def read_alignment(self): if not self.vars['add_sequence']: _modeller.mod_alignment_clear(self.get_aln()) self.__default_file('file', '.A', ('', '.ali')) fh = modfile.File(self.vars['file'], 'r') AutoCommands.read_alignment(self, allow_alternates=False, fh=fh.file_pointer) fh.close()
def sequence_to_ali(self): aln = self.get_aln() if not self.vars['add_sequence']: _modeller.mod_alignment_clear(aln) nseq = _modeller.mod_alignment_nseq_get(aln) try: align_codes = self.vars['align_codes'][nseq] except IndexError: align_codes = '' try: atom_files = self.vars['atom_files'][nseq] except IndexError: atom_files = '' AutoCommands.sequence_to_ali(self, align_codes=align_codes, atom_files=atom_files)
def clear(self): """Remove all sequences from the alignment""" return _modeller.mod_alignment_clear(self.modpt)
def prof_to_aln(self): if not self.vars['append_aln']: _modeller.mod_alignment_clear(self.get_aln()) AutoCommands.prof_to_aln(self)
def read_alignment2(self): if not self.vars['add_sequence']: _modeller.mod_alignment_clear(self.get_aln(2)) self.__default_file('file', '.A', ('', '.ali')) AutoCommands.read_alignment2(self)