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()