From 1b09d8378a54ef8b24fc45ba109982352f908a72 Mon Sep 17 00:00:00 2001 From: Fanwang Meng Date: Fri, 6 Oct 2023 23:59:02 -0400 Subject: [PATCH] Clean up files --- .gitignore | 1 - MANIFEST.in | 1 - README.md | 8 ++++---- b3clf/feature_list.txt | 2 +- b3clf/geometry_opt.py | 2 +- b3clf/test/test_SMILES.csv | 2 +- b3clf/test/test_input_sdf.sdf | 36 +++++++++++++++++------------------ 7 files changed, 25 insertions(+), 27 deletions(-) diff --git a/.gitignore b/.gitignore index b6060ce..6249d96 100644 --- a/.gitignore +++ b/.gitignore @@ -108,4 +108,3 @@ tags # version file generated by rob procrustes/_version.py - diff --git a/MANIFEST.in b/MANIFEST.in index d7bcf5d..788231f 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,4 +1,3 @@ include b3clf/pre_trained/* include b3clf/feature_list.txt include b3clf/data/B3clf_thresholds.xlsx - diff --git a/README.md b/README.md index c1c2466..1c5b775 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,13 @@ ## About The blood-brain barrier (BBB) protects and regulations the microvasculature in the central nervous system (CNS) -by inhibiting the transportation or passage of toxins and pathogens from the blood. Because of its resistance to +by inhibiting the transportation or passage of toxins and pathogens from the blood. Because of its resistance to exogenous compounds, the BBB also poses a challenge for the -delivery of neuroactive molecules (i.e. drugs) into the CNS. -Understanding small molecules' BBB permeability is therefore vital for CNS drug discovery, and should +delivery of neuroactive molecules (i.e. drugs) into the CNS. +Understanding small molecules' BBB permeability is therefore vital for CNS drug discovery, and should be considered at an early stage in the drug-development pipeline to avoid costly late-stage failures. -`B3clf` uses data from 7407 molecules, taken from our curated dataset, +`B3clf` uses data from 7407 molecules, taken from our curated dataset, [B3DB](https://github.com/theochem/B3DB). It supports 24 different models, with four different classification algorithms (_dtree_ for decision trees, _logreg_ for logistical regression, _knn_ for KNN, _xgb_ for XGBoost) and six resampling diff --git a/b3clf/feature_list.txt b/b3clf/feature_list.txt index ba8161d..6998c1c 100644 --- a/b3clf/feature_list.txt +++ b/b3clf/feature_list.txt @@ -472,4 +472,4 @@ Dm E1v E2v E3v -Dv \ No newline at end of file +Dv diff --git a/b3clf/geometry_opt.py b/b3clf/geometry_opt.py index 8febf82..a9861cd 100644 --- a/b3clf/geometry_opt.py +++ b/b3clf/geometry_opt.py @@ -96,7 +96,7 @@ def minimize_with_rdkit(input_molfname, mols = [] for idx, smi in enumerate(smile_list): mol = Chem.MolFromSmiles(smi) - # This will overwrite + # This will overwrite if mol is not None: mol.SetProp("_Name", mol_name_list[idx]) mols.append(mol) diff --git a/b3clf/test/test_SMILES.csv b/b3clf/test/test_SMILES.csv index ce04ea8..13b7c0a 100644 --- a/b3clf/test/test_SMILES.csv +++ b/b3clf/test/test_SMILES.csv @@ -4,4 +4,4 @@ CCC CCCC CC(=O)OC1=CC=CC=C1C(=O)O -CC(=O)OC1=C(C=C(C=C1)Cl)C(=O)OC(=O)C2=C(C=CC(=C2)Cl)OC(=O)C \ No newline at end of file +CC(=O)OC1=C(C=C(C=C1)Cl)C(=O)OC(=O)C2=C(C=CC(=C2)Cl)OC(=O)C diff --git a/b3clf/test/test_input_sdf.sdf b/b3clf/test/test_input_sdf.sdf index e640575..6ce532d 100644 --- a/b3clf/test/test_input_sdf.sdf +++ b/b3clf/test/test_input_sdf.sdf @@ -109,22 +109,22 @@ H1_Bepotastine 26 50 1 0 27 51 1 0 M END -> (1) +> (1) H1_Bepotastine -> (1) +> (1) [H]OC(=O)C([H])([H])C([H])([H])C([H])([H])N1C([H])([H])C([H])([H])C([H])(OC([H])(c2nc([H])c([H])c([H])c2[H])c2c([H])c([H])c(Cl)c([H])c2[H])C([H])([H])C1([H])[H] -> (1) +> (1) 2350 -> (1) +> (1) N -> (1) +> (1) InChI=1S/C21H25ClN2O3/c22-17-8-6-16(7-9-17)21(19-4-1-2-12-23-19)27-18-10-14-24(15-11-18)13-3-5-20(25)26/h1-2,4,6-9,12,18,21H,3,5,10-11,13-15H2,(H,25,26)/t21-/m1/s1 -> (1) +> (1) 49.1758 $$$$ @@ -226,22 +226,22 @@ H1_Quifenadine 21 44 1 0 22 45 1 0 M END -> (2) +> (2) H1_Quifenadine -> (2) +> (2) [H]OC(c1c([H])c([H])c([H])c([H])c1[H])(c1c([H])c([H])c([H])c([H])c1[H])C1([H])C([H])([H])N2C([H])([H])C([H])([H])C1([H])C([H])([H])C2([H])[H] -> (2) +> (2) 65600 -> (2) +> (2) N -> (2) +> (2) InChI=1S/C20H23NO/c22-20(17-7-3-1-4-8-17,18-9-5-2-6-10-18)19-15-21-13-11-16(19)12-14-21/h1-10,16,19,22H,11-15H2/t19-/m1/s1 -> (2) +> (2) 84.891 $$$$ @@ -366,22 +366,22 @@ H1_Rupatadine 30 55 1 0 30 56 1 0 M END -> (3) +> (3) H1_Rupatadine -> (3) +> (3) [H]c1nc2c(c([H])c1[H])C([H])([H])C([H])([H])c1c([H])c(Cl)c([H])c([H])c1C2=C1C([H])([H])C([H])([H])N(C([H])([H])c2c([H])nc([H])c(C([H])([H])[H])c2[H])C([H])([H])C1([H])[H] -> (3) +> (3) 133017 -> (3) +> (3) N -> (3) +> (3) InChI=1S/C26H26ClN3/c1-18-13-19(16-28-15-18)17-30-11-8-20(9-12-30)25-24-7-6-23(27)14-22(24)5-4-21-3-2-10-29-26(21)25/h2-3,6-7,10,13-16H,4-5,8-9,11-12,17H2,1H3 -> (3) +> (3) 119.976 $$$$