def write(self, file, model_format='PDB', no_ter=False):
"""Write coordinates to a file"""
if isinstance(file, str):
file = modfile.File(file, 'w')
return _modeller.mod_model_write(self.modpt, self.env.libs.modpt, (),
file.file_pointer, model_format,
no_ter, True)
def write(self, file):
"""Write current coordinates to a PDB file"""
if isinstance(file, str):
file = modfile.File(file, 'w')
return _modeller.mod_alnstructure_write(self.cdpt, self.seqpt,
file.file_pointer,
self.aln.env.libs.modpt)
def write(self, file, model_format='PDB', no_ter=False):
"""Write selection coordinates to a file"""
(inds, mdl) = self.__require_indices()
if isinstance(file, str):
file = modfile.File(file, 'w')
return _modeller.mod_model_write(mdl.modpt, mdl.env.libs.modpt, inds,
file.file_pointer, model_format,
no_ter, False)
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 read_profile(self):
fmt = self.vars['profile_format']
prf = self.get_prf()
libs = self.get_libs()
fname = self.vars['file']
if fmt.upper() == 'BINARY':
_modeller.mod_profile_read_binary(prf, libs, fname)
else:
fh = modfile.File(fname, 'r')
_modeller.mod_profile_read_text(prf, libs, fh.file_pointer)
fh.close()
def write(self, file, alignment_format='PIR',
alignment_features='INDICES CONSERVATION', align_block=0,
align_alignment=False):
"""Write the alignment to a file"""
if isinstance(file, str):
file = modfile.File(file, 'w')
return _modeller.mod_alignment_write(self.modpt, self.env.libs.modpt,
file.file_pointer,
alignment_format,
alignment_features, align_block,
align_alignment)
def read_model(self):
self.__default_file('file', 'B')
(file, model_segment) = self.__seg_from_aln('model_segment')
io = self.get_io()
file = _modeller.mod_pdb_filename_get(file, io.atom_files_directory)
fh = modfile.File(file, 'r')
AutoCommands.read_model(self,
fh=fh.file_pointer,
model_segment=model_segment,
keep_disulfides=False)
fh.close()
self.__pickall()
def write(self,
file,
atom_file,
align_code,
comment='',
format='PIR',
chop_nonstd_termini=True):
"""Write this chain out to an alignment file"""
f = _modeller.mod_chain_write
if isinstance(file, str):
file = modfile.File(file, 'w')
return f(self.seq.seqpt, self.seq.cdpt, self._num, file.file_pointer,
atom_file, align_code, comment, format, chop_nonstd_termini,
self.seq.env.libs.modpt)
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
def write_model(self):
self.__default_file('file', '.B')
fh = modfile.File(self.__add_outdir('file'), 'w')
AutoCommands.write_model(self, fh=fh.file_pointer, extra_data='')
fh.close()
def write_restraints(self):
self.__default_file('file', '.C')
fh = modfile.File(self.__add_outdir('file'), 'w')
AutoCommands.write_restraints(self, fh=fh.file_pointer)
def read_density(self):
fh = modfile.File(self.vars['file'], 'rb')
AutoCommands.read_density(self, fh=fh.file_pointer, read_origin=False)
fh.close()
def read_atom_classes(self):
fh = modfile.File(self.vars['atom_classes_file'], 'r')
AutoCommands.read_atom_classes(self, fh=fh.file_pointer)
fh.close()
def read_restraints(self):
if not self.vars['add_restraints']:
_modeller.mod_restraints_clear(self.get_mdl())
self.__default_file('file', '.C', ('', '.rsr'))
fh = modfile.File(self.vars['file'], 'r')
AutoCommands.read_restraints(self, fh=fh.file_pointer)
def read_restyp_lib(self):
fh = modfile.File(self.vars['restyp_lib_file'], 'r')
AutoCommands.read_restyp_lib(self, fh=fh.file_pointer)
def write_topology_model(self):
self.__default_file('file', '.toplib')
fh = modfile.File(self.__add_outdir('file'), 'w')
AutoCommands.write_topology_model(self, fh=fh.file_pointer)
fh.close()
def read_topology(self):
if not self.vars['add_topology']:
_modeller.mod_topology_clear(self.get_tpl(), self.get_libs())
self.__default_file('file', '.T', ('', '.lib'))
fh = modfile.File(self.vars['file'], 'r')
AutoCommands.read_topology(self, fh=fh.file_pointer)
def write_alignment(self):
self.__default_file('file', '.A')
fh = modfile.File(self.__add_outdir('file'), 'w')
AutoCommands.write_alignment(self, fh=fh.file_pointer)
fh.close()