def append(self, file, align_codes='all', atom_files=None, remove_gaps=True,
alignment_format='PIR', io=None, allow_alternates=False):
"""Add sequence(s) from an alignment file"""
if io is None:
io = self.env.io
new_align_codes = align_codes
new_atom_files = atom_files
align_codes = [seq.code for seq in self]
atom_files = [seq.atom_file for seq in self]
if new_align_codes is not None:
if modutil.non_string_iterable(new_align_codes):
align_codes.extend(new_align_codes)
else:
align_codes.append(new_align_codes)
if new_atom_files is not None:
fmt = alignment_format.upper()
if fmt != 'PAP' and fmt != 'INSIGHT':
raise TypeError("atom_files is only used for PAP and " + \
"INSIGHT alignment files")
if modutil.non_string_iterable(new_atom_files):
atom_files.extend(new_atom_files)
else:
atom_files.append(new_atom_files)
fh = modfile._get_filehandle(file, 'r')
func = _modeller.mod_alignment_read
return func(self.modpt, io.modpt, self.env.libs.modpt, align_codes,
atom_files, fh.file_pointer, remove_gaps, alignment_format,
allow_alternates)
def only_atom_types(self, atom_types):
"""Create and return a new selection, containing only atoms from
the current selection of the given type(s).
:param str atom_types: A space-separated list of type(s)
(e.g. 'CA CB').
:return: A new selection containing only atoms of the given type(s).
:rtype: :class:`selection`"""
if modutil.non_string_iterable(atom_types):
atom_types = " ".join(atom_types)
return self.__filter(_modeller.mod_selection_atom_types, atom_types)
def patch(self, residue_type, residues):
"""Patch the model topology"""
if not modutil.non_string_iterable(residues):
residues = [residues]
for r in residues:
if not isinstance(r, coordinates.Residue) or r.mdl is not self:
raise TypeError("expecting one or more 'Residue' objects")
return _modeller.mod_model_patch(mdl=self.modpt,
libs=self.env.libs.modpt,
residue_type=residue_type,
residue_ids=[r.index \
for r in residues])
def only_residue_types(self, residue_types):
"""Create and return a new selection, containing only atoms from
the current selection in residues of the given type(s).
:param str residue_types: A space-separated list of type(s)
(e.g. 'ALA ASP').
:return: A new selection containing only atoms in residues
of the given type(s).
:rtype: :class:`selection`"""
if modutil.non_string_iterable(residue_types):
residue_types = " ".join(residue_types)
libs = self.__get_libs()
return self.__filter(_modeller.mod_selection_residue_types,
residue_types, libs)
def _parse_values(self, values, modal, param, idim):
if len(modal) <= idim:
modal.append(len(values))
else:
if modal[idim] != len(values):
raise ValueError("Spline parameters should be a " +
"rectangular matrix")
for elmnt in values:
if modutil.non_string_iterable(elmnt):
self._parse_values(elmnt, modal, param, idim + 1)
else:
if idim + 1 != len(modal):
raise ValueError("Spline parameters should be a " +
"rectangular matrix")
param.append(elmnt)
def __get_list_atom_indices(self, atoms):
inds = []
mdl = None
for obj in atoms:
if modutil.non_string_iterable(obj) \
and not hasattr(obj, 'get_atom_indices'):
(objinds, objmdl) = self.__get_list_atom_indices(obj)
else:
(objinds, objmdl) = obj.get_atom_indices()
if mdl is None:
mdl = objmdl
elif mdl != objmdl:
raise ValueError("All atoms must be from the same model")
inds.extend(objinds)
return (inds, mdl)
def remove(self, obj):
"""Removes an object (e.g. atom, residue) from the selection;
raises KeyError if not present"""
if not hasattr(obj, "get_atom_indices") \
and modutil.non_string_iterable(obj):
for x in obj:
self.remove(x)
else:
if obj not in self:
raise KeyError(obj)
(inds, mdl) = obj.get_atom_indices()
if self.__mdl is not mdl:
raise ValueError("All atoms must be in the same model!")
for ind in inds:
del self.__selection[ind]
def add(self, obj):
"""Adds a new object (e.g. atom, residue) to the selection"""
if not hasattr(obj, "get_atom_indices") \
and modutil.non_string_iterable(obj):
for x in obj:
self.add(x)
else:
self.__check_object(obj)
(inds, mdl) = obj.get_atom_indices()
if self.__mdl is None:
self.__mdl = mdl
elif self.__mdl is not mdl:
raise ValueError("All atoms must be in the same model!")
for ind in inds:
self.__selection[ind] = None