1.1 --- a/allpy/structure.py	Fri Mar 25 23:09:58 2011 +0300
     1.2 +++ b/allpy/structure.py	Fri Mar 25 23:12:21 2011 +0300
     1.3 @@ -59,13 +59,13 @@
     1.4  
     1.5      *   pdb_chain -- Bio.PDB.Chain
     1.6  
     1.7 -    Monomers from this sequence get attribute "pdb_residue"
     1.8 +    Monomers from this sequence get attribute "pdb_residue", "ca_xyz"
     1.9  
    1.10      ?TODO: global pdb_structures
    1.11      """
    1.12  
    1.13      def set_pdb_chain(self, pdb_file, pdb_id, pdb_chain='A', pdb_model=0,
    1.14 -            max_mutations=config.max_mutations):
    1.15 +            max_mutations=config.max_mutations, xyz_only=False):
    1.16          """ Read Pdb chain from file
    1.17  
    1.18          max_mutations -- max number of monomer type mismatches
    1.19 @@ -75,7 +75,8 @@
    1.20          """
    1.21          structure = get_structure(pdb_file, self.name)
    1.22          chain = structure[pdb_model][pdb_chain]
    1.23 -        self.pdb_chain = chain
    1.24 +        if not xyz_only:
    1.25 +            self.pdb_chain = chain
    1.26          pdb_sequence = self.__class__.from_pdb_chain(chain)
    1.27          Alignment = self.types.Alignment
    1.28          a = Alignment()
    1.29 @@ -86,7 +87,9 @@
    1.30          for monomer, pdb_monomer in a.columns_as_lists():
    1.31              if monomer and hasattr(pdb_monomer, 'pdb_residue'):
    1.32                  if monomer == pdb_monomer:
    1.33 -                    monomer.pdb_residue = pdb_monomer.pdb_residue
    1.34 +                    monomer.ca_xyz = pdb_monomer.pdb_residue['CA'].get_vector()
    1.35 +                    if not xyz_only:
    1.36 +                        monomer.pdb_residue = pdb_monomer.pdb_residue
    1.37                  else:
    1.38                      mutations += 1
    1.39          assert mutations <= max_mutations
    1.40 @@ -118,7 +121,7 @@
    1.41                  sequence.append(monomer)
    1.42          return sequence
    1.43  
    1.44 -    def auto_pdb(self, conformity=None, pdb_getter=download_pdb):
    1.45 +    def auto_pdb(self, conformity=None, pdb_getter=download_pdb, xyz_only=False):
    1.46          """ Add pdb information to each monomer
    1.47  
    1.48          raise AssertionError if info has not been successfully added
    1.49 @@ -131,7 +134,7 @@
    1.50          chain = match['chain']
    1.51          model = match['model']
    1.52          pdb_file = pdb_getter(code)
    1.53 -        self.set_pdb_chain(pdb_file, code, chain, model)
    1.54 +        self.set_pdb_chain(pdb_file, code, chain, model, xyz_only=xyz_only)
    1.55  
    1.56      def save_pdb(self, out_filename, new_chain=None, new_model=None):
    1.57          """ Save pdb_chain to out_file """
    1.58 @@ -306,12 +309,9 @@
    1.59                          if sequence in column1 and sequence in column2:
    1.60                              m1 = column1[sequence]
    1.61                              m2 = column2[sequence]
    1.62 -                            if hasattr(m1, 'pdb_residue') and hasattr(m2, 'pdb_residue'):
    1.63 -                                r1 = m1.pdb_residue
    1.64 -                                r2 = m2.pdb_residue
    1.65 -                                ca1 = r1['CA']
    1.66 -                                ca2 = r2['CA']
    1.67 -                                d = ca1 - ca2 # Bio.PDB feature
    1.68 +                            if hasattr(m1, 'ca_xyz') and hasattr(m2, 'ca_xyz'):
    1.69 +                                delta_vector = m1.ca_xyz - m2.ca_xyz
    1.70 +                                d = sum([C**2 for C in delta_vector.get_array()]) ** 0.5
    1.71                                  distances.append(d)
    1.72                      if len(distances) == len(self.sequences):
    1.73                          delta = max(distances) - min(distances)