def main():
# parse args
parser = argparse.ArgumentParser(description="make data file")
parser.add_argument("-a",
"--atom",
nargs=1,
dest="atom_path",
default=False)
parser.add_argument("-g",
"--grid",
nargs=1,
dest="grid_path",
default=False)
parser.add_argument("-m",
"--mulliken",
nargs=1,
dest="mulliken_path",
default=False)
parser.add_argument(
"-o",
"--output",
nargs=1,
dest="data_path",
)
# read the data
fatom = open(args.atom_path[0], "r")
Atom_List = fl_read.read_pdb_file(fatom)
fgrid = open(args.grid_path[0], "rb")
Grid_List = fl_read.read_grid_msg_file(fgrid)
fesp = open(args.grid_path[0], "rb")
ESP_List = fl_read.read_esp_msg_file(fesp)
fmulliken = open(args.mulliken_path[0], "r")
Mulliken_List = fl_read.read_mulliken_file(fmulliken)
# calculate the data
X = mkmat.matrixX(Atom_List, Grid_List)
Y = mkmat.matrixY(Grid_List)
# write the msgpack file
fw_path = args.data_path[0]
fw = open(fw_path, "wb")
data = {}
data["atoms"] = Atom_List
data["grids"] = Grid_List
data["ESP"] = ESP_List
data["mulliken"] = Mulliken_List
data["matrixX"] = np.array(X)
data["matrixY"] = np.array(Y)
data["net_charge"] = -2
data["Nelec"] = 3000
packed = msgpack.packb(data)
fw.write(packed)
fw.close()
def main():
# parse args
parser = argparse.ArgumentParser(description="make data file")
parser.add_argument("-a", "--atom",
nargs=1,
dest="atom_path",
default=False)
parser.add_argument("-g", "--grid",
nargs=1,
dest="grid_path",
default=False)
parser.add_argument("-m", "--mulliken",
nargs=1,
dest="mulliken_path",
default=False)
parser.add_argument("-o", "--output",
nargs=1,
dest="data_path",)
# read the data
fatom = open(args.atom_path[0], "r")
Atom_List = fl_read.read_pdb_file(fatom)
fgrid = open(args.grid_path[0], "rb")
Grid_List = fl_read.read_grid_msg_file(fgrid)
fesp = open(args.grid_path[0], "rb")
ESP_List = fl_read.read_esp_msg_file(fesp)
fmulliken = open(args.mulliken_path[0], "r")
Mulliken_List = fl_read.read_mulliken_file(fmulliken)
# calculate the data
X = mkmat.matrixX(Atom_List, Grid_List)
Y = mkmat.matrixY(Grid_List)
# write the msgpack file
fw_path = args.data_path[0]
fw = open(fw_path, "wb")
data = {}
data["atoms"] = Atom_List
data["grids"] = Grid_List
data["ESP"] = ESP_List
data["mulliken"] = Mulliken_List
data["matrixX"] = np.array(X)
data["matrixY"] = np.array(Y)
data["net_charge"] = -2
data["Nelec"] = 3000
packed = msgpack.packb(data)
fw.write(packed)
fw.close()
def add_Grid_List(File): fr = open(File, "rb") Grid_List = fl_read.read_grid_msg_file(fr) return Grid_List