* check seen_bonds after popping connectedBondsQ
* use references for arguments
* add release note
* add example required by Dan
* add example requested by Dan
* 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.
* when shifting double bonds in tautomerization, set double bond stereo to STEREOANY
fixes#9102
notably, do this only to non-ring bonds
move tests over to assert this
avoid index-based bond lookup in test assertions
since bond indexing can move in tautomers
* inchi unittest check
* fast rings
* Cannot push_back std::string to boost json array
`boost::json::array.push_back` expects a `value`
* prefer emplace_back to avoid casting
* Ensure every MINIMAL_LIB option is tested in CI
Also remove Chemdraw support from the compilation. This does not change the final size of the output (not exported anyways) but it reduces the compilation time by 1 min (-10% on my local machine)
* Expose MMPA with other options
* Fix MMPA compilation: Implicitly binding raw pointers is illegal
Applying same pattern as in `get_frags_helper`
* use queues instead of sets for trimBonds
* skip 2 last atoms: if these were in rings, we'd have already noticed
* refactor duplicate detection in findRingsD2nodes
* make smallestRingsBfs a free function
* move things around
* fix paper reference; fix other comments
* Fixes#9068
* fix a problem with empty labels in s-group parsing
* fix empty column names in smiles suppliers
* add the check to setPODVal()
---------
Co-authored-by: = <=>
* Don't silent ignore missing atoms (and replace them with atom #0) in copymolsubet
* Fail if explicitly set atoms/bonds are not present
* Add tests
* Simplify optimization (copy whole molecule) add test for no bonds
* get BertzCT working with numpy 2.4
* test pass with with Pandas 3.0
(on windows at least)
* update testRanker too
* update nb test
* run win32 CI tests with different pandas versions
also updates boost version
* works with pandas 2.0?
* update linux_build_py311 -> linux_build_py312
test both old and new pandas
can't go higher with the python version yet because the older pandas and numpy are not available.
* doctest fix?
---------
Co-authored-by: = <=>
* 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
* added flag to allow chiral settings on Atoms with 2 hydrogens for SCSR treatment
* added parameter to allow chiral 2Hs on template mols in SCSR parser
* fixed testShapeHelpers for arm64 build
* Remove checking for two Hs in chiral atom in atomChiralTypeFromBondDirPseudo3D
* removal of flag for allow2Hs
* remove setup.bat file
* do not write extra separators
* add a test
* update tests
* Update Code/GraphMol/SmilesParse/CXSmilesOps.cpp
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
