ost.conop.cleanup Namespace Reference

Functions
def	Cleanup (entity, strip_water=True, canonicalize=True, remove_ligands=True)

Function Documentation

Cleanup()

def ost.conop.cleanup.Cleanup	(		entity,
			strip_water = True,
			canonicalize = True,
			remove_ligands = True
	)

This function returns a cleaned-up (simplified) version of the protein
structure. Different parameters affect the behaviour of the function.

:param strip_water: Whether to remove water from the structure
:param canonicalize: Whether to strip off modifications of amino acids and map
   them back to their parent standard amino acid, e.g. selenium methionine to
   methionine.For more complex amino acids, where the relation between the
   modified and the standard parent amino acid is not known, sidechain atoms
   are removed. D-peptide-linking residues are completely removed as well.
:param remove_ligands: Whether to remove ligands from the structure

:return: a cleaned version of the entity

Definition at line 3 of file cleanup.py.