1.1 --- a/allpy/structure.py	Fri Jul 15 03:03:39 2011 +0400
     1.2 +++ b/allpy/structure.py	Fri Jul 15 02:06:23 2011 +0400
     1.3 @@ -232,6 +232,32 @@
     1.4          self.set_pdb_chain(pdb_file, code, chain, model, xyz_only=xyz_only,
     1.5              resi_begin=resi_begin, resi_end=resi_end)
     1.6  
     1.7 +    def superimpose(self, main_sequence, gc, extra_columns=False):
     1.8 +        """ Superimpose structure of this to main_sequence
     1.9 +
    1.10 +         * gc -- collection of columns to use as for superimposition
    1.11 +         * extra_columns -- allow columns with gaps or without structure
    1.12 +        """
    1.13 +        fixed_gc = []
    1.14 +        moving_gc = []
    1.15 +        for column in gc:
    1.16 +            if main_sequence in column and self in column:
    1.17 +                if hasattr(column[main_sequence], 'pdb_residue') \
    1.18 +                and hasattr(column[self], 'pdb_residue'):
    1.19 +                    fixed_gc.append(column[main_sequence].pdb_residue['CA'])
    1.20 +                    moving_gc.append(column[self].pdb_residue['CA'])
    1.21 +                else:
    1.22 +                    assert extra_columns
    1.23 +            else:
    1.24 +                assert extra_columns
    1.25 +        sup = Superimposer()
    1.26 +        sup.set_atoms(fixed_gc, moving_gc)
    1.27 +        moving = self.pdb_chain.get_atoms()
    1.28 +        sup.apply(moving)
    1.29 +        for monomer in self:
    1.30 +            if hasattr(monomer, 'pdb_residue'):
    1.31 +                monomer.ca_xyz = monomer.pdb_residue['CA'].get_vector()
    1.32 +
    1.33      def save_pdb(self, out_filename, new_chain=None, new_model=None):
    1.34          """ Save pdb_chain to out_file """
    1.35          chain = self.pdb_chain
    1.36 @@ -428,25 +454,7 @@
    1.37              sequences = copy(self.sequences)
    1.38              main_sequence = sequences.pop()
    1.39              for sequence in sequences:
    1.40 -                fixed_gc = []
    1.41 -                moving_gc = []
    1.42 -                for column in gc:
    1.43 -                    if main_sequence in column and sequence in column:
    1.44 -                        if hasattr(column[main_sequence], 'pdb_residue') \
    1.45 -                        and hasattr(column[sequence], 'pdb_residue'):
    1.46 -                            fixed_gc.append(column[main_sequence].pdb_residue['CA'])
    1.47 -                            moving_gc.append(column[sequence].pdb_residue['CA'])
    1.48 -                        else:
    1.49 -                            assert extra_columns
    1.50 -                    else:
    1.51 -                        assert extra_columns
    1.52 -                sup = Superimposer()
    1.53 -                sup.set_atoms(fixed_gc, moving_gc)
    1.54 -                moving = sequence.pdb_chain.get_atoms()
    1.55 -                sup.apply(moving)
    1.56 -                for monomer in sequence:
    1.57 -                    if hasattr(monomer, 'pdb_residue'):
    1.58 -                        monomer.ca_xyz = monomer.pdb_residue['CA'].get_vector()
    1.59 +                sequence.superimpose(main_sequence, gc, extra_columns=extra_columns)
    1.60  
    1.61      def save_pdb(self, out_file):
    1.62          """ Save all sequences