MolecularDiffusion.modules.models.diffsmol.bond_tables

Reference bond-length tables, vendored verbatim from DiffSMol.

others/DiffSMol/source/utils/analyze.py bonds1..bonds4 (single / double / triple / aromatic, in 0.01 A units, -1 = “no such bond order for this pair”).

These are not interchangeable with the platform’s own utils.geom_analyzer.bonds{1,2,3}: 26 entries of bonds1 and one of bonds2 differ numerically (mostly Br/I pairs, plus S-C double). Those tables drive the 5-class edge feature that every attention layer sees, so the pretrained DiffSMol checkpoint only reproduces upstream’s numbers against these values. The element-vocab path built before this module existed keeps using the platform tables and is untouched.

Attributes

BONDS_AROMATIC
BONDS_DOUBLE
BONDS_SINGLE
BONDS_TRIPLE
DIFFSMOL_BOND_TABLES

Module Contents

MolecularDiffusion.modules.models.diffsmol.bond_tables.BONDS_AROMATIC: dict[str, dict[str, int]]

MolecularDiffusion.modules.models.diffsmol.bond_tables.BONDS_DOUBLE: dict[str, dict[str, int]]

MolecularDiffusion.modules.models.diffsmol.bond_tables.BONDS_SINGLE: dict[str, dict[str, int]]

MolecularDiffusion.modules.models.diffsmol.bond_tables.BONDS_TRIPLE: dict[str, dict[str, int]]

MolecularDiffusion.modules.models.diffsmol.bond_tables.DIFFSMOL_BOND_TABLES