1.1 --- a/allpy/structure.py	Wed Jul 06 18:05:51 2011 +0400
     1.2 +++ b/allpy/structure.py	Wed Jul 06 20:49:31 2011 +0200
     1.3 @@ -68,7 +68,8 @@
     1.4              xyz_only=False,
     1.5              min_continuous_match=config.min_continuous_match,
     1.6              min_match=config.min_match,
     1.7 -            max_waste_in_pdb=config.max_waste_in_pdb):
     1.8 +            max_waste_in_pdb=config.max_waste_in_pdb,
     1.9 +            resi_begin=None, resi_end=None):
    1.10          """ Read Pdb chain from file
    1.11  
    1.12          and align each Monomer with PDB.Residue
    1.13 @@ -77,6 +78,11 @@
    1.14              * min_continuous_match
    1.15              * min_match
    1.16              * max_waste_in_pdb
    1.17 +            * resi_begin and resi_end -- identifiers of first and last pdb
    1.18 +                residues of residue range to be used. If only one is provided,
    1.19 +                another parameter is set to first or last residue of chain.
    1.20 +                Id of residue is (hetero_flag, sequence_id, insertion_code),
    1.21 +                see biopdb documantation for more information.
    1.22  
    1.23          The sequence is aligned with pdb_sequence using muscle.
    1.24          The alignment is splitted to continuous_blocks
    1.25 @@ -93,6 +99,12 @@
    1.26          if not xyz_only:
    1.27              self.pdb_chain = chain
    1.28          pdb_sequence = self.__class__.from_pdb_chain(chain)
    1.29 +        if resi_begin:
    1.30 +            while pdb_sequence[0].pdb_residue.get_id() != resi_begin:
    1.31 +                pdb_sequence.pop(0)
    1.32 +        if resi_end:
    1.33 +            while pdb_sequence[-1].pdb_residue.get_id() != resi_end:
    1.34 +                pdb_sequence.pop()
    1.35          Alignment = self.types.Alignment
    1.36          a = Alignment()
    1.37          a.append_sequence(self)
    1.38 @@ -158,9 +170,12 @@
    1.39                  sequence.append(monomer)
    1.40          return sequence
    1.41  
    1.42 -    def auto_pdb(self, conformity=None, pdb_getter=download_pdb, xyz_only=False):
    1.43 +    def auto_pdb(self, conformity=None, pdb_getter=download_pdb, xyz_only=False,
    1.44 +            resi_begin=None, resi_end=None):
    1.45          """ Add pdb information to each monomer
    1.46  
    1.47 +        * resi_begin and resi_end -- see set_pdb_chain
    1.48 +
    1.49          raise AssertionError if info has not been successfully added
    1.50  
    1.51          TODO: conformity_file
    1.52 @@ -171,7 +186,8 @@
    1.53          chain = match['chain']
    1.54          model = match['model']
    1.55          pdb_file = pdb_getter(code)
    1.56 -        self.set_pdb_chain(pdb_file, code, chain, model, xyz_only=xyz_only)
    1.57 +        self.set_pdb_chain(pdb_file, code, chain, model, xyz_only=xyz_only,
    1.58 +            resi_begin=resi_begin, resi_end=resi_end)
    1.59  
    1.60      def save_pdb(self, out_filename, new_chain=None, new_model=None):
    1.61          """ Save pdb_chain to out_file """