Python Nautilus示例

示例#1

文件： nautilus-traj2cell.py 项目： Steboss/Sire

    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)

示例#2

文件： nautilus-focusgrid.py 项目： yueguangzoum/Sire

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)

示例#3

文件： nautilus-avggrids.py 项目： yueguangzoum/Sire

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)

示例#4

文件： nautilus-avggrids.py 项目： Steboss/Sire

    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)

示例#5

文件： nautilus-traj2cell.py 项目： yueguangzoum/Sire

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)

示例#6

文件： nautilus-subgrids.py 项目： Steboss/Sire

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)

示例#7

文件： nautilus-regionproperties.py 项目： Steboss/Sire

    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)

示例#8

文件： nautilus-regionproperties.py 项目： yueguangzoum/Sire

    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)

示例#9

文件： nautilus-boxgrid.py 项目： yueguangzoum/Sire

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)

示例#10

文件： nautilus-cell2grid.py 项目： yueguangzoum/Sire

    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)

示例#11

文件： nautilus-boxgrid.py 项目： Steboss/Sire

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)

示例#12

文件： nautilus-clustergrids.py 项目： Steboss/Sire

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)

示例#13

文件： nautilus-clustergrids.py 项目： yueguangzoum/Sire

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)

示例#14

文件： nautilus-cell2grid.py 项目： Steboss/Sire

    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)