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

source code


Calculation of residue depth (using Michel Sanner's MSMS program for the
surface calculation).

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)

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]
  standard_aa_names = ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY',...
  to_one_letter_code = {'2AS': 'D', '3AH': 'H', '5HP': 'E', 'ACL...
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.


Variables Details [hide private]

standard_aa_names

Value:
['ALA',
 'CYS',
 'ASP',
 'GLU',
 'PHE',
 'GLY',
 'HIS',
 'ILE',
...

to_one_letter_code

Value:
{'2AS': 'D',
 '3AH': 'H',
 '5HP': 'E',
 'ACL': 'R',
 'AGM': 'R',
 'AIB': 'A',
 'ALA': 'A',
 'ALM': 'A',
...