ost.bindings.dssp Namespace Reference

Functions
	_SkipHeader (stream)
	_Cleanup (temp_dssp_path, pdb_path)
	_CalcRelativeSA (residue_type, absolute_sa)
	AssignDSSP (ent, pdb_path="", extract_burial_status=False, tmp_dir=None, dssp_bin=None)
	LoadDSSP (file_name, model, extract_burial_status=False, entity_saved=False, calculate_relative_sa=True)

Detailed Description

Utility functions to load secondary structure information from DSSP files
and assign them to entities.

Authors: Pascal Benkert, Marco Biasini

Function Documentation

_CalcRelativeSA()

_CalcRelativeSA (   residue_type,   absolute_sa  )

protected

Definition at line 47 of file dssp.py.

_Cleanup()

_Cleanup (   temp_dssp_path,   pdb_path  )

protected

Definition at line 41 of file dssp.py.

_SkipHeader()

_SkipHeader (   stream )

protected

Definition at line 33 of file dssp.py.

AssignDSSP()

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 replaces the "old" AssignDSSP which relies on the DSSP command line
program and uses OpenStructure internal functionality only. The sole purpose
is to retain the "old" interface and you're adviced to directly use
:func:`ost.mol.alg.AssignSecStruct` and :func:`ost.mol.alg.Accessibility`.  

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 - deprecated, has no effect
:param dssp_bin: The path to the DSSP executable - deprecated, has no effect

Definition at line 142 of file dssp.py.

LoadDSSP()

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 190 of file dssp.py.