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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)
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ResidueDepth Calculate residue and CA depth for all residues. |
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__package__ =
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standard_aa_names =
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to_one_letter_code =
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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) |
Return average distance to surface for all atoms in a residue, ie. the residue depth. |
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standard_aa_names
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to_one_letter_code
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