autofragment.core.bonds

Bond detection and interfragment bond representation.

This module provides: - InterfragmentBond: Represents a bond between two fragments - COVALENT_RADII: Standard covalent radii for common elements - Bond detection utilities

Functions

get_covalent_radius(element)	Get the covalent radius for an element.
infer_bonds_from_atoms(atoms[, tolerance])	Infer bonds from a list of Atom objects using covalent radii.
is_bonded(atom1_symbol, atom1_coords, ...[, ...])	Determine if two atoms are bonded based on distance.

Classes

InterfragmentBond(fragment1_id, atom1_index, ...)

Represents a bond between two fragments.