def append(self, file):
"""Read interaction parameters from a file"""
self.__param_files.append(file)
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_group_restraints_read(self._modpt,
self.env.libs.modpt,
fh.file_pointer)
def write(self, file, model_format='PDB', no_ter=False, extra_data=""):
"""Write selection coordinates to a file"""
(inds, mdl) = self.__require_indices()
fh = modfile._get_filehandle(file, 'w')
return _modeller.mod_model_write(mdl.modpt, mdl.env.libs.modpt, inds,
fh.file_pointer, model_format, no_ter,
False, extra_data)
def read(self, file, io=None):
"""Read coordinates from a PDB file"""
if io is None:
io = self.aln.env.io
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_alnstructure_read_pdb(
fh.file_pointer, self.aln.modpt, self.__num, io.modpt,
self.aln.env.libs.modpt)
def write(self, file, alignment_format='PIR',
alignment_features='INDICES CONSERVATION', align_block=0,
align_alignment=False):
"""Write the alignment to a file"""
fh = modfile._get_filehandle(file, 'w')
return _modeller.mod_alignment_write(self.modpt, self.env.libs.modpt,
fh.file_pointer,
alignment_format,
alignment_features, align_block,
align_alignment)
def read(self,
file,
model_format='PDB',
model_segment=('FIRST:@', 'LAST:'),
io=None,
keep_disulfides=False):
"""Read coordinates from a file"""
if io is None:
io = self.env.io
if isinstance(file, str):
file = _modeller.mod_pdb_filename_get(file,
io.atom_files_directory)
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_model_read2(self.modpt, io.modpt,
self.env.libs.modpt, fh.file_pointer,
model_format, model_segment,
keep_disulfides)
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_one
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]
else:
file = modfile._get_filehandle(file, 'r')
return func(self.modpt, file.file_pointer, io.modpt,
self.env.libs.modpt, remove_gaps, alignment_format,
allow_alternates) == 0
def write(self, file):
"""Writes topology library to a file"""
fh = modfile._get_filehandle(file, 'w')
return _modeller.mod_topology_model_write(self._modpt,
self.__libs.modpt,
fh.file_pointer)
def append(self, file):
"""Appends information from a residue topology file"""
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_topology_read(self._modpt, self.__libs.modpt,
fh.file_pointer)
def write(self, file):
"""Write currently selected restraints to a file"""
fh = modfile._get_filehandle(file, 'w')
return _modeller.mod_restraints_write(self.__mdl.modpt,
fh.file_pointer)
def append(self, file):
"""Append restraints from a file, and select them"""
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_restraints_read(self.__mdl.modpt, fh.file_pointer)
def write(self, file):
"""Write current coordinates to a PDB file"""
fh = modfile._get_filehandle(file, 'w')
return _modeller.mod_alnstructure_write(self.cdpt, self.seqpt,
fh.file_pointer,
self.aln.env.libs.modpt)
def __read_libs(self):
fh = modfile._get_filehandle(self.__restyp_lib_file, 'r')
_modeller.mod_libraries_read_libs(self.modpt, fh.file_pointer)
def write(self, file, model_format='PDB', no_ter=False, extra_data=''):
"""Write coordinates to a file"""
fh = modfile._get_filehandle(file, 'w')
return _modeller.mod_model_write(self.modpt, self.env.libs.modpt, (),
fh.file_pointer, model_format, no_ter,
True, extra_data)
def append(self, file):
"""Append information from a CHARMM parameter file"""
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_parameters_read(self._modpt, self.__libs.modpt,
fh.file_pointer)
def __read_classes(self, file):
"""Read atom classes from a file"""
self.__class_file = file
fh = modfile._get_filehandle(file, 'r')
return _modeller.mod_atom_classes_read(self._modpt, fh.file_pointer)