DSSP Tools
This module defines functions for executing DSSP program and parsing
its output.
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execDSSP(pdb, outputname=None, outputdir=None, stderr=True)[source]
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 gzip library. When no outputname is given, output name
will be pdb.dssp. .dssp extension will be appended
automatically to outputname. If outputdir is 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.
For more information on DSSP see http://swift.cmbi.ru.nl/gv/dssp/.
If you benefited from DSSP, please consider citing [WK83].
[WK83] | Kabsch W, Sander C. Dictionary of protein secondary structure:
pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers 1983 22:2577-2637. |
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parseDSSP(dssp, ag, parseall=False)[source]
Parse DSSP data from file dssp into AtomGroup instance
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 parseall=True is passed:
- 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.
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performDSSP(pdb, parseall=False, stderr=True)[source]
Perform DSSP calculations and parse results. DSSP data is returned
in an AtomGroup instance. See also execDSSP()
and parseDSSP().