Runs the PDB parser.

def parse_pdb_file(self):
        """Runs the PDB parser."""
        self.pdb_parse_tree = {'info': {},
                               'data': {
                                   self.state: {}}
                               }
        try:
            for line in self.pdb_lines:
                self.current_line = line
                record_name = line[:6].strip()
                if record_name in self.proc_functions:
                    self.proc_functions[record_name]()
                else:
                    if record_name not in self.pdb_parse_tree['info']:
                        self.pdb_parse_tree['info'][record_name] = []
                    self.pdb_parse_tree['info'][record_name].append(line)
        except EOFError:
            # Raised by END record
            pass
        if self.new_labels:
            ampal_data_session.commit()
        return