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)