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")

    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)