biopython v1.71.0 Bio.PDB.ResidueDepth

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:

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

Direct MSMS interface, typical use:

     >>> parser = PDBParser()
     >>> structure = parser.get_structure('1FAT.pdb')
     >>> model = structure[0]
     >>> surface = get_surface(model)

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)

Link to this section Summary

Functions

_get_atom_radius()

Translates an atom object to an atomic radius defined in MSMS

_read_vertex_array()

Read the vertex list into a Numeric array

get_surface()

Represent molecular surface as a vertex list array

min_dist()

Return minimum distance between coord and surface

residue_depth()

Residue depth as average depth of all its atoms

Link to this section Functions

_get_atom_radius()

Translates an atom object to an atomic radius defined in MSMS.

Uses information from the parent residue and the atom object to define the atom type.

Returns the radius (float) according to the selected type:

explicit (reads hydrogens)
united (default)

_read_vertex_array()

Read the vertex list into a Numeric array.

get_surface()

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 os.system)

min_dist()

Return minimum distance between coord and surface.

residue_depth()

Residue depth as average depth of all its atoms.

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