dssp

Process output from dssp.

dssp can be used to calculate secondary structure and solvent accessibility information from a PDB structure. This module can process that output.

dms_tools2.dssp.MAX_ASA_TIEN = {'A': 129.0, 'C': 167.0, 'D': 193.0, 'E': 223.0, 'F': 240.0, 'G': 104.0, 'H': 224.0, 'I': 197.0, 'K': 236.0, 'L': 201.0, 'M': 224.0, 'N': 195.0, 'P': 159.0, 'Q': 225.0, 'R': 274.0, 'S': 155.0, 'T': 172.0, 'V': 174.0, 'W': 285.0, 'Y': 263.0}

max accessible surface area (square angstroms) for amino acids, from Tien et al (2013). MAX_ASA_TIEN[a] is the max surface area for amino acid a.

dms_tools2.dssp.processDSSP(dsspfile, chain=None, max_asa={'A': 129.0, 'C': 167.0, 'D': 193.0, 'E': 223.0, 'F': 240.0, 'G': 104.0, 'H': 224.0, 'I': 197.0, 'K': 236.0, 'L': 201.0, 'M': 224.0, 'N': 195.0, 'P': 159.0, 'Q': 225.0, 'R': 274.0, 'S': 155.0, 'T': 172.0, 'V': 174.0, 'W': 285.0, 'Y': 263.0})[source]

Get secondary structure and solvent accessibility from dssp.

dssp is a program that calculates secondary structure and absolute solvent accessibility from a PDB file.

This function processes the text output provided by the dssp webserver, at least given the format of that output as of Sept-4-2017.

It returns a pandas.DataFrame that gives the secondary structure and solvent accessibility for each residue in the dssp output.

Args:
dsspfile (str)

Name of text file containing dssp output.

chain (str or None)

If the PDB file analyzed by dssp to create dsspfile has more than one chain, specify the letter code for one of those chains with this argument.

max_asa (dict)

Max surface area for each amino acid in square angstroms.

Returns:

A pandas.DataFrame with the following columns:

  • site: residue number for all sites in dsspfile.

  • amino_acid: amino acid identity of site in dsspfile.

  • ASA: absolute solvent accessibility of the residue.

  • RSA: relative solvent accessibility of the residue.

  • SS: dssp secondary structure code, one of:

    • G: 3-10 helix

    • H: alpha helix

    • I: pi helix

    • B: beta bridge

    • E: beta bulge

    • T: turn

    • S: high curvature

    • -: loop

  • SS_class: broader secondary structure class:

    • helix: SS value of G, H, or I

    • strand: SS value of B or E

    • loop: any of the other SS values.