class tester():
def setup(self):
self.p = ArgumentParser()
def cmd(self, value):
sys.argv = [os.path.abspath(__file__)]
for e in value.split():
sys.argv.append(e)
@property
def v(self):
return self.p.parse_args(print_banner=False)
def add(self, *args, **kwargs):
self.p.add_argument(*args, **kwargs)
def test_0(self):
self.add('a', nargs='+')
self.cmd('-a 1 2')
eq_(self.v.a, ['1', '2'])
def test_1(self):
self.add('a', nargs='+', type=int)
self.cmd('-a 1 2')
eq_(self.v.a, [1, 2])
def test_2(self):
self.add('a', type=int)
self.cmd('-a 4')
eq_(self.v.a, 4)
def test_3(self):
self.add('a', type=float)
self.cmd('-a 5')
eq_(self.v.a, 5.0)
@raises(SystemExit)
def test_4(self):
sys.stderr = open('/dev/null', 'w')
self.add('a', choices=[1, 2], type=float)
self.cmd('-a 5')
eq_(self.v.a, 5.0)
sys.stderr = sys.__stderr__
def test_5(self):
self.add('a', choices=['1', '2'], type=int)
self.cmd('-a 1')
eq_(self.v.a, 1.0)
# @expected_failure
def test_6(self):
self.add('a', choices=[1, 2], type=int)
self.cmd('-a 1')
eq_(self.v.a, 1)
def test_7(self):
self.add('a', action='store_true', type=bool)
self.cmd('-a')
eq_(self.v.a, True)
def test_71(self):
self.add('a', action='store_false', type=bool)
self.cmd('-a')
eq_(self.v.a, False)
def test_8(self):
self.add('a', action='store_true')
self.cmd('-a')
eq_(self.v.a, True)
def test_81(self):
self.add('b', action='store_false')
self.cmd('-b')
eq_(self.v.b, False)
def test_9(self):
self.add('a', default=False, action='store_true', type=bool)
self.cmd('')
eq_(self.v.a, False)
def test_10(self):
self.add('a', action='store_true', type=bool)
self.cmd('')
eq_(self.v.a, False)
together. The glob pattern used would be XTC/*/*.xtc'. If 'fah', then standard
folding@home-style directory architecture is required.''',
default='file', choices=['fah', 'file', 'file_dcd'])
parser.add_argument('min_length', help='''Minimum number of frames per trajectory
required to include data in Project. Used to discard extremely short
trajectories.''', default=0, type=int)
parser.add_argument('stride', help='''Integer number to subsample by.
Every "u-th" frame will be taken from the data and converted to msmbuilder
format''', default=1, type=int)
parser.add_argument('rmsd_cutoff', help='''A safe-guard that discards any
structure with and RMSD higher than the specified value (in nanometers,
with respect to the input PDB file). Pass -1 to disable this feature''',
default=-1, type=float)
#parser.add_argument('parallel', help='''Run the conversion in parallel.
# multiprocessing launches multiple python interpreters to use all of your cores.
# dtm uses mpi, and requires python's "deap" module to be installed. To execute the
# code over mpi using dtm, you need to start the command with mpirun -np <num_procs>.
# Note that in many circumstates, the conversion done by this script is IO bound,
# not CPU bound, so parallelism can actually be detrememtal.''', default='None',
# choices=['None', 'multiprocessing', 'dtm'])
args = parser.parse_args()
rmsd_cutoff = args.rmsd_cutoff
if rmsd_cutoff <= 0.0:
rmsd_cutoff = None
else:
logger.warning("Will discard any frame that is %f nm from the PDB conformation...", rmsd_cutoff)
run(args.project, args.pdb, args.input_dir, args.source,
args.min_length, args.stride, rmsd_cutoff)
help='''Integer number to subsample by.
Every "u-th" frame will be taken from the data and converted to msmbuilder
format''',
default=1,
type=int)
parser.add_argument('rmsd_cutoff',
help='''A safe-guard that discards any
structure with and RMSD higher than the specified value (in nanometers,
with respect to the input PDB file). Pass -1 to disable this feature''',
default=-1,
type=float)
#parser.add_argument('parallel', help='''Run the conversion in parallel.
# multiprocessing launches multiple python interpreters to use all of your cores.
# dtm uses mpi, and requires python's "deap" module to be installed. To execute the
# code over mpi using dtm, you need to start the command with mpirun -np <num_procs>.
# Note that in many circumstates, the conversion done by this script is IO bound,
# not CPU bound, so parallelism can actually be detrememtal.''', default='None',
# choices=['None', 'multiprocessing', 'dtm'])
args = parser.parse_args()
rmsd_cutoff = args.rmsd_cutoff
if rmsd_cutoff <= 0.0:
rmsd_cutoff = None
else:
logger.warning(
"Will discard any frame that is %f nm from the PDB conformation...",
rmsd_cutoff)
run(args.project, args.pdb, args.input_dir, args.source, args.min_length,
args.stride, rmsd_cutoff)
class tester():
def setup(self):
self.p = ArgumentParser()
def cmd(self, value):
sys.argv = [os.path.abspath(__file__)]
for e in value.split():
sys.argv.append(e)
@property
def v(self):
return self.p.parse_args(print_banner=False)
def add(self, *args, **kwargs):
self.p.add_argument(*args, **kwargs)
def test_0(self):
self.add('a', nargs='+')
self.cmd('-a 1 2')
eq_(self.v.a, ['1', '2'])
def test_1(self):
self.add('a', nargs='+', type=int)
self.cmd('-a 1 2')
eq_(self.v.a, [1, 2])
def test_2(self):
self.add('a', type=int)
self.cmd('-a 4')
eq_(self.v.a, 4)
def test_3(self):
self.add('a', type=float)
self.cmd('-a 5')
eq_(self.v.a, 5.0)
@raises(SystemExit)
def test_4(self):
sys.stderr = open('/dev/null', 'w')
self.add('a', choices=[1,2], type=float)
self.cmd('-a 5')
eq_(self.v.a, 5.0)
sys.stderr = sys.__stderr__
def test_5(self):
self.add('a', choices=['1', '2'], type=int)
self.cmd('-a 1')
eq_(self.v.a, 1.0)
def test_6(self):
self.add('a', choices=[1, 2], type=int)
self.cmd('-a 1')
eq_(self.v.a, 1)
def test_7(self):
self.add('a', action='store_true', type=bool)
self.cmd('-a')
eq_(self.v.a, True)
def test_71(self):
self.add('a', action='store_false', type=bool)
self.cmd('-a')
eq_(self.v.a, False)
def test_8(self):
self.add('a', action='store_true')
self.cmd('-a')
eq_(self.v.a, True)
def test_81(self):
self.add('b', action='store_false')
self.cmd('-b')
eq_(self.v.b, False)
def test_9(self):
self.add('a', default=False, action='store_true', type=bool)
self.cmd('')
eq_(self.v.a, False)
def test_10(self):
self.add('a', action='store_true', type=bool)
self.cmd('')
eq_(self.v.a, False)
