Relative Solvent Accessibilities using Biopython and DSSP

bio_dssp.py

#!/usr/bin/env python

"""
Demonstration of calling DSSP and accessing accessibilities using Biopython
"""

from Bio.PDB import PDBParser, DSSP

# Make sure you downloaded 1ctf in PDB format first..
pdb_filepath = '1ctf.pdb'

parser = PDBParser(QUIET=1)
structure = parser.get_structure('randompdb', pdb_filepath)
dssp_data = DSSP(structure[0], pdb_filepath)

# Option 1
# Use DSSP dictionary directly, each key being (<str chain>, <tuple resid>)
# e.g. ('A', (' ', 120, ' '))
print(dssp_data[('A', (' ', 120, ' '))])
# (68, 'K', '-', 0.7414634146341463, -133.3, 360.0, -65, -2.2, -65, -2.5, -2, -0.4, -2, -0.0)

# Option 2
# Iterate over structure and get .xtra method of each residue
# DSSP automatically populates fields there
for residue in structure.get_residues():
    resid = residue.id[1]
    resname = residue.resname
    abs_sasa = residue.xtra['EXP_DSSP_ASA']
    rel_sasa = residue.xtra['EXP_DSSP_RASA']
    print('{}{}\t{:6.3f}\t{:6.3f}'.format(resname, resid, abs_sasa, rel_sasa))

# Returns:
# GLU53   190.000  0.979
# PHE54   56.000   0.284
# ASP55   46.000   0.282
# VAL56    0.000   0.000
# ILE57   18.000   0.107
# LEU58    0.000   0.000
# LYS59   85.000   0.415
# ...