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)
relevant XTCs inside that directory (PROJECT/TRAJ*/frame*.xtc).
Output:
-- 'Trajectories' directory containing all the merged lh5 files
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project', type=str, help='''The ProjectInfo (.h5) to
write to disk. Contains metadata associated with your project''')
parser.add_argument('pdb')
parser.add_argument('input_dir', help='''Path to the parent directory
containing subdirectories with MD (.xtc/.dcd) data. See the description above
for the appropriate formatting for directory architecture.''')
parser.add_argument('source', help='''Data source: "file", "file_dcd" or
"fah". For "file" & "file_dcd" formats, each of the trajectories needs to be
in a different directory. For example, if you supply input_dir='XTC', then
it is expected that the directory 'XTC' contains a set of subdirectories, each
of which contains one or more files of a single MD trajectory that will be concatenated
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)
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project',
type=str,
help='''The ProjectInfo (.h5) file
that contains a mapping of the previous work done. If you specify a file that
exists on disk, conversion will pick up where it left off and simply add data
to what has already been done. If you specify a file that doesn't exist, the
conversion starts from the beginning and writes a ProjectInfo file with that name
at the end of the conversion. NOTE: If you specify a ProjectInfo file, the conversion
automatically retrieves the conversion parameters you were using before and uses
them - all other options you specify will be IGNORED.''')
parser.add_argument('pdb')
parser.add_argument('input_dir',
help='''Path to the parent directory
containing subdirectories with MD (.xtc/.dcd) data. See the description above
for the appropriate formatting for directory architecture.''')
parser.add_argument('source',
help='''Data source: "file", "file_dcd" or
"fah". This is the style of trajectory data that gets fed into MSMBuilder.
If a file, then it requires each trajectory be housed in a separate directory
like (PROJECT/TRAJ*/frame*.xtc). If 'fah', then standard FAH-style directory
architecture is required.''',
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)
relevant XTCs inside that directory (PROJECT/TRAJ*/frame*.xtc).
Output:
-- 'Trajectories' directory containing all the merged lh5 files
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project', type=str, help='''The ProjectInfo (.h5) to
write to disk. Contains metadata associated with your project''')
parser.add_argument('pdb')
parser.add_argument('input_dir', help='''Path to the parent directory
containing subdirectories with MD (.xtc/.dcd) data. See the description above
for the appropriate formatting for directory architecture.''')
parser.add_argument('source', help='''Data source: "file", "file_dcd" or
"fah". This is the style of trajectory data that gets fed into MSMBuilder.
If a file, then it requires each trajectory be housed in a separate directory
like (PROJECT/TRAJ*/frame*.xtc). If 'fah', then standard FAH-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)
Can read any format compatible with mdtraj.
Output:
-- 'Trajectories' directory containing all the merged h5 files
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project', type=str, help='''The ProjectInfo (.h5) to
write to disk. Contains metadata associated with your project''')
parser.add_argument('pdb')
parser.add_argument('input_dir', help='''Path to the parent directory
containing subdirectories with MD data. See the description above
for the appropriate formatting for directory architecture.''')
parser.add_argument('source', help='''Data source: "file", or
"fah". For "file" format, each of the trajectories needs to be
in a different directory. For example, if you supply input_dir='XTC', then
it is expected that the directory 'XTC' contains a set of subdirectories, each
of which contains one or more files of a single MD trajectory that will be concatenated
together. The glob pattern used would be XTC/*/*.*'. If 'fah', then standard
folding@home-style directory architecture is required. If the IEXT option
is given, the glob pattern will be restricted to the given file extension
(behavior is the same for file and fah)''',
default='file', choices=['fah', 'file'])
parser.add_argument('min_length', help='''Minimum number of frames per trajectory
-- 'Trajectories' directory containing all the merged lh5 files
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project', type=str, help='''The ProjectInfo (.h5) file
that contains a mapping of the previous work done. If you specify a file that
exists on disk, conversion will pick up where it left off and simply add data
to what has already been done. If you specify a file that doesn't exist, the
conversion starts from the beginning and writes a ProjectInfo file with that name
at the end of the conversion. NOTE: If you specify a ProjectInfo file, the conversion
automatically retrieves the conversion parameters you were using before and uses
them - all other options you specify will be IGNORED.''')
parser.add_argument('pdb')
parser.add_argument('input_dir', help='''Path to the parent directory
containing subdirectories with MD (.xtc/.dcd) data. See the description above
for the appropriate formatting for directory architecture.''')
parser.add_argument('source', help='''Data source: "file", "file_dcd" or
"fah". This is the style of trajectory data that gets fed into MSMBuilder.
If a file, then it requires each trajectory be housed in a separate directory
like (PROJECT/TRAJ*/frame*.xtc). If 'fah', then standard FAH-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)
Can read any format compatible with mdtraj.
Output:
-- 'Trajectories' directory containing all the merged h5 files
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project',
type=str,
help='''The ProjectInfo (.h5) to
write to disk. Contains metadata associated with your project''')
parser.add_argument('pdb')
parser.add_argument('input_dir',
help='''Path to the parent directory
containing subdirectories with MD data. See the description above
for the appropriate formatting for directory architecture.''')
parser.add_argument('source',
help='''Data source: "file", or
"fah". For "file" format, each of the trajectories needs to be
in a different directory. For example, if you supply input_dir='XTC', then
it is expected that the directory 'XTC' contains a set of subdirectories, each
of which contains one or more files of a single MD trajectory that will be concatenated
together. The glob pattern used would be XTC/*/*.*'. If 'fah', then standard
folding@home-style directory architecture is required. If the IEXT option
is given, the glob pattern will be restricted to the given file extension