Skip to main content Module graph Copy item path Source 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. 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. 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.