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 http://www.cmbi.kun.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]
{}
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]')
  standard_aa_names = ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY',...
  to_one_letter_code = {'2AS': 'D', '3AH': 'H', '5HP': 'E', 'ACL...
Function Details [hide private]

dssp_dict_from_pdb_file(in_file, DSSP='dssp')

source code 

Create a DSSP dictionary from a PDB file.

Example:

>>> dssp_dict=dssp_dict_from_pdb_file("1fat.pdb")
>>> aa, ss, acc=dssp_dict[('A', 1)]
Parameters:
  • in_file (string) - pdb file
  • DSSP (string) - DSSP executable (argument to os.system)
Returns: {}
a dictionary that maps (chainid, resid) to amino acid type, secondary structure code and accessibility.

make_dssp_dict(filename)

source code 

Return a DSSP dictionary that maps (chainid, resid) to aa, ss and accessibility, from a DSSP file.

Parameters:
  • filename (string) - the DSSP output file

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,
...

standard_aa_names

Value:
['ALA',
 'CYS',
 'ASP',
 'GLU',
 'PHE',
 'GLY',
 'HIS',
 'ILE',
...

to_one_letter_code

Value:
{'2AS': 'D',
 '3AH': 'H',
 '5HP': 'E',
 'ACL': 'R',
 'AGM': 'R',
 'AIB': 'A',
 'ALA': 'A',
 'ALM': 'A',
...