File size: 4,486 Bytes
d05f89f |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 |
# -*- coding: utf-8 -*-
# The B3clf library computes the blood-brain barrier (BBB) permeability
# of organic molecules with resampling strategies.
#
# Copyright (C) 2021 The Ayers Lab
#
# This file is part of B3clf.
#
# B3clf is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# B3clf is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
# --
"""Package for BBB predictions."""
import argparse
from .b3clf import b3clf
try:
from .version import __version__
except ImportError:
__version__ = "0.0.0.post0"
def main():
# https://docs.python.org/3/library/argparse.html
parser = argparse.ArgumentParser(
description="b3clf predicts if molecules can pass blood-brain barrier with resampling "
"strategies.",
)
parser.add_argument("-mol",
default="input.sdf",
type=str,
help="Input file with descriptors.")
parser.add_argument("-sep",
type=str,
default="\s+|\t+",
help="""Separator for input file. Default="\s+|\\t+".""")
parser.add_argument("-clf",
type=str,
default="xgb",
help="Classification algorithm type. Default=xgb.")
parser.add_argument("-sampling",
type=str,
default="classic_ADASYN",
help="Resampling method type. Default=classic_ADASYN.")
parser.add_argument("-output",
type=str,
default="B3clf_output.xlsx",
help="Name of output file, CSV or XLSX format. Default=B3clf_output.xlsx.")
parser.add_argument("-verbose",
type=int,
default=1,
help="If verbose is not zero, B3clf will print out the predictions. "
"Default=1.")
parser.add_argument("-random_seed",
type=int,
default=42,
help="""Romdom seed to control randonness. If set to be "None", """
"""it will result in a randomness of the predictions. Default=42.""")
parser.add_argument("-time_per_mol",
type=int,
default=-1,
help="""Time per molecule in seconds. If set to be -1, no time limit. """
"""Default=-1.""")
parser.add_argument("-keep_features",
type=str,
default="no",
help="""To keep computed feature file ("yes") or not ("no"). Default=no.""")
parser.add_argument("-keep_sdf",
type=str,
default="no",
help="""To keep computed molecular geometries ("yes") or not ("no"). Default=no.""")
parser.add_argument("-threshold",
type=str,
default="none",
help="""Threshold used for the classification which can be "none", """
""""J_threshold" and "F_threshold". "J_threshold" will use """
"""threshold optimized from Youden’s J statistic. "F_threshold" will """
"""use threshold optimized from F score. Default="none".""")
args = parser.parse_args()
_ = b3clf(mol_in=args.mol,
sep=args.sep,
clf=args.clf,
sampling=args.sampling,
output=args.output,
verbose=args.verbose,
random_seed=args.random_seed,
time_per_mol=args.time_per_mol,
keep_features=args.keep_features,
keep_sdf=args.keep_sdf,
threshold=args.threshold,
)
if __name__ == "__main__":
"""B3clf command-line interface."""
main()
|