When converting molecules with wavy bonds (Bond::STEREOANY on double
bonds) through InChI and back, the stereo information was silently
dropped. This affected any workflow using InChI roundtrips for
canonicalization (e.g. with -SUU flag).
Two bugs in External/INCHI-API/inchi.cpp:
Reverse path (InchiToMol): The stereo0D processing loop skipped
INCHI_PARITY_UNDEFINED entries before they could reach the double bond
handler. The handler already had an else clause that correctly sets
Bond::STEREOANY, but it was never reached. Fix: only skip
INCHI_PARITY_NONE at the top level, and add a guard in the Tetrahedral
case to prevent UNDEFINED/UNKNOWN from incorrectly setting chirality.
Forward path (MolToInchi): STEREOANY double bonds were only handled by
collapsing the coordinates — InChI then produced no stereo annotation
under -SUU. Fix: also emit a stereo0D entry with INCHI_PARITY_UNKNOWN
parity so InChI's -SUU output correctly carries the "stereo unknown"
designation. StereoAtoms may be cleared for STEREOANY, so we locate
the two outer neighbors by iterating bonds.
New test testStereoAnyRoundtrip in External/INCHI-API/test.cpp covers
9 representative cases (Schiff base, oxime, cinnamic acid, chalcone,
crotonaldehyde, tamoxifen-like, retinal-like, plus two molecules with
a chiral center adjacent to the wavy bond).
Counts in rdkit/Chem/UnitTestInchi.py shift by 1 (689 same, 492
reasonable) because the new STEREOANY emission produces a more
accurate roundtrip for one entry in the test inventory.
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
MolToInchi has called MolOps::Kekulize(*m, false) for years, but PR #9125 changed the default traversal to canonical=true. That pulls rankFragmentAtoms() and the canonicalization path into the InChI conversion even though the tested InChI outputs stay the same.
Validation:
- rdkit.Chem.UnitTestInchi passed before and after this change on upstream/master (18 tests, OK in both runs).
- No InChI output drift was observed between stock and patched builds on Regress/Data/mols.1000.sdf.gz, rdkit/Chem/test_data/pubchem-hard-set.sdf.gz, or the atom-order regression molecules added in Code/GraphMol/catch_graphmol.cpp.
Performance:
- Release_2026_03_1 Python MolToInchi on Regress/Data/mols.1000.sdf.gz improved from 0.40712s to 0.38871s median (-4.52%).
- Release_2026_03_1 rdinchi MolToInchi on the same dataset improved from 0.39755s to 0.37814s median (-4.88%).
- Release_2026_03_1 standalone C++ MolToInchi on /tmp/mols.1000.sdf improved from 7.66775s to 7.03474s wall time (-8.26%), from 20.57B to 19.04B cycles (-7.46%), and from 121.78M to 114.05M cache misses (-6.35%).
* Add MolFromInchiAndAuxInfo to restore original atom order from AuxInfo
Add a new function that reconstructs molecules from InChI + AuxInfo strings,
restoring the original atom ordering and 2D/3D coordinates from the /N: and
/rC: AuxInfo layers. Includes comprehensive tests for round-tripping, stereo
preservation, coordinate restoration, edge cases, and multi-fragment molecules.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* Update rdkit/Chem/UnitTestInchi.py
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add MolTransforms library.
* Transform to inertial frame of reference before overlay.
* Vital fix of typo in comment.
* Tidy up debugging cruft.
* Comment in CMakeLists.txt.
* Fix python wrappers.
* Extra tidy.
* Response to review.
* Tidy includes.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Add function to compute shape scores without overlay.
* Update docstrings.
* Rename function to ScoreMolecule/ScoreMol.
Add extra functions analogous to the overlay ones.
* Windows export crap.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
The iterator in the loop over bonds (changed in utils.cpp) is potentially
invalidated by adding bonds to the molecule. We copy the bonds into a vector to
ensure safety.
* patch RapidJSON to make sure it builds on all platforms
* remove unnecessary sed command from Docker recipe
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Fix an out of bounds access when replacing fragments
* Add segfaulting US patent CDXs
* Return false when we can't find the bond idx for better handling
* Remove useless REQUIRE
* Only sniff when in format AUTO
* Add test for reading wrong format
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* support providing custom features
* expose that to python
* switch to tuples (on get) and objects (on set) for attributes
* allow aligning mols directly with ShapeInputOptions
* changes for review
* add warning
isascii() (which is the standard) or __isascii(), but it guesses wrong for
Emscripten builds (which I do during sketcher compilation). This change
passes -D__isascii=isascii when building InChi,
which means that the wrong guess will still wind up with the right
function name.
* 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>
* Fixes a bug with bad H positions in output conformer
This would only trigger when the number of H atoms is equal
to the number of features, but it was terrible when it happened.
* spell that better
* docs
---------
Co-authored-by: = <=>
* 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
* Rev chemdraw version
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* - avoid a large number of warnings when building MinimalLib with emscripten, which does not support SHARED
- fix indentation in CoordGen CMakeLists.txt
* disable RDK_USE_BOOST_STACKTRACE on emscripten platform
* revert change done by mistake
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Make shape on subset of atoms in molecule.
Optional radius for dummy atoms.
* Re-factor.
Add ShapeInputOptions.
* Python wrapper for options.
* Add non-standard radii option.
Add function to align a shape on a shape.
Add function to align conformer based on shape-shape transformation.
* Python wrappers for AlignShapes and TransformConformer.
* Add the new thing for Python options.
* Add option for excluding atoms from color features.
No partial color features if using atomSubset.
* In AlignShapes, don't change the fit shape (apart from transforming it) in case it will be used again.
* Rename it AlignShape to be consistent with AlignMolecule.
* Response to review.
* Undo clang-format
* Fix botched merge.
* Typo.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* c++20 builds working
* get MolStandardize building with clang19
* get FMCS building with clang-19
* set cxx version to c++20
* remove a few more compiler warnings
* bump min boost version, CI cleanup
* boost 1.81 is not available from conda-forge
* remove unused constants
* bump linux version for CI
* remove another unused variable
* fix (hopefully) cartridge CI builds
* simplify cartridge environment
* try postgresql14 in CI
* start the postgresql service
* change the columns used in the pandastools nbtest
* remove missed merge conflict artifact
* get github4823 test to pass with numpy 2.2
* remove a compiler warning/error with g++13
* avoid a segfault in CoordGen when a double bond has stereo spec but no stereo atoms
* changes in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* refactor the code to determine whether or not an atom is in brackets
* move the definition of isMetal to QueryOps
* atoms bound to metals in SMILES should always be in square brackets
Implementation and some test updates
needs confirmation that all of tests run
* basic tests pass
* java tests pass
* update js tests
* doc updates
* Update Code/GraphMol/catch_graphmol.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Update Code/GraphMol/SmilesParse/test.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* finish fixing tests
* bump yaehmop version to allow compilation to work
---------
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
