ost.bindings.dssp Namespace Reference

Functions
def	AssignDSSP
def	LoadDSSP

Function Documentation

def ost.bindings.dssp.AssignDSSP	(		ent,
			pdb_path = "",
			extract_burial_status = False,
			tmp_dir = None,
			dssp_bin = None
	)

Assign secondary structure states to peptide residues in the structure. This
function uses the DSSP command line program.

If you already have a DSSP output file and would like to assign the secondary 
structure states to an entity, use :func:`LoadDSSP`.

:param ent: The entity for which the secondary structure should be calculated
:type ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
:param extract_burial_status: If true, also extract burial status and store
                              as float-property
                              ``relative_solvent_accessibility`` at residue
                              level
:param tmp_dir: If set, overrides the default tmp directory of the
                operating system
:param dssp_bin: The path to the DSSP executable
:raises: :class:`~ost.settings.FileNotFound` if the dssp executable is not 
    in the path.
:raises: :class:`RuntimeError` when dssp is executed with errors

Definition at line 81 of file dssp.py.

def ost.bindings.dssp.LoadDSSP	(		file_name,
			model,
			extract_burial_status = False,
			entity_saved = False,
			calculate_relative_sa = True
	)

Loads DSSP output and assigns secondary structure states to the peptidic
residues.

If you would like to run dssp *and* assign the secondary structure,
use :func:`AssignDSSP` instead.

:param file_name: The filename of the DSSP output file
:param model: The entity to which the secondary structure states should be
              assigned
:param extract_burial_status: If true also calculates burial status of
    residues and assigns it to the burial_status string property.
:param calculate_relative_sa: If true also relative solvent accessibility and
    and assigns it to the relative_solvent_accessibility float property of
    the residue.
:param entity_save: Whether the entity was saved.

Definition at line 134 of file dssp.py.