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()