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Biskit
Package Biskit :: Module DSSP :: Class Dssp
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Class Dssp

source code

Run Dssp

The DSSP program will define the secondary structure of a given structure. The secondary structure elements defined are: 
 H = alpha helix
 B = residue in isolated beta-bridge
 E = extended strand, participates in beta ladder
 G = 3-helix (3/10 helix)
 I = 5 helix (pi helix)
 T = hydrogen bonded turn
 S = bend
 . = loop or irregular

Example usage

>>> d = Dssp( model )
>>> result = d.run()

References



Instance Methods [hide private]
  __init__(self, model, **kw)
  prepare(self)
Overrides Executor method.
  cleanup(self)
Tidy up the mess you created.
[str] parse_result(self)
Parse the secondary structure from tha DSSP output file.
  finish(self)
Overrides Executor method

Method Details [hide private]

__init__(self, model, **kw)
(Constructor)

source code 
Parameters:
  • model (PDBModel) - model analyze
  • kw (key=value pairs : 
     debug    - 0|1, keep all temporary files (default: 0)
 verbose  - 0|1, print progress messages to log (log != STDOUT)
 node     - str, host for calculation (None->local) NOT TESTED
                 (default: None)
 nice     - int, nice level (default: 0)
 log      - Biskit.LogFile, program log (None->STOUT) (default: None)
    ) - additional key=value parameters for Executor:

prepare(self)

source code 

Overrides Executor method.

cleanup(self)

source code 

Tidy up the mess you created.

parse_result(self)

source code 

Parse the secondary structure from tha DSSP output file.
Returns: [str]
a list with the standard DSSP secondary structure description (one letter code) with the exception that a blank " " has been replaced by a dot "."

finish(self)

source code 

Overrides Executor method

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