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

source code

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

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.


>>> 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]
>>> # (dssp index, amino acid, secondary structure, relative ASA, phi, psi,
>>> # NH_O_1_relidx, NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy,
>>> # NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx, O_NH_2_energy)
>>> dssp[a_key]
(3, 'A', 'H', 0.7075471698113207, -61.2, -42.4,
 -2, -0.7, 4, -3.0, 1, -0.2, 5, -0.2)
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')

source code 

Create a DSSP object.


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__