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

source code

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

Run DSSP and parse secondary structure and accessibility.

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 = 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= >,
'H',
72,
0.67924528301886788,
-61.200000000000003,
-42.399999999999999)
Instance Methods [hide private]
 
__init__(self, model, in_file, dssp='dssp', acc_array='Sander', file_type='PDB')
Create a DSSP object.
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, in_file, dssp='dssp', acc_array='Sander', file_type='PDB')
(Constructor)

source code 

Create a DSSP object.

Parameters

model : Model
The first model of the structure
in_file : string
Either a PDB file or a DSSP file.
dssp : string
The dssp executable (ie. the argument to os.system)
acc_array : string
Accessible surface area (ASA) from either Miller et al. (1987), Sander & Rost (1994), or Wilke: Tien et al. 2013, as string Sander/Wilke/Miller. Defaults to Sander.
file_type: string
File type switch, either PDB or DSSP with PDB as default.
Overrides: object.__init__