def main():
"""
Run everythin from the command line
"""
# Command line parsing
args = define_options(sys.argv[1:])
try:
title, atoms, box = groIO.parse_file(args.filin)
except groIO.FormatError as e:
print(e, file=sys.stderr)
return 1
if args.verbose:
print("The input coordinate file is {0}".format(args.filin))
print("The output file will be {0}".format(args.filout))
print("The reference atom for the lipid bilayer is {0}".format(
args.lipid_atom))
print("The reference atom for the water is {0}".format(
args.water_atom))
try:
if args.sphere is None:
output_atoms, nb_water = perform_bilayer_removing(
atoms, args.lipid_atom, args.water_atom, args.verbose)
else:
output_atoms, nb_water = perform_sphere_removing(
atoms, args.sphere, args.radius, args.water_residue,
args.verbose)
if args.verbose:
print()
print("The old system contained {0} atoms.".format(len(atoms)))
print("{0} water molecules have been removed.".format(nb_water))
print("The new system contains {0} atoms.".format(len(output_atoms)))
# Write in the output file
with open(args.filout, "w") as fout:
for line in groIO.write_gro(title, output_atoms, box):
print(line, end='', file=fout)
except RefObjectError as e:
print(e)
return 1
return 0
def main():
"""
Run everythin from the command line
"""
# Command line parsing
args = define_options(sys.argv[1:])
try:
title, atoms, box = groIO.parse_file(args.filin)
except groIO.FormatError as e:
print(e, file=sys.stderr)
return 1
if args.verbose:
print("The input coordinate file is {0}".format(args.filin))
print("The output file will be {0}".format(args.filout))
print("The reference atom for the lipid bilayer is {0}".format(args.lipid_atom))
print("The reference atom for the water is {0}".format(args.water_atom))
try:
if args.sphere is None:
output_atoms, nb_water = perform_bilayer_removing(atoms, args.lipid_atom,
args.water_atom, args.verbose)
else:
output_atoms, nb_water = perform_sphere_removing(atoms, args.sphere, args.radius,
args.water_residue, args.verbose)
if args.verbose:
print()
print("The old system contained {0} atoms.".format(len(atoms)))
print("{0} water molecules have been removed.".format(nb_water))
print("The new system contains {0} atoms.".format(len(output_atoms)))
# Write in the output file
with open(args.filout, "w") as fout:
for line in groIO.write_gro(title, output_atoms, box):
print(line, end='', file=fout)
except RefObjectError as e:
print(e)
return 1
return 0
def test_write(self):
"""
Test the writing of a gro file
"""
# Create a random file
title, atoms, box = _generate_file()
# Write it
test_write = os.path.join(REFDIR, "test_write.gro")
with open(test_write, "w") as fout:
for line in groIO.write_gro(title, atoms, box):
print(line, end='', file=fout)
# Reference file
ref_write = os.path.join(REFDIR, "write.gro")
with open(ref_write) as f1, open(test_write) as f2:
ref_readlines = f1.readlines()
test_readlines = f2.readlines()
self.assertEqual(ref_readlines, test_readlines)
os.remove(test_write)
