This module defines functions for executing DSSP program and parsing its output.
execDSSP(pdb, outputname=None, outputdir=None, stderr=True)¶
Execute DSSP for given pdb. pdb can be a PDB identifier or a PDB file path. If pdb is a compressed file, it will be decompressed using Python
gziplibrary. When no outputname is given, output name will be
.dsspextension will be appended automatically to outputname. If
outputdiris given, DSSP output and uncompressed PDB file will be written into this folder. Upon successful execution of dssp pdb > out command, output filename is returned. On Linux platforms, when stderr is false, standard error messages are suppressed, i.e.
dssp pdb > outputname 2> /dev/null.
[WK83] Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983 22:2577-2637.
parseDSSP(dssp, ag, parseall=False)¶
Parse DSSP data from file dssp into
AtomGroupinstance ag. DSSP output file must be in the new format used from July 1995 and onwards. When dssp file is parsed, following attributes are added to ag:
- dssp_resnum: DSSP’s sequential residue number, starting at the first residue actually in the data set and including chain breaks; this number is used to refer to residues throughout.
- dssp_acc: number of water molecules in contact with this residue *10. or residue water exposed surface in Angstrom^2.
- dssp_kappa: virtual bond angle (bend angle) defined by the three Cα atoms of residues I-2,I,I+2. Used to define bend (structure code ‘S’).
- dssp_alpha: virtual torsion angle (dihedral angle) defined by the four Cα atoms of residues I-1,I,I+1,I+2.Used to define chirality (structure code ‘+’ or ‘-‘).
- dssp_phi and dssp_psi: IUPAC peptide backbone torsion angles
The following attributes are parsed when
- dssp_bp1, dssp_bp2, and dssp_sheet_label: residue number of first and second bridge partner followed by one letter sheet label
- dssp_tco: cosine of angle between C=O of residue I and C=O of residue I-1. For α-helices, TCO is near +1, for β-sheets TCO is near -1. Not used for structure definition.
- dssp_NH_O_1_index, dssp_NH_O_1_energy, etc.: hydrogen bonds; e.g. -3,-1.4 means: if this residue is residue i then N-H of I is h-bonded to C=O of I-3 with an electrostatic H-bond energy of -1.4 kcal/mol. There are two columns for each type of H-bond, to allow for bifurcated H-bonds.
See http://swift.cmbi.ru.nl/gv/dssp/DSSP_3.html for details.