autofragment.multilevel.link_atoms

Advanced link atom positioning for QM/MM boundaries.

This module provides sophisticated link atom positioning using g-factor approach and supporting different element pairs.

Functions

calculate_g_factor(qm_element, mm_element[, ...])	Calculate g-factor for link atom positioning.
create_link_atoms_for_cut_bonds(coords, ...)	Create link atoms for all cut bonds.
get_bond_length(element1, element2)	Get typical bond length between two elements.
position_link_atom_fixed_distance(...[, ...])	Position link atom at fixed distance from QM atom.
position_link_atom_gfactor(qm_position, ...)	Position link atom using g-factor approach.
validate_link_atoms(link_atoms, coords[, ...])	Validate link atom positions.

Classes

LinkAtomInfo(qm_atom_index, mm_atom_index[, ...])

Complete information about a link atom.