color=args.color_seq) + '\n' try: sys.stdout.write(output) sys.stdout.flush() except IOError: pass if args.get_ss: # quick fix - make a list on the spot if list != type(args.file): args.file = [args.file] ################################## for f in args.file: output = f + '\n' p = x3DNA(f) output += p.get_secstruc() + '\n' try: sys.stdout.write(output) sys.stdout.flush() except IOError: pass # getchain if args.get_chain: s = RNAStructure(args.file) ## s.std_resn() ## s.remove_hydrogen() ## s.remove_ion() ## s.remove_water() ## s.renum_atoms()
output += s.get_seq(compact=args.compact, chainfirst=args.chain_first) + '\n' try: sys.stdout.write(output) sys.stdout.flush() except IOError: pass if args.get_ss: # quick fix - make a list on the spot if list != type(args.file): args.file = [args.file] ################################## for f in args.file: output = f + '\n' p = x3DNA(f) output += p.get_secstruc() + '\n' try: sys.stdout.write(output) sys.stdout.flush() except IOError: pass if args.get_chain: s = RNAStructure(args.file) s.std_resn() s.remove_hydrogen() s.remove_ion() s.remove_water() s.renum_atoms() s.fix_O_in_UC()