def delete_restraint(self):
atom_names = self.vars['atom_ids']
mdl = self.get_mdl(1)
cd = _modeller.mod_model_cd_get(mdl)
seq = _modeller.mod_model_seq_get(mdl)
atom_ids = [_modeller.mod_coordinates_find_atom(cd, seq, a) \
for a in atom_names]
if 0 in atom_ids:
log.warning("delete_restraint",
"One or more atoms absent from MODEL: " \
+ " ".join(atom_names))
else:
AutoCommands.unpick_restraints(self, atom_ids=atom_ids)
def __set_atfil(self, val):
if isinstance(val, tuple):
self.__atom_files_directory = list(val)
elif isinstance(val, list):
self.__atom_files_directory = val
elif isinstance(val, str):
spl = val.split(':')
log.warning("io_data",
"""Setting io.atom_files_directory to a colon-delimited string is
deprecated, as it is not robust on Windows systems. Set it to
a list of directories instead. For example:
env.io.atom_files_directory = """ + str(spl))
self.__atom_files_directory = spl
else:
raise TypeError("atom_files_directory should be a list")
def read_one(self, file, remove_gaps=False, alignment_format='PIR',
io=None, allow_alternates=False):
"""Read sequences from the file, one by one. Return False when no more
can be read."""
if io is None:
io = self.env.io
self.clear()
func = _modeller.mod_alignment_read_one2
if isinstance(file, str):
# Cache one file handle per alignment:
if self.__read_one_pair is None or self.__read_one_pair[0] != file:
log.warning("read_one",
"Filename arguments to read_one() are " + \
"deprecated.\nPlease use a handle " + \
"(modfile.File object) instead.")
self.__read_one_pair = (file, modfile.File(file, 'r'))
file = self.__read_one_pair[1]
return func(self.modpt, file.file_pointer, io.modpt,
self.env.libs.modpt, remove_gaps, alignment_format,
allow_alternates) == 0