biopython v1.71.0 Bio.PDB.DSSP.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")
 >>> 
 >>> a_key = list(dssp.keys())[2]
 >>> 
 >>> 
 >>> 
 >>> dssp[a_key]
 (3, 'A', 'H', 0.7075471698113207, -61.2, -42.4,
  -2, -0.7, 4, -3.0, 1, -0.2, 5, -0.2)

Link to this section Summary

Functions

__init__()

Create a DSSP object

resid2code()

Serialize a residue’s resseq and icode for easy comparison

Link to this section Functions

__init__()

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.

resid2code()

Serialize a residue’s resseq and icode for easy comparison.