dssp.rst

:mod:`~ost.bindings.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/.

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