def add_Atom_List(File): fr = open(File, "r") Atom_List = [] fl_read.read_pdb_file(fr, Atom_List) return Atom_List
def main():
# parse args
parser = argparse.ArgumentParser(description="output the CHELPG grid points")
parser.add_argument("FILE",
nargs=1,
help="input file(.pdb)")
parser.add_argument("-o", "--output",
nargs=1,
dest="grid_path",
default="grid.mpac",
help="output file")
args = parser.parse_args()
# setting
pdb_path = args.FILE[0]
fr = open(pdb_path, "r")
Atom_List = fl_read.read_pdb_file(fr)
# calculation
range_List = grid_chelpg.range_List(Atom_List)
all_grid_List = grid_chelpg.CHELPG_List_all(range_List)
chelpg_List = grid_chelpg.CHELPG_List(Atom_List, all_grid_List)
# output
fw_path = args.grid_path[0]
fw = open(fw_path, "wb")
data = {}
data["atoms"] = Atom_List
data["grids"] = chelpg_List
packed = msgpack.packb(data)
fw.write(packed)
fw.close()
def main():
# parse args
parser = argparse.ArgumentParser(
description="output the CHELPG grid points")
parser.add_argument("FILE", nargs=1, help="input file(.pdb)")
parser.add_argument("-o",
"--output",
nargs=1,
dest="grid_path",
default="grid.mpac",
help="output file")
args = parser.parse_args()
# setting
pdb_path = args.FILE[0]
fr = open(pdb_path, "r")
Atom_List = fl_read.read_pdb_file(fr)
# calculation
range_List = grid_chelpg.range_List(Atom_List)
all_grid_List = grid_chelpg.CHELPG_List_all(range_List)
chelpg_List = grid_chelpg.CHELPG_List(Atom_List, all_grid_List)
# output
fw_path = args.grid_path[0]
fw = open(fw_path, "wb")
data = {}
data["atoms"] = Atom_List
data["grids"] = chelpg_List
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 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="output the MK grid points")
parser.add_argument("FILE",
nargs=1,
help="input file(.pdb)")
parser.add_argument("-o", "--output",
nargs=1,
dest="grid_path",
default="grid.mpac",
help="output file")
args = parser.parse_args()
# setting
pdb_path = args.FILE[0]
fr = open(pdb_path, "r")
Atom_List = fl_read.read_pdb_file(fr)
# calculation
All_Layer1 = grid_mk.generate_All_Grid_List(Atom_List, 1)
All_Layer2 = grid_mk.generate_All_Grid_List(Atom_List, 2)
All_Layer3 = grid_mk.generate_All_Grid_List(Atom_List, 3)
All_Layer4 = grid_mk.generate_All_Grid_List(Atom_List, 4)
Layer1 = grid_mk.position_check(Atom_List, All_Layer1, 1)
Layer2 = grid_mk.position_check(Atom_List, All_Layer2, 2)
Layer3 = grid_mk.position_check(Atom_List, All_Layer3, 3)
Layer4 = grid_mk.position_check(Atom_List, All_Layer4, 4)
Grid_List = Layer1 + Layer2 + Layer3 + Layer4
# output
fw_path = args.grid_path[0]
fw = open(fw_path, "wb")
data = {}
data["atoms"] = Atom_List
data["grids"] = Grid_List
packed = msgpack.packb(data)
fw.write(packed)
fw.close()
def main():
# parse args
parser = argparse.ArgumentParser(description="output the MK grid points")
parser.add_argument("FILE", nargs=1, help="input file(.pdb)")
parser.add_argument("-o",
"--output",
nargs=1,
dest="grid_path",
default="grid.mpac",
help="output file")
args = parser.parse_args()
# setting
pdb_path = args.FILE[0]
fr = open(pdb_path, "r")
Atom_List = fl_read.read_pdb_file(fr)
# calculation
All_Layer1 = grid_mk.generate_All_Grid_List(Atom_List, 1)
All_Layer2 = grid_mk.generate_All_Grid_List(Atom_List, 2)
All_Layer3 = grid_mk.generate_All_Grid_List(Atom_List, 3)
All_Layer4 = grid_mk.generate_All_Grid_List(Atom_List, 4)
Layer1 = grid_mk.position_check(Atom_List, All_Layer1, 1)
Layer2 = grid_mk.position_check(Atom_List, All_Layer2, 2)
Layer3 = grid_mk.position_check(Atom_List, All_Layer3, 3)
Layer4 = grid_mk.position_check(Atom_List, All_Layer4, 4)
Grid_List = Layer1 + Layer2 + Layer3 + Layer4
# output
fw_path = args.grid_path[0]
fw = open(fw_path, "wb")
data = {}
data["atoms"] = Atom_List
data["grids"] = Grid_List
packed = msgpack.packb(data)
fw.write(packed)
fw.close()