Bio.PDB.ResidueDepth module

Calculation of residue depth using command line tool MSMS.

This module uses Michel Sanner’s MSMS program for the surface calculation. 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:

from Bio.PDB.ResidueDepth import ResidueDepth
from Bio.PDB.PDBParser import PDBParser
parser = PDBParser()
structure = parser.get_structure("1a8o", "Tests/PDB/1A8O.pdb")
model = structure[0]
rd = ResidueDepth(model)
print(rd['A',(' ', 152, ' ')])

Direct MSMS interface, typical use:

from Bio.PDB.ResidueDepth import get_surface
surface = get_surface(model)

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

Distance to surface:

from Bio.PDB.ResidueDepth import min_dist
coord = (1.113, 35.393,  9.268)
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):

from Bio.PDB.ResidueDepth import residue_depth
chain = model['A']
res152 = chain[152]
rd = residue_depth(res152, surface)

Bio.PDB.ResidueDepth.get_surface(model, PDB_TO_XYZR=None, MSMS='msms')

Represent molecular surface as a vertex list array.

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

Arguments:

• PDB_TO_XYZR - deprecated, ignore this.

• MSMS - msms executable (used as argument to subprocess.call)

Bio.PDB.ResidueDepth.min_dist(coord, surface)

Return minimum distance between coord and surface.

Bio.PDB.ResidueDepth.residue_depth(residue, surface)

Residue depth as average depth of all its atoms.

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

Bio.PDB.ResidueDepth.ca_depth(residue, surface)

Return CA depth.

class Bio.PDB.ResidueDepth.ResidueDepth(model, pdb_file=None, msms_exec=None)

Bases: Bio.PDB.AbstractPropertyMap.AbstractPropertyMap

Calculate residue and CA depth for all residues.

__init__(self, model, pdb_file=None, msms_exec=None)

Initialize the class.