rdkit-montai 2.0.0

RDKit fork with enhanced stereochemistry InChI support

rdkit-montai

Fork of RDKit 2026.03.1pre with enhanced stereochemistry InChI support.

Install

Pre-built wheels for Linux (x86_64, aarch64) and macOS (ARM):

pip install rdkit-montai

What's different from upstream RDKit?

Upstream RDKit silently drops enhanced stereo group annotations (ABS, OR, AND) during InChI generation. This means a racemic mixture and a single enantiomer produce identical InChI Keys — they are indistinguishable.

This fork fixes that:

• Mol → InChI: Stereo groups (ABS/OR/AND) are passed to the InChI library via the GetINCHIEx extended API, producing a /s layer that encodes the stereo group type
• InChI → Mol: The /s layer is parsed back into StereoGroup objects, so round-trips preserve stereo annotations
• Stable keys: Enhanced stereo InChIs produce standard InChI=1S/ output (not Beta 1B), so keys will match the eventual official IUPAC release
• InChI v1.07.5: Upgraded from v1.05 (2017) to the IUPAC-InChI dev branch with enhanced stereochemistry support

Group Type	Meaning	InChI /s prefix
ABS	Absolute configuration	1(...)
OR	This enantiomer or its mirror	2(...)
AND	Racemic mixture	3(...)

Usage

from rdkit import Chem
from rdkit.Chem.inchi import MolToInchi, MolFromInchi

# Create a molecule with an AND stereo group (racemic)
mol = Chem.MolFromSmiles('[C@@H](F)(Cl)Br |&1:0|')

# Generate InChI — stereo group is preserved in /s layer
inchi = MolToInchi(mol)
print(inchi)  # Contains /s3(...) for AND group

# Round-trip back — stereo group is restored
mol2 = MolFromInchi(inchi)
groups = mol2.GetStereoGroups()
print(len(groups))  # 1

Preserving atom order with AuxInfo

from rdkit.Chem.inchi import MolToInchiAndAuxInfo, MolFromInchiAndAuxInfo

mol = Chem.MolFromSmiles('c1cc(O)ccc1N')
inchi, aux = MolToInchiAndAuxInfo(mol)
mol2 = MolFromInchiAndAuxInfo(inchi, aux)
# Atom order and coordinates are preserved

Upstream status

Change	Upstream PR	Status
MolFromInchiAndAuxInfo	rdkit/rdkit #9158	Merged into rdkit:main
Enhanced stereo InChI	—	Not yet submitted (waiting for IUPAC official release)
InChI v1.07 upgrade	—	Depends on IUPAC official release

Base commit: RDKit 2026.03.1pre (22be7245d)

License

Code released under the BSD license.