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arguments.py
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import argparse
def str2bool(v):
if v.lower() in ("yes", "true", "t", "y", "1"):
return True
elif v.lower() in ("no", "false", "f", "n", "0"):
return False
else:
raise argparse.ArgumentTypeEror("Boolean value expected")
def parser(command):
arg_command = command[1:]
parser = argparse.ArgumentParser(description="parser for train and test")
parser.add_argument("--dim_gnn",
help="dim_gnn",
type=int,
default=128)
parser.add_argument("--n_gnn",
help="depth of gnn layer",
type=int,
default=3)
parser.add_argument("--ngpu",
help="ngpu",
type=int,
default=1)
parser.add_argument("--restart_file",
help="restart file",
type=str,
default="")
parser.add_argument("--potential",
help="potential",
type=str,
default="harmonic",
choices=["morse",
"harmonic",
"morse_all_pair",
"gnn",
"cnn3d",
"cnn3d_kdeep"])
parser.add_argument("--pos_noise_std",
help="std of noise added to the position",
type=float,
default=0.0)
parser.add_argument("--filter_gamma",
help="filter gamma",
type=float,
default=10.0)
parser.add_argument("--filter_spacing",
help="filter spacing",
type=float,
default=0.5)
parser.add_argument("--interaction_net",
action="store_true",
help="edge conv")
parser.add_argument("--no_rotor_penalty",
action="store_true",
help="rotor penaly")
parser.add_argument("--vdw_N",
help="vdw N",
type=float,
default=6.0)
parser.add_argument("--max_vdw_interaction",
help="max vdw _interaction",
type=float,
default=0.0356)
parser.add_argument("--min_vdw_interaction",
help="min vdw _interaction",
type=float,
default=0.0178)
parser.add_argument("--dev_vdw_radius",
help="deviation of vdw radius",
type=float,
default=0.2)
parser.add_argument("--dropout_rate",
help="dropout rate",
type=float,
default=0.1)
if "train.py" in command[0] or "test.py" in command[0]:
parser.add_argument("--filename",
help="filename",
type=str,
default="")
parser.add_argument("--key_dir",
help="key directory",
type=str,
default="")
parser.add_argument("--data_dir",
help="data file path",
type=str,
default="")
parser.add_argument("--batch_size",
help="batch size",
type=int,
default=8)
parser.add_argument("--num_workers",
help="number of workers",
type=int,
default=7)
parser.add_argument("--grid_rotation",
help="whether rotate the grid or not",
action="store_true")
parser.add_argument("--lattice_dim",
help="lattice size for 3D CNN",
type=int,
default=20)
parser.add_argument("--scaling",
help="scaling constant for 3D CNN",
type=float,
default=0.5)
parser.add_argument("--with_uncertainty",
help="with aleatoric uncertainty or not",
action="store_true")
# for train
if "train.py" in command[0]:
parser.add_argument("--lr",
help="learning rate",
type=float,
default=1e-4)
parser.add_argument("--lr_decay",
help="learning rate decay",
type=float,
default=1.0)
parser.add_argument("--weight_decay",
help="weight decay",
type=float,
default=0.0)
parser.add_argument("--num_epochs",
help="number of epochs",
type=int,
default=1001)
parser.add_argument("--train_result_filename",
help="train result filename",
type=str,
default="./result/train_result.txt")
parser.add_argument("--test_result_filename",
help="test result filename",
type=str,
default="./result/test_result.txt")
parser.add_argument("--train_result_docking_filename",
help="train result docking_filename",
type=str,
default="./result/train_result_docking.txt")
parser.add_argument("--test_result_docking_filename",
help="test result docking filename",
type=str,
default="./result/test_result_docking.txt")
parser.add_argument("--train_result_screening_filename",
help="train result screening filename",
type=str,
default="./result/train_result_screening.txt")
parser.add_argument("--test_result_screening_filename",
help="test result screening filename",
type=str,
default="./result/test_result_screening.txt")
parser.add_argument("--loss_der1_ratio",
help="loss der1 ratio",
type=float,
default=10.0)
parser.add_argument("--loss_der2_ratio",
help="loss der2 ratio",
type=float,
default=10.0)
parser.add_argument("--min_loss_der2",
help="min loss der2",
type=float,
default=-20.0)
parser.add_argument("--loss_docking_ratio",
help="loss docking ratio",
type=float,
default=10.0)
parser.add_argument("--min_loss_docking",
help="min loss docking",
type=float,
default=-1.0)
parser.add_argument("--loss_screening_ratio",
help="loss screening ratio",
type=float,
default=5.0)
parser.add_argument("--loss_screening2_ratio",
help="loss screening ratio",
type=float,
default=5.0)
parser.add_argument("--save_dir",
help="save directory of model save files",
type=str,
default="results/run01")
parser.add_argument("--save_every",
help="saver every n epoch",
type=int,
default=100)
parser.add_argument("--tensorboard_dir",
help="save directory of tensorboard log files",
type=str,
default="run/run01")
parser.add_argument("--filename2",
help="filename2",
default="")
parser.add_argument("--key_dir2",
help="key directory",
type=str,
default="")
parser.add_argument("--data_dir2",
help="data file path",
type=str,
default="")
parser.add_argument("--filename3",
help="filename",
default="")
parser.add_argument("--key_dir3",
help="key directory",
type=str,
default="")
parser.add_argument("--data_dir3",
help="data file path",
type=str,
default="")
parser.add_argument("--filename4",
help="filename",
default="")
parser.add_argument("--key_dir4",
help="key directory",
type=str,
default="")
parser.add_argument("--data_dir4",
help="data file path",
type=str,
default="")
if "--with_uncertainty" in command:
parser.add_argument("--var_agg",
help="var agg",
type=str,
default="product")
parser.add_argument("--var_abs",
help="var abs",
type=str,
default="abs")
parser.add_argument("--var_log",
help="log var or var",
type=str2bool,
default=False)
parser.add_argument("--loss_var_ratio",
help="loss var ratio",
type=float,
default=1e-4)
parser.add_argument("--mc_dropout",
help="to turn on or off MC dropout",
type=str2bool,
default=False)
# for test
if "test.py" in command[0]:
parser.add_argument("--test_result_filename",
help="test result filename",
type=str,
default="./result/test_result.txt")
if "--with_uncertainty" in command:
parser.add_argument("--n_mc_sampling",
help="number of mc sampling",
type=int,
default=3)
parser.add_argument("--var_agg",
help="var agg",
type=str,
default="product")
parser.add_argument("--var_abs",
help="var abs",
type=str,
default="abs")
# for predict
if "predict.py" in command[0]:
parser.add_argument("--ligand_files",
help="list of ligand file",
nargs="+",
type=str,)
parser.add_argument("--protein_files",
help="list of protein file",
nargs="+",
type=str,)
parser.add_argument("--output_files",
help="list of output file",
nargs="+",
type=str,)
parser.add_argument("--ligand_opt_output_files",
help="list of output file",
nargs="+",
type=str,)
parser.add_argument("--local_opt",
action="store_true",
help="local_opt")
parser.add_argument("--ligand_prop",
action="store_true",
help="ligand_prop")
args = parser.parse_args(arg_command)
return args