Package Bio :: Package PDB :: Module DSSP'
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Module DSSP'

source code

Use the DSSP program to calculate secondary structure and accessibility.

You need to have a working version of DSSP (and a license, free for academic use) in order to use this. For DSSP, see U{}.

The DSSP codes for secondary structure used here are:

Classes [hide private]
Run DSSP on a pdb file, and provide a handle to the DSSP secondary structure and accessibility.
Functions [hide private]
Return a DSSP dictionary that maps (chainid, resid) to an amino acid, secondary structure symbol, solvent accessibility value, and hydrogen bond information (relative dssp indices and hydrogen bond energies) from an open DSSP file object.
source code
dssp_dict_from_pdb_file(in_file, DSSP='dssp')
Create a DSSP dictionary from a PDB file.
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Return a DSSP dictionary that maps (chainid, resid) to aa, ss and accessibility, from a DSSP file.
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Secondary structure symbol to index.
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Variables [hide private]
  MAX_ACC = {'ALA': 106.0, 'ARG': 248.0, 'ASN': 157.0, 'ASP': 16...
  __package__ = 'Bio.PDB'
  _dssp_cys = re.compile(r'[a-z]')
Function Details [hide private]


source code 
Secondary structure symbol to index. H=0 E=1 C=2

Variables Details [hide private]


{'ALA': 106.0,
 'ARG': 248.0,
 'ASN': 157.0,
 'ASP': 163.0,
 'CYS': 135.0,
 'GLN': 198.0,
 'GLU': 194.0,
 'GLY': 84.0,