def __init__(self, fname, model, **kwargs):
self._skip = 0
self._stride = 1
self._iterator = None
if 'skip' in kwargs:
self._skip = kwargs['skip']
if 'stride' in kwargs:
self._stride = kwargs['stride']
if 'iterator' in kwargs:
self._iterator = kwargs['iterator']
if 'subset' in kwargs:
self._subset = loos.selectAtoms(model, kwargs['subset'])
else:
self._subset = model
self._model = model
self._fname = fname
self._traj = loos.createTrajectory(fname, model)
self._stale = 1
self._initFrameList()
def __init__(self, fname, model, **kwargs):
self._skip = 0
self._stride = 1
self._iterator = None
if 'skip' in kwargs:
self._skip = kwargs['skip']
if 'stride' in kwargs:
self._stride = kwargs['stride']
if 'iterator' in kwargs:
self._iterator = kwargs['iterator']
if 'subset' in kwargs:
self._subset = loos.selectAtoms(model, kwargs['subset'])
else:
self._subset = model
self._model = model
self._fname = fname
self._traj = loos.createTrajectory(fname, model)
self._stale = 1
self._initFrameList()
system_filename = sys.argv[1]
traj_filename = sys.argv[2]
skip = int(sys.argv[3])
zmin = float(sys.argv[4])
zmax = float(sys.argv[5])
padding = float(sys.argv[6])
selection_strings = sys.argv[
7:] # first selection gives the all atoms to use
# in area calculations, all others tell you
# how to group the areas
print("# ", " ".join(sys.argv))
system = loos.createSystem(system_filename)
traj = loos.createTrajectory(traj_filename, system)
traj.readFrame(skip)
traj.updateGroupCoords(system)
slicer = ZSliceSelector(zmin, zmax)
selections = []
selections.append(loos.selectAtoms(system, selection_strings[0]))
for s in selection_strings[1:]:
selections.append(loos.selectAtoms(selections[0], s))
frame = skip
string = ""
for i in range(len(selections)):
string += "\tArea" + str(i)
)
parser.add_argument("-d",
"--directory",
help="Directory to create output files",
default=".")
parser.add_argument(
"-t",
"--threshold",
default=7,
type=int,
help="Number of atoms inside for the chain to be considered inside")
args = parser.parse_args()
system = loos.createSystem(args.system_file)
traj = loos.createTrajectory(args.traj_file, system)
protein = loos.selectAtoms(system, args.protein_string)
output_directory = args.directory
if not os.path.exists(output_directory):
try:
os.mkdir(output_directory)
except OSError as inst:
print 'Error creating output directory %s : ' % output_directory
print inst
sys.exit(1)
if not os.access(output_directory, os.W_OK):
print "Error: no permission to write to output directory ", output_directory
sys.exit(1)
nargs="+",
help="list of colon-delimited residue number ranges specifying where the helices are")
parser.add_argument("-d", "--directory",
help="Directory to create output files",
default=".")
parser.add_argument("-t", "--threshold",
default=7,
type=int,
help="Number of atoms inside for the chain to be considered inside")
args = parser.parse_args()
system = loos.createSystem(args.system_file)
traj = loos.createTrajectory(args.traj_file, system)
protein = loos.selectAtoms(system, args.protein_string)
output_directory = args.directory
if not os.path.exists(output_directory):
try:
os.mkdir(output_directory)
except OSError as inst:
print 'Error creating output directory %s : ' % output_directory
print inst
sys.exit(1)
if not os.access(output_directory, os.W_OK):
print "Error: no permission to write to output directory ", output_directory
sys.exit(1)
system_filename = sys.argv[1]
traj_filename = sys.argv[2]
skip = int(sys.argv[3])
zmin = float(sys.argv[4])
zmax = float(sys.argv[5])
padding = float(sys.argv[6])
selection_strings = sys.argv[7:] # first selection gives the all atoms to use
# in area calculations, all others tell you
# how to group the areas
print "# ", " ".join(sys.argv)
system = loos.createSystem(system_filename)
traj = loos.createTrajectory(traj_filename, system)
traj.readFrame(skip)
traj.updateGroupCoords(system)
slicer = ZSliceSelector(zmin, zmax)
selections = []
selections.append(loos.selectAtoms(system, selection_strings[0]))
for s in selection_strings[1:]:
selections.append(loos.selectAtoms(selections[0], s))
frame = skip
string = ""
for i in range(len(selections)):
string += "\tArea" + str(i)
