Package Bio :: Package PDB :: Module DSSP'
[hide private]
[frames] | no frames]

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{http://swift.cmbi.ru.nl/gv/dssp/}.

The DSSP codes for secondary structure used here are:

Classes [hide private]
  DSSP
Run DSSP on a pdb file, and provide a handle to the DSSP secondary structure and accessibility.
Functions [hide private]
 
_make_dssp_dict(handle)
Return a DSSP dictionary that maps (chainid, resid) to aa, ss and accessibility, 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.
source code
 
make_dssp_dict(filename)
Return a DSSP dictionary that maps (chainid, resid) to aa, ss and accessibility, from a DSSP file.
source code
 
ss_to_index(ss)
Secondary structure symbol to index.
source code
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]

ss_to_index(ss)

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

Variables Details [hide private]

MAX_ACC

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