params["trajfile"] = traj_file
if args.start_frame:
start_frame = int(args.start_frame)
params["start_frame"] = start_frame
if args.end_frame:
end_frame = int(args.end_frame)
params["end_frame"] = end_frame
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(coord_file) and os.path.exists(top_file)):
parser.print_help()
print("\nPlease supply the name of an existing topology and coordinate file.")
if not os.path.exists(coord_file):
print("(cannot find coordinate file %s)" % coord_file)
if not os.path.exists(top_file):
print("(cannot find topology file %s)" % top_file)
sys.exit(-1)
if not (os.path.exists(traj_file)):
parser.print_help()
print("\nPlease supply the name of an existing trajectory file.")
sys.exit(-1)
print("\nRunning nautilus-traj2cell.py using files %s, %s and %s " % (top_file, coord_file, traj_file) )
Nautilus.traj2cell(params)
if args.gridforces:
gridforces = args.gridforces
params["gridforces"] = gridforces
elif "gridforces" in params:
gridforces = params["gridforces"]
else:
gridforces = "grid.forces"
params["gridforces"] = gridforces
if args.R:
R = float(args.R)
params["R"] = R
else:
R = 6
params["R"] = R
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces)):
parser.print_help()
print(
"\nPlease supply the name of an existing grid force file and coordinates"
)
if not os.path.exists(gridforces):
print("(cannot find grid file %s)" % gridforces)
sys.exit(-1)
print("\nRunning nautilus-subgrids.py using file %s" % (gridforces))
Nautilus.subgrids(params)
if args.avggridfiles:
print(args.avggridfiles)
avggridfiles = ast.literal_eval(str(args.avggridfiles))
params["avggridfiles"] = avggridfiles
else:
parser.print_help()
print("\nNo grid files to average specified")
sys.exit(-1)
if args.avgdx:
grid2 = args.avgdx
params["avgdx"] = avgdx
elif "avgdx" in params:
avgdx = params["avgdx"]
else:
avgdx = "avg.dx"
params["avgdx"] = avgdx
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(avggridfiles[0])):
parser.print_help()
print("\nPlease supply the names of relevant dx files.")
if not os.path.exists(avggridfiles[0]):
print("(cannot find dx files %s)" % (avggridfiles[0]))
sys.exit(-1)
print("\nRunning nautilus-avggrids.py using list of files %s" % (avggridfiles))
Nautilus.avggrids(params)
print (args.avggridfiles)
avggridfiles = ast.literal_eval(str(args.avggridfiles))
params["avggridfiles"] = avggridfiles
else:
parser.print_help()
print ("\nNo grid files to average specified")
sys.exit(-1)
if args.avgdx:
grid2 = args.avgdx
params["avgdx"] = avgdx
elif "avgdx" in params:
avgdx = params["avgdx"]
else:
avgdx = "avg.dx"
params["avgdx"] = avgdx
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(avggridfiles[0])):
parser.print_help()
print("\nPlease supply the names of relevant dx files.")
if not os.path.exists(avggridfiles[0]):
print("(cannot find dx files %s)" % (avggridfiles[0]))
sys.exit(-1)
print("\nRunning nautilus-avggrids.py using list of files %s" % (avggridfiles) )
Nautilus.avggrids(params)
if args.start_frame:
start_frame = int(args.start_frame)
params["start_frame"] = start_frame
if args.end_frame:
end_frame = int(args.end_frame)
params["end_frame"] = end_frame
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(coord_file) and os.path.exists(top_file)):
parser.print_help()
print(
"\nPlease supply the name of an existing topology and coordinate file."
)
if not os.path.exists(coord_file):
print("(cannot find coordinate file %s)" % coord_file)
if not os.path.exists(top_file):
print("(cannot find topology file %s)" % top_file)
sys.exit(-1)
if not (os.path.exists(traj_file)):
parser.print_help()
print("\nPlease supply the name of an existing trajectory file.")
sys.exit(-1)
print("\nRunning nautilus-traj2cell.py using files %s, %s and %s " %
(top_file, coord_file, traj_file))
Nautilus.traj2cell(params)
elif "gridl" in params:
gridl = params["gridl"]
else:
gridl = "gridl.dx"
params["gridl"] = gridl
if args.diffdx:
diffdx = args.diffdx
params["diffdx"] = diffdx
elif "diffdx" in params:
diffdx= params["diffdx"]
else:
diffdx = "diff.dx"
params["diffdx"] = diffdx
if args.benchmark:
params["benchmark"] = True
#print (params)
if not (os.path.exists(gridf) and os.path.exists(gridl)):
parser.print_help()
print("\nPlease supply the names of an dx files to be subtracted.")
if not os.path.exists(os.path.exists(gridf) and os.path.exists(gridl)):
print("(cannot find dx files %s %s)" % (gridf, gridl))
sys.exit(-1)
print("\nRunning nautilus-subgrids.py using files %s %s" % (gridf, gridl) )
Nautilus.subgrids(params)
gridforces = params["gridforces"]
else:
gridforces = "grid.forces"
params["gridforces"] = gridforces
if args.regionfile:
regionfile = args.regionfile
params["regionfile"] = regionfile
elif "regionfile" in params:
regionfile = params["regionfile"]
else:
regionfile = "all.region"
params["regionfile"] = regionfile
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces) and os.path.exists(regionfile)):
parser.print_help()
print("\nPlease supply the name of an existing grid and region file.")
if not os.path.exists(regionfile):
print("cannot find region file %s" % regionfile)
if not os.path.exists(gridforces):
print("cannot find grid file %s" % gridforces)
sys.exit(-1)
#print (params,args)
print("\nRunning nautilus-regionproperties.py using files %s and %s" % (gridforces, regionfile) )
Nautilus.regionproperties(params)
gridforces = params["gridforces"]
else:
gridforces = "grid.forces"
params["gridforces"] = gridforces
if args.regionfile:
regionfile = args.regionfile
params["regionfile"] = regionfile
elif "regionfile" in params:
regionfile = params["regionfile"]
else:
regionfile = "all.region"
params["regionfile"] = regionfile
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces) and os.path.exists(regionfile)):
parser.print_help()
print("\nPlease supply the name of an existing grid and region file.")
if not os.path.exists(regionfile):
print("cannot find region file %s" % regionfile)
if not os.path.exists(gridforces):
print("cannot find grid file %s" % gridforces)
sys.exit(-1)
#print (params,args)
print("\nRunning nautilus-regionproperties.py using files %s and %s" %
(gridforces, regionfile))
Nautilus.regionproperties(params)
if args.R:
R = float(args.R)
params["R"] = R
else:
R = 10
params["R"] = R
if args.center:
center = ast.literal_eval(center)
params["center"] = center
elif "center" in params:
center = parms["center"]
else:
print("Using grid center specified in config file")
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces)):
parser.print_help()
print(
"\nPlease supply the name of an existing grid force file and a center coordinate and the distance from it"
)
if not os.path.exists(gridforces):
print("(cannot find grid file %s)" % gridforces)
sys.exit(-1)
print("\nRunning nautilus-boxgrid.py using file %s" % (gridforces))
Nautilus.boxgrid(params)
print("Loading configuration information from file %s" % args.config)
params = readParams(args.config)
if args.cell_dir:
cell_dir = args.cell_dir
params["cell_dir"] = cell_dir
elif "cell_dir" in params:
cell_dir = params["cell_dir"]
else:
cell_dir = "cell"
params["cell_dir"] = cell_dir
if args.start_frame:
start_frame = int(args.start_frame)
params["start_frame"] = start_frame
if args.end_frame:
end_frame = int(args.end_frame)
params["end_frame"] = end_frame
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(cell_dir)):
parser.print_help()
print("\nPlease supply the cell file directory, it is missing")
sys.exit(-1)
print("\nRunning nautilus-cell2grid.py using files %s " % (cell_dir))
Nautilus.cell2grid(params)
if args.R:
R = float(args.R)
params["R"] = R
else:
R = 10
params["R"] = R
if args.center:
center = ast.literal_eval(center)
params["center"] = center
elif "center" in params:
center = parms["center"]
else:
print ("Using grid center specified in config file")
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces)):
parser.print_help()
print("\nPlease supply the name of an existing grid force file and a center coordinate and the distance from it")
if not os.path.exists(gridforces):
print("(cannot find grid file %s)" % gridforces)
sys.exit(-1)
print("\nRunning nautilus-boxgrid.py using file %s" % (gridforces) )
Nautilus.boxgrid(params)
if args.gridforces:
gridforces = args.gridforces
params["gridforces"] = gridforces
elif "gridforces" in params:
gridforces = params["gridforces"]
else:
gridforces = "grid.forces"
params["gridforces"] = gridforces
if args.neighcut:
neighcut = float(args.neighcut)
params["neighcut"] = neighcut
if args.lowt:
lowt = float(args.lowt)
params["lowt"] = lowt
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces)):
parser.print_help()
print("\nPlease supply the name of an existing grid force file.")
if not os.path.exists(gridforces):
print("(cannot find grid file %s)" % gridforces)
sys.exit(-1)
print("\nRunning nautilus-clustergrids.py using file %s" % (gridforces) )
Nautilus.clustergrids(params)
if args.gridforces:
gridforces = args.gridforces
params["gridforces"] = gridforces
elif "gridforces" in params:
gridforces = params["gridforces"]
else:
gridforces = "grid.forces"
params["gridforces"] = gridforces
if args.neighcut:
neighcut = float(args.neighcut)
params["neighcut"] = neighcut
if args.lowt:
lowt = float(args.lowt)
params["lowt"] = lowt
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(gridforces)):
parser.print_help()
print("\nPlease supply the name of an existing grid force file.")
if not os.path.exists(gridforces):
print("(cannot find grid file %s)" % gridforces)
sys.exit(-1)
print("\nRunning nautilus-clustergrids.py using file %s" % (gridforces))
Nautilus.clustergrids(params)
params = readParams(args.config)
if args.cell_dir:
cell_dir = args.cell_dir
params["cell_dir"] = cell_dir
elif "cell_dir" in params:
cell_dir = params["cell_dir"]
else:
cell_dir= "cell"
params["cell_dir"] = cell_dir
if args.start_frame:
start_frame = int(args.start_frame)
params["start_frame"] = start_frame
if args.end_frame:
end_frame = int(args.end_frame)
params["end_frame"] = end_frame
if args.benchmark:
params["benchmark"] = True
if not (os.path.exists(cell_dir)):
parser.print_help()
print("\nPlease supply the cell file directory, it is missing")
sys.exit(-1)
print("\nRunning nautilus-cell2grid.py using files %s " % (cell_dir) )
Nautilus.cell2grid(params)