Truncation utils

Module containing functions utilized by truncation_schemes.py.

QMzyme.truncation_utils.cap_H(replace_atom, fixed_atom, bond_length=1.09, base_atom=None)

Parameters:

• replace_atom -- The Atom to be converted to hydrogen.

• fixed_atom -- The Atom bound to replace_atom that serves as reference point for bond vector calculation.

QMzyme.truncation_utils.balance_charge(region, truncated_region)

To be used if original region has atom charge information, so the QMzymeRegion guess_charge() and read_charges() methods do not get messed up. Within a residue, any atoms added should distribute the charges of any atoms removed.

QMzyme.truncation_utils.set_bond_length(mobile_coords, fixed_coords, new_length)

QMzyme.truncation_utils.create_new_atom(base_atom, new_atom_dict)

QMzyme.truncation_utils.get_preceding_Catom(region, resid)

QMzyme.truncation_utils.get_following_Natom(region, resid)

QMzyme.truncation_utils.has_Nterm_neighbor(atom)

QMzyme.truncation_utils.has_Cterm_neighbor(atom)