# 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 NumPy 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, MSMS='msms')

  Represent molecular surface as a vertex list array.

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

  Arguments:

    - model - BioPython PDB model object (used to get atoms for input model)

    - 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, msms_exec=None)

  Bases: `AbstractPropertyMap`

  Calculate residue and CA depth for all residues.

  __init__(model, msms_exec=None)

    Initialize the class.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 587
  __static_attributes__ = ()

Biopython v: 1.86

Versions
  Previous
  Latest
  Develop

Biopython Project
  Homepage
  On GitHub