Logo Search packages:      
Sourcecode: python-biopython version File versions

test_PDB.py

# Copyright (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be)
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.  

from Bio.PDB import *


# first make a PDB parser object
p=PDBParser(PERMISSIVE=1) 

# get the structure, call it "example"
structure=p.get_structure("example", "PDB/a_structure.pdb")

# now loop over content and print some info
for model in structure.get_list():
      model_id=model.get_id()
      print "Model %i contains %i chains." % (model_id, len(model))
      for chain in model.get_list():
            chain_id=chain.get_id()
            print "\tChain '%s' contains %i residues." % (chain_id, len(chain))
            for residue in chain.get_list():
                  residue_id=residue.get_id()
                  hetfield, resseq, icode=residue_id
                  print "\t\tResidue ('%s', %i, '%s') contains %i atoms." % (hetfield, resseq, icode, len(residue))
                  # check if there is disorder due to a point mutation --- this is rare
                  if residue.is_disordered()==2:
                        print "\t\t\tThere is a point mutation present in the crystal at this position."
                        s="\t\t\tResidues at this position are "
                        for resname in residue.disordered_get_id_list():
                              s=s+resname+" "
                        print s[:-1]+"."
                  # count the number of disordered atoms
                  if residue.is_disordered()==1:
                        disordered_count=0
                        for atom in residue.get_list():
                              if atom.is_disordered():
                                    disordered_count=disordered_count+1
                        if disordered_count>0:
                              print "\t\t\tThe residue contains %i disordered atoms." % disordered_count


print "Polypeptides using C-N"
ppb=PPBuilder()
for pp in ppb.build_peptides(structure, 1):
      print pp

print "Polypeptides using CA-CA"
ppb=CaPPBuilder()
for pp in ppb.build_peptides(structure, 1):
      print pp

                              

Generated by  Doxygen 1.6.0   Back to index