Update headers

b3clf/__init__.py

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

b3clf/__main__.py

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

b3clf/b3clf.py

@@ -1,3 +1,26 @@
+# -*- 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/>
+#
+# --
+
 """
 Main B3clf Script.
 
@@ -17,69 +40,48 @@
 ]
 
 
-def b3clf(descriptors_path,
+def b3clf(mol_in,
           sep,
-          clf_str,
-          sampling_str,
-          xlsx_output,
+          classification,
+          sampling,
+          output,
           ):
     """Use B3clf for BBB classifications."""
 
     features_out = "internal_padel_descriptors.xlsx"
     internal_sdf = "internal.sdf"
 
-    # ===================
-    # Pipeline
-    # ===================
-
-    # ===================
     # Geometry optimization
-    # ===================
     # Input:
     # * Either an SDF file with molecular geometries or a text file with SMILES strings
 
-    geometry_optimize(input_fname=descriptors_path, output_sdf=internal_sdf, sep=sep)
+    geometry_optimize(input_fname=mol_in, output_sdf=internal_sdf, sep=sep)
 
-    # ===================
     # Compute descriptors with PaDel
-    # ===================
     # Internal file name passed should be relative to this directory I think
     _ = compute_descriptors(sdf_file=internal_sdf, excel_out=features_out)
 
-    # ===================
     # Get computed descriptors
-    # ===================
     X_features, info_df = get_descriptors(df=features_out)
     # X_features, info_df = get_descriptors(internal_df)
 
-    # ===================
     # Select descriptors
-    # ===================
     X_features = select_descriptors(df=X_features)
 
-    # ===================
     # Scale descriptors
-    # ===================
     X_features = scale_descriptors(df=X_features)
 
-    # ===================
     # Get classifier
-    # ===================
-
-    clf = get_clf(clf_str=clf_str, sampling_str=sampling_str)
+    clf = get_clf(clf_str=classification, sampling_str=sampling)
 
-    # ===================
     # Get classifier
-    # ===================
     result_df = predict_permeability(clf=clf, features_df=X_features, info_df=info_df)
 
-    # ===================
     # Get classifier
-    # ===================
     display_cols = ["ID", "SMILES", "B3clf_predicted_probability", "B3clf_predicted_label"]
 
     display_df = result_df[[col for col in result_df.columns.to_list() if col in display_cols]]
     # print(display_df)
 
-    display_df.to_excel(xlsx_output, index=None)
+    display_df.to_excel(output, index=None)
     return display_df

b3clf/descriptor_padel.py

@@ -1,3 +1,26 @@
+# -*- 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/>
+#
+# --
+
 import pandas as pd
 from padelpy import from_sdf
 from rdkit import Chem

b3clf/geometry_opt.py

@@ -1,5 +1,25 @@
-# import os
-# import subprocess
+# -*- 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/>
+#
+# --
 
 import pandas as pd
 from rdkit import Chem

b3clf/utils.py

@@ -1,3 +1,26 @@
+# -*- 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/>
+#
+# --
+
 """
 B3clf utility functions
 

b3clf/version.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
-# The B3clf library provides a set of functions for transforming
-# a matrix to make it as similar as possible to a target matrix.
+# The B3clf library computes the blood-brain barrier (BBB) permeability
+# of organic molecules with resampling strategies.
 #
 # Copyright (C) 2021 The Ayers Lab
 #
@@ -20,6 +20,7 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
+
 """Version Information for B3clf."""
 
 VERSION = (0, 0, 1, "beta")

setup.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
-# The B3clf library provides a set of functions for transforming
-# a matrix to make it as similar as possible to a target matrix.
+# The B3clf library computes the blood-brain barrier (BBB) permeability
+# of organic molecules with resampling strategies.
 #
 # Copyright (C) 2021 The Ayers Lab
 #
@@ -20,6 +20,7 @@
 # along with this program; if not, see <http://www.gnu.org/licenses/>
 #
 # --
+
 """Installation script for B3clf.
 
 Directly calling this script is only needed by B3clf developers in special