Module graph 

Molecular graph representation backed by petgraph.

Defines Atom, Bond, and Molecule — the core data model consumed by conformer generation, force fields, electronic methods, and all property modules. Atoms carry hybridization, chirality, and aromaticity; bonds carry order and stereo.

Structs

Atom

A single atom node in the molecular graph.

Bond

A bond edge in the molecular graph.

Molecule

Molecular graph: atoms as nodes, bonds as edges. Constructed from a SMILES string via Molecule::from_smiles.

NodeIndex

Node identifier.

Enums

BondOrder

Bond order: single, double, triple, aromatic, or unknown.

BondStereo

E/Z (cis/trans) stereochemistry of a double bond.

ChiralType

Tetrahedral chirality type derived from the SMILES @/@@ specification.

Hybridization

Hybridization state of an atom, used to compute bond angles and geometry.

Functions

atom_in_ring

Check if an atom is in any ring (has an alternative path of length ≤ 8 through any neighbor).

bond_in_ring_of_size

Check if a bond (edge between a and b) is in a ring of exactly the given size.

get_corrected_ideal_angle

Returns the ideal 1–2–3 bond angle (radians) between atoms n1–center–n2, accounting for ring strain in small rings (3-, 4-, 5-membered).

get_covalent_radius

Returns the covalent radius (in Å) for a given atomic number Data derived from RDKit’s atomic_data.cpp

get_ideal_angle

Returns the ideal bond angle (in radians) for a given hybridization

get_vdw_radius

Returns the Van der Waals radius (in Å)

min_path_excluding

BFS shortest path (in bonds) from start to target in the molecular graph, excluding the node exclude. Used to detect ring membership and ring sizes. Returns None if no path exists within limit bonds.

min_path_excluding2

BFS shortest path from start to target, excluding two intermediate nodes.