Package Bio :: Package PDB :: Module DSSP'

Module DSSP'

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://www.cmbi.kun.nl/gv/dssp/}.

The DSSP codes for secondary structure used here are:

    - H        Alpha helix (4-12)
    - B        Isolated beta-bridge residue
    - E        Strand
    - G        3-10 helix
    - I        pi helix
    - T        Turn
    - S        Bend
    - -        None

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...

_dssp_cys = re.compile(r'[a-z]')

to_one_letter_code = {'00C': 'C', '01W': 'X', '02K': 'A', '03Y...

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)]

@param in_file: pdb file
@type in_file: string

@param DSSP: DSSP executable (argument to os.system)
@type DSSP: string

@return: a dictionary that maps (chainid, resid) to
    amino acid type, secondary structure code and
    accessibility.
@rtype: {}

make_dssp_dict(filename)

source code


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

@param filename: the DSSP output file
@type filename: string

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,
...

to_one_letter_code

Value:

{'00C': 'C',
 '01W': 'X',
 '02K': 'A',
 '03Y': 'C',
 '07O': 'C',
 '08P': 'C',
 '0A0': 'D',
 '0A1': 'Y',
...

Module DSSP'

dssp_dict_from_pdb_file(in_file, DSSP='dssp')

make_dssp_dict(filename)

ss_to_index(ss)

MAX_ACC

to_one_letter_code

dssp_dict_from_pdb_file(in_file, DSSP=`'dssp'`)