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

Class DSSP

source code

   AbstractPropertyMap.AbstractPropertyMap --+    
                                             |    
AbstractPropertyMap.AbstractResiduePropertyMap --+
                                                 |
                                                DSSP

Run DSSP on a pdb file, and provide a handle to the DSSP secondary structure and accessibility.

Note that DSSP can only handle one model.

Example:

>>> p=PDBParser()
>>> structure=parser.get_structure("1fat.pdb")
>>> model=structure[0]
>>> dssp=DSSP(model, "1fat.pdb")
>>> # print dssp data for a residue
>>> secondary_structure, accessibility=dssp[(chain_id, res_id)]
Instance Methods [hide private]
 
__init__(self, model, pdb_file, dssp='dssp') source code

Inherited from AbstractPropertyMap.AbstractPropertyMap: __getitem__, __iter__, __len__, has_key, keys

Method Details [hide private]

__init__(self, model, pdb_file, dssp='dssp')
(Constructor)

source code 
Parameters:
  • model (Model) - the first model of the structure
  • pdb_file (string) - a PDB file
  • dssp (string) - the dssp executable (ie. the argument to os.system)
Overrides: AbstractPropertyMap.AbstractPropertyMap.__init__