def main(pdb_path, tls_out_path, calc_tls): struct = FileIO.LoadStructure(file=pdb_path) ## calculate one set of TLS tensors from all the amino acid atoms if calc_tls == True: tls = TLS.TLSGroup() for res in struct.iter_amino_acids(): for atm in res.iter_atoms(): tls.append(atm) tls.origin = tls.calc_centroid() tls.calc_tls_tensors() print_TLSGroup(tls) else: tls_file = TLS.TLSFile() ## get TLS groups from REMARK statments in PDB file if tls_out_path == None: tls_file.set_file_format(TLS.TLSFileFormatPDB()) try: tls_file.load(open(pdb_path, "r"), pdb_path) except IOError, e: print "[Error] %s: %s" % (str(e), pdb_path) ## or get TLS groups from REFMAC TLSOUT file else:
def LoadStructure(struct_source): """Loads Structure, chooses a unique struct_id string. Also, search the REMARK records for TLS group records. If they are found, then add the TLS group ADP magnitude to the B facors of the ATOM records. """ ## determine the argument type if isinstance(struct_source, str): file_path = struct_source console.kvformat("LOADING STRUCTURE", file_path) fobj = open(file_path, "r") elif hasattr(struct_source, "__iter__") and hasattr(struct_source, "seek"): console.kvformat("LOADING STRUCTURE", str(struct_source)) fobj = struct_source else: raise ValueError ## load struct struct = FileIO.LoadStructure(file = fobj, distance_bonds = True) console.kvformat("HEADER", struct.header) console.kvformat("TITLE", struct.title) console.kvformat("EXPERIMENTAL METHOD", struct.experimental_method) ## set the structure ID if conf.globalconf.struct_id is not None: struct_id = conf.globalconf.struct_id else: struct_id = struct.structure_id conf.globalconf.struct_id = struct_id struct.structure_id = struct_id console.endln() ## if there are REFMAC5 TLS groups in the REMARK records of ## the PDB file, then add those in tls_file = TLS.TLSFile() tls_file.set_file_format(TLS.TLSFileFormatPDB()) ## return to the beginning of the file and read the REMARK/TLS records fobj.seek(0) tls_file.load(fobj) if len(tls_file.tls_desc_list) > 0: console.stdoutln("ADDING TLS GROUP Bequiv TO ATOM TEMPERATURE FACTORS") console.stdoutln(" NUM TLS GROUPS: %d" % (len(tls_file.tls_desc_list))) ## assume REFMAC5 groups where Utotal = Utls + Biso(temp_factor) for tls_desc in tls_file.tls_desc_list: tls_group = tls_desc.construct_tls_group_with_atoms(struct) console.stdoutln(" TLS GROUP: %s" % (tls_group.name)) for atm, Utls in tls_group.iter_atm_Utls(): bresi = atm.temp_factor atm.temp_factor = bresi + (Constants.U2B * numpy.trace(Utls) / 3.0) atm.U = (Constants.B2U * bresi * numpy.identity(3, float)) + Utls console.endln() return struct