from sklearn.neighbors import KNeighborsClassifier import streamlit as st from rdkit.Chem import MACCSkeys from rdkit import Chem import numpy as np import pandas as pd import xgboost as xgb from sklearn.svm import SVC import matplotlib.pyplot as plt from sklearn.model_selection import train_test_split, cross_val_score from sklearn.metrics import classification_report, confusion_matrix, average_precision_score, roc_auc_score import pickle global header model_path = 'model/' def load_tpr_fpr(ml, enzyme): tpr_file = 'AUC/' + ml + '_' + enzyme + '_tpr.pickle' fpr_file = 'AUC/' + ml + '_' + enzyme + '_fpr.pickle' with open(tpr_file, 'rb') as f: tpr = pickle.load(f) with open(fpr_file, 'rb') as f: fpr = pickle.load(f) return tpr, fpr def smile_list_to_MACCS(smi_list): MACCS_list = [] for smi in smi_list: mol = Chem.MolFromSmiles(smi) maccs = list(MACCSkeys.GenMACCSKeys(mol).ToBitString()) MACCS_list.append(maccs) return MACCS_list st.write(""" # Area Under the Curve Ploting """) st.sidebar.header('User Input Parameters') def user_input_features(): # name = st.text_input('compound name', 'Fedratinib') # if name == None: # name = 'test' # smi = st.text_input('compound SMILES', 'CC1=CN=C(N=C1NC2=CC(=CC=C2)S(=O)(=O)NC(C)(C)C)NC3=CC=C(C=C3)OCCN4CCCC4') # if name == None and smi == None: # name ='Fedratinib' # smi = 'CC1=CN=C(N=C1NC2=CC(=CC=C2)S(=O)(=O)NC(C)(C)C)NC3=CC=C(C=C3)OCCN4CCCC4' # enzyme = st.multiselect( # 'Choose JAK: ', # ['JAK1', 'JAK2', 'JAK3', 'TYK2']) # if enzyme == None: # enzyme = 'JAK1' st.write('Select JAK kinase: ') JAK1 = st.checkbox('JAK1') JAK2 = st.checkbox('JAK2') JAK3 = st.checkbox('JAK3') TYK2 = st.checkbox('TYK2') all_enzyme = st.checkbox('Select all JAKs') enzyme = [] if JAK1 == True: enzyme.append('JAK1') if JAK2 == True: enzyme.append('JAK2') if JAK3 == True: enzyme.append('JAK3') if TYK2 == True: enzyme.append('TYK2') if all_enzyme == True: enzyme = ['JAK1', 'JAK2', 'JAK3', 'TYK2'] # model = st.multiselect( # 'Choose model: ', # ['knn','SVM_linear', 'SVM_poly', 'SVM_rbf', 'SVM_sigmoid', 'XGBoost']) model = [] st.write('Select model: ') knn = st.checkbox('KNN') SVM_linear = st.checkbox('SVM_linear') SVM_poly = st.checkbox('SVM_poly') SVM_rbf = st.checkbox('SVM_rbf') SVM_sigmoid = st.checkbox('SVM_sigmoid') RF = st.checkbox('RF') XGBoost = st.checkbox('XGBoost') CNN = st.checkbox('CNN') GVAE = st.checkbox('GraphVAE') chemBERTa = st.checkbox('chembert') all_model = st.checkbox('Select all models') if knn == True: model.append('knn') if SVM_linear == True: model.append('SVM_linear') if SVM_poly == True: model.append('SVM_poly') if SVM_rbf == True: model.append('SVM_rbf') if SVM_sigmoid == True: model.append('SVM_sigmoid') if RF == True: model.append('RF') if XGBoost == True: model.append('XGBoost') if CNN == True: model.append('CNN') if GVAE == True: model.append('GVAE') if chemBERTa == True: model.append('chembert') if all_model == True: model = ['knn', 'SVM_linear', 'SVM_poly', 'SVM_rbf', 'SVM_sigmoid', 'RF', 'XGBoost', 'CNN', 'GVAE', 'chembert'] return enzyme, model with st.sidebar: enzymes, model_chosen = user_input_features() st.subheader('User Input parameters:') # st.write('Current compound: ', name) # st.write('Current compound SMILE: ', smi) st.write('Selected JAK:', enzymes) st.write('Selected model: ', model_chosen) if st.button('Start Plot AUC'): if model_chosen==[]: st.write('Did not choose model!') if enzymes==[]: st.write('Did not choose JAK kinase!') elif model_chosen != [] and enzymes != []: for enzyme in enzymes: title = enzyme + ' Receiver Operating Characteristic Curve' models = model_chosen fig, ax = plt.subplots(figsize=(10,10)) for ml in models: tpr, fpr = load_tpr_fpr(ml, enzyme) ax.plot(fpr, tpr, label=ml) ax.plot(np.linspace(0, 1, 100), np.linspace(0, 1, 100), label='baseline', linestyle='--') plt.title(title, fontsize=18) plt.ylabel('TPR', fontsize=16) plt.xlabel('FPR', fontsize=16) plt.legend(fontsize=12) # plt.savefig('figures/'+enzyme+'.png') st.pyplot(fig)