Package Bio :: Package PDB :: Module DSSP' :: Class DSSP
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Class DSSP

source code

                                object --+        
   AbstractPropertyMap.AbstractPropertyMap --+    
AbstractPropertyMap.AbstractResiduePropertyMap --+

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.


>>> p = PDBParser()
>>> structure = p.get_structure("1MOT", "1MOT.pdb")
>>> model = structure[0]
>>> dssp = DSSP(model, "1MOT.pdb")
>>> # DSSP data is accessed by a tuple (chain_id, res_id)
>>> a_key = list(dssp.keys())[2]
>>> # residue object, secondary structure, solvent accessibility,
>>> # relative accessiblity, phi, psi
>>> dssp[a_key]
(<Residue ALA het=  resseq=251 icode= >,
Instance Methods [hide private]
__init__(self, model, pdb_file, dssp='dssp')
@param pdb_file: a PDB file @type pdb_file: string
source code

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

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

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

source code 
@param model: the first model of the structure
@type model: L{Model} ::

@param pdb_file: a PDB file @type pdb_file: string

@param dssp: the dssp executable (ie. the argument to os.system)
@type dssp: string
Overrides: object.__init__