ost.conop.cleanup Namespace Reference

Functions
	Cleanup (entity, strip_water=True, canonicalize=True, remove_ligands=True)
	_StripWater (clean_entity, ed)
	_RemoveLigands (clean_entity, ed)
	_CanonicalizeResidues (clean_entity, ed, compound_lib)
	_Replacement (res, ed, old_name)
	_Deletion (res, ed)
	_Addition (res, ed, additional_modif_atoms)
	_Unchanged (res, ed)
	_DeleteSidechain (res, ed)

Function Documentation

_Addition()

_Addition (   res,   ed,   additional_modif_atoms  )

protected

Definition at line 141 of file cleanup.py.

_CanonicalizeResidues()

_CanonicalizeResidues (   clean_entity,   ed,   compound_lib  )

protected

This function strips off modifications of amino acids and maps
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.

Definition at line 59 of file cleanup.py.

_DeleteSidechain()

_DeleteSidechain (   res,   ed  )

protected

Definition at line 159 of file cleanup.py.

_Deletion()

_Deletion (   res,   ed  )

protected

Definition at line 135 of file cleanup.py.

_RemoveLigands()

_RemoveLigands (   clean_entity,   ed  )

protected

This function removes ligands from the structure

Definition at line 47 of file cleanup.py.

_Replacement()

_Replacement (   res,   ed,   old_name  )

protected

Definition at line 120 of file cleanup.py.

_StripWater()

_StripWater (   clean_entity,   ed  )

protected

This function removes water residues from the structure

Definition at line 36 of file cleanup.py.

_Unchanged()

_Unchanged (   res,   ed  )

protected

Definition at line 150 of file cleanup.py.

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.