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)