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FanwangMFanwangM
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Update headers
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‎b3clf/__init__.py

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@@ -1,6 +1,6 @@
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# -*- coding: utf-8 -*-
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# The B3clf library provides a set of functions for transforming
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# a matrix to make it as similar as possible to a target matrix.
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# The B3clf library computes the blood-brain barrier (BBB) permeability
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# of organic molecules with resampling strategies.
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#
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# Copyright (C) 2021 The Ayers Lab
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#

‎b3clf/__main__.py

Lines changed: 6 additions & 6 deletions
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@@ -1,6 +1,6 @@
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# -*- coding: utf-8 -*-
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# The B3clf library provides a set of functions for transforming
3-
# a matrix to make it as similar as possible to a target matrix.
2+
# The B3clf library computes the blood-brain barrier (BBB) permeability
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# of organic molecules with resampling strategies.
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#
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# Copyright (C) 2021 The Ayers Lab
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#
@@ -61,11 +61,11 @@ def main():
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args = parser.parse_args()
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# Input variables
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_ = b3clf(descriptors_path=args.mol,
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_ = b3clf(mol_in=args.mol,
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sep=args.sep,
66-
clf_str=args.clf,
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sampling_str=args.sampling,
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xlsx_output=args.output,
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classification=args.clf,
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sampling=args.sampling,
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output=args.output,
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)
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‎b3clf/b3clf.py

Lines changed: 30 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,26 @@
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# -*- coding: utf-8 -*-
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# The B3clf library computes the blood-brain barrier (BBB) permeability
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# of organic molecules with resampling strategies.
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#
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# Copyright (C) 2021 The Ayers Lab
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#
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# This file is part of B3clf.
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#
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# B3clf is free software; you can redistribute it and/or
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# modify it under the terms of the GNU General Public License
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# as published by the Free Software Foundation; either version 3
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# of the License, or (at your option) any later version.
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#
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# B3clf is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program; if not, see <http://www.gnu.org/licenses/>
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#
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# --
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"""
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Main B3clf Script.
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@@ -17,69 +40,48 @@
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]
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def b3clf(descriptors_path,
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def b3clf(mol_in,
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sep,
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clf_str,
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sampling_str,
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xlsx_output,
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classification,
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sampling,
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output,
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):
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"""Use B3clf for BBB classifications."""
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features_out = "internal_padel_descriptors.xlsx"
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internal_sdf = "internal.sdf"
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31-
# ===================
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# Pipeline
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# ===================
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35-
# ===================
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# Geometry optimization
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# ===================
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# Input:
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# * Either an SDF file with molecular geometries or a text file with SMILES strings
4057

41-
geometry_optimize(input_fname=descriptors_path, output_sdf=internal_sdf, sep=sep)
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geometry_optimize(input_fname=mol_in, output_sdf=internal_sdf, sep=sep)
4259

43-
# ===================
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# Compute descriptors with PaDel
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# ===================
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# Internal file name passed should be relative to this directory I think
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_ = compute_descriptors(sdf_file=internal_sdf, excel_out=features_out)
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49-
# ===================
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# Get computed descriptors
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# ===================
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X_features, info_df = get_descriptors(df=features_out)
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# X_features, info_df = get_descriptors(internal_df)
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55-
# ===================
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# Select descriptors
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# ===================
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X_features = select_descriptors(df=X_features)
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# ===================
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# Scale descriptors
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# ===================
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X_features = scale_descriptors(df=X_features)
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# ===================
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# Get classifier
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# ===================
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69-
clf = get_clf(clf_str=clf_str, sampling_str=sampling_str)
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clf = get_clf(clf_str=classification, sampling_str=sampling)
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71-
# ===================
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# Get classifier
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# ===================
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result_df = predict_permeability(clf=clf, features_df=X_features, info_df=info_df)
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# ===================
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# Get classifier
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# ===================
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display_cols = ["ID", "SMILES", "B3clf_predicted_probability", "B3clf_predicted_label"]
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display_df = result_df[[col for col in result_df.columns.to_list() if col in display_cols]]
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# print(display_df)
8385

84-
display_df.to_excel(xlsx_output, index=None)
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display_df.to_excel(output, index=None)
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return display_df

‎b3clf/descriptor_padel.py

Lines changed: 23 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,26 @@
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# -*- coding: utf-8 -*-
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# The B3clf library computes the blood-brain barrier (BBB) permeability
3+
# of organic molecules with resampling strategies.
4+
#
5+
# Copyright (C) 2021 The Ayers Lab
6+
#
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# This file is part of B3clf.
8+
#
9+
# B3clf is free software; you can redistribute it and/or
10+
# modify it under the terms of the GNU General Public License
11+
# as published by the Free Software Foundation; either version 3
12+
# of the License, or (at your option) any later version.
13+
#
14+
# B3clf is distributed in the hope that it will be useful,
15+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
16+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17+
# GNU General Public License for more details.
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#
19+
# You should have received a copy of the GNU General Public License
20+
# along with this program; if not, see <http://www.gnu.org/licenses/>
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#
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# --
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import pandas as pd
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from padelpy import from_sdf
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from rdkit import Chem

‎b3clf/geometry_opt.py

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,25 @@
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# import os
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# import subprocess
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# -*- coding: utf-8 -*-
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# The B3clf library computes the blood-brain barrier (BBB) permeability
3+
# of organic molecules with resampling strategies.
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#
5+
# Copyright (C) 2021 The Ayers Lab
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#
7+
# This file is part of B3clf.
8+
#
9+
# B3clf is free software; you can redistribute it and/or
10+
# modify it under the terms of the GNU General Public License
11+
# as published by the Free Software Foundation; either version 3
12+
# of the License, or (at your option) any later version.
13+
#
14+
# B3clf is distributed in the hope that it will be useful,
15+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
16+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17+
# GNU General Public License for more details.
18+
#
19+
# You should have received a copy of the GNU General Public License
20+
# along with this program; if not, see <http://www.gnu.org/licenses/>
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#
22+
# --
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424
import pandas as pd
525
from rdkit import Chem

‎b3clf/utils.py

Lines changed: 23 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,26 @@
1+
# -*- coding: utf-8 -*-
2+
# The B3clf library computes the blood-brain barrier (BBB) permeability
3+
# of organic molecules with resampling strategies.
4+
#
5+
# Copyright (C) 2021 The Ayers Lab
6+
#
7+
# This file is part of B3clf.
8+
#
9+
# B3clf is free software; you can redistribute it and/or
10+
# modify it under the terms of the GNU General Public License
11+
# as published by the Free Software Foundation; either version 3
12+
# of the License, or (at your option) any later version.
13+
#
14+
# B3clf is distributed in the hope that it will be useful,
15+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
16+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17+
# GNU General Public License for more details.
18+
#
19+
# You should have received a copy of the GNU General Public License
20+
# along with this program; if not, see <http://www.gnu.org/licenses/>
21+
#
22+
# --
23+
124
"""
225
B3clf utility functions
326

‎b3clf/version.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
# -*- coding: utf-8 -*-
2-
# The B3clf library provides a set of functions for transforming
3-
# a matrix to make it as similar as possible to a target matrix.
2+
# The B3clf library computes the blood-brain barrier (BBB) permeability
3+
# of organic molecules with resampling strategies.
44
#
55
# Copyright (C) 2021 The Ayers Lab
66
#
@@ -20,6 +20,7 @@
2020
# along with this program; if not, see <http://www.gnu.org/licenses/>
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#
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# --
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2324
"""Version Information for B3clf."""
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2526
VERSION = (0, 0, 1, "beta")

‎setup.py

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
# -*- coding: utf-8 -*-
2-
# The B3clf library provides a set of functions for transforming
3-
# a matrix to make it as similar as possible to a target matrix.
2+
# The B3clf library computes the blood-brain barrier (BBB) permeability
3+
# of organic molecules with resampling strategies.
44
#
55
# Copyright (C) 2021 The Ayers Lab
66
#
@@ -20,6 +20,7 @@
2020
# along with this program; if not, see <http://www.gnu.org/licenses/>
2121
#
2222
# --
23+
2324
"""Installation script for B3clf.
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2526
Directly calling this script is only needed by B3clf developers in special

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