dssp - Secondary structure assignment
Introduction
DSSP is a program developed by Wolfgang Kabsch and Chris Sander to assign
secondary structure states to protein structures. The assignment is based on
hydrogen bonding patterns and geometric features.
The program can be downloaded from http://swift.cmbi.ru.nl/gv/dssp/.
Warning
Support of the DSSP program has been deprecated. OpenStructure provides
functionality to assign equivalent secondary structures
(ost.mol.alg.AssignSecStruct()) and solvent accessibility
(ost.mol.alg.Accessibility()). You’re advised to use these
algorithms.
AssignDSSP() still exists and provides the “old” interface but
internally uses the OpenStructure impmlementations and does not call
an external program anymore.
Examples
The following example assigns secondary structure states to an entity by using
the DSSP program.
from ost.bindings import dssp
ent=io.LoadPDB('1ake.pdb')
dssp.AssignDSSP(ent)
Now we fetch structure information plus solvent accessibility for an entity
using the mmCIF interface.
from ost.bindings import dssp
ent=io.LoadMMCIF('1ake.cif')
dssp.AssignDSSP(ent, extract_burial_status=True)
for chain in ent.chains:
if chain.is_polypeptide:
for res in chain.residues:
print(res.GetFloatProp('relative_solvent_accessibility'))
DSSP bindings Usage
-
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
ost.mol.alg.AssignSecStruct() and 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 LoadDSSP().
| Parameters: |
- ent (
EntityHandle or EntityView) – The entity for which the secondary structure should be calculated
- extract_burial_status – If true, also extract burial status and store
as float-property
relative_solvent_accessibility at residue
level
- tmp_dir – If set, overrides the default tmp directory of the
operating system - deprecated, has no effect
- dssp_bin – The path to the DSSP executable - deprecated, has no effect
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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 AssignDSSP() instead.
| Parameters: |
- file_name – The filename of the DSSP output file
- model – The entity to which the secondary structure states should be
assigned
- extract_burial_status – If true also calculates burial status of
residues and assigns it to the burial_status string property.
- calculate_relative_sa – If true also relative solvent accessibility and
and assigns it to the relative_solvent_accessibility float property of
the residue.
- entity_save – Whether the entity was saved.
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