#!/usr/bin/python

# Xavier Ambroggio, 2012

# ambroggiox@niaid.nih.gov

from Bio.PDB import PDBIO

from Bio.PDB.PDBParser import PDBParser

from optparse import OptionParser

parser=OptionParser()

parser.add_option("-f", "--pdbfile", default = None, type = "string", help="pdb structure file for additional 3-coord cartesian per residue")

(options,args)=parser.parse_args()

parser=PDBParser()

structure=parser.get_structure("mystruct", options.pdbfile)

model=structure[0]

average_bfactors = {}

for residue in model["X"] :

average_bfactors[ residue.get_id()[1] ] = 0.0

for chain in model.get_list():

for residue in chain.get_list():

sum_over_natoms = 0

if residue.has_id("N"):

ca=residue["N"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("H"):

ca=residue["H"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("H1"):

ca=residue["H1"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("CA"):

ca=residue["CA"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("C"):

ca=residue["C"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("O"):

ca=residue["O"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("OXT"):

ca=residue["OXT"]

average_bfactors[ residue.get_id()[1] ] += float( ca.get_bfactor() )

sum_over_natoms += 1

if residue.has_id("CA"):

average_bfactors[ residue.get_id()[1] ] /= sum_over_natoms

for chain in model.get_list():

for residue in chain.get_list():

for atom in residue.get_list():

atom.set_bfactor( average_bfactors[ residue.get_id()[1] ] )

w = PDBIO()

w.set_structure(structure)

w.save('avg_b_backbone_'+options.pdbfile)