Package Bio :: Package PDB :: Module ResidueDepth'
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Module ResidueDepth'

source code

Calculation of residue depth using command line tool MSMS.

This module uses Michel Sanner's MSMS program for the surface calculation (specifically commands msms and pdb_to_xyzr). See: http://mgltools.scripps.edu/packages/MSMS

Residue depth is the average distance of the atoms of a residue from the solvent accessible surface.

Residue Depth:

>>> rd = ResidueDepth(model, pdb_file)
>>> print(rd[(chain_id, res_id)])

Direct MSMS interface, typical use:

>>> surface = get_surface("1FAT.pdb")

The surface is a Numeric array with all the surface vertices.

Distance to surface:

>>> dist = min_dist(coord, surface)

where coord is the coord of an atom within the volume bound by the surface (ie. atom depth).

To calculate the residue depth (average atom depth of the atoms in a residue):

>>> rd = residue_depth(residue, surface)
Classes [hide private]
  ResidueDepth
Calculate residue and CA depth for all residues.
Functions [hide private]
 
_read_vertex_array(filename)
Read the vertex list into a Numeric array.
source code
 
ca_depth(residue, surface) source code
 
get_surface(pdb_file, PDB_TO_XYZR='pdb_to_xyzr', MSMS='msms')
Return a Numeric array that represents the vertex list of the molecular surface.
source code
 
min_dist(coord, surface)
Return minimum distance between coord and surface.
source code
 
residue_depth(residue, surface)
Return average distance to surface for all atoms in a residue, ie.
source code
Variables [hide private]
  __package__ = 'Bio.PDB'
Function Details [hide private]

get_surface(pdb_file, PDB_TO_XYZR='pdb_to_xyzr', MSMS='msms')

source code 

Return a Numeric array that represents the vertex list of the molecular surface.

PDB_TO_XYZR --- pdb_to_xyzr executable (arg. to os.system) MSMS --- msms executable (arg. to os.system)

residue_depth(residue, surface)

source code 
Return average distance to surface for all atoms in a residue, ie. the residue depth.