luna.mol.standardiser module

class ResidueStandard(value)[source]

Bases: enum.Enum

An enumeration of protonation states for standard residues.

CYM = 5
CYS = 4
HID = 1
HIE = 2
HIP = 3
class ResiduesStandardiser(break_metal_bonds=False, his_type=ResidueStandard.HIE)[source]

Bases: object

Standardize residues.

Parameters

  • break_metal_bonds (bool) – If True, break covalent bonds with metals and correct the topology of the involved atoms.

  • his_type ({HID, HIE, HIP}) – Define which histidine protonation state to use. Currently, this option is still not been used.

standardise(atom_pairs)[source]

Standardize residues.

Parameters

atom_pairs (iterable of tuple of (MolWrapper, Atom)) – The atoms to standardise.