RF.py

# -*- coding: utf-8 -*-
"""
Created on Mon Sep  4 10:38:59 2023

@author: BM109X32G-10GPU-02
"""


from sklearn.metrics import confusion_matrix
import matplotlib.pyplot as plt
import numpy as np

from sklearn.datasets import make_blobs
import json
import numpy as np
import math
from tqdm import tqdm
from scipy import sparse
from sklearn.metrics import median_absolute_error,r2_score, mean_absolute_error,mean_squared_error
import pickle


import pandas as pd
import matplotlib.pyplot as plt
from rdkit import Chem

from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import MinMaxScaler
from sklearn.neural_network import MLPClassifier
from sklearn.svm import SVC
from tensorflow.keras.models import Model, load_model
from tensorflow.keras.layers import Dense, Input, Flatten, Conv1D, MaxPooling1D, concatenate
from tensorflow.keras import metrics, optimizers
from tensorflow.keras.callbacks import ModelCheckpoint, EarlyStopping, ReduceLROnPlateau

def split_smiles(smiles, kekuleSmiles=True):
    try:
        mol = Chem.MolFromSmiles(smiles)
        smiles = Chem.MolToSmiles(mol, kekuleSmiles=kekuleSmiles)
    except:
        pass
    splitted_smiles = []
    for j, k in enumerate(smiles):
        if len(smiles) == 1:
            return [smiles]
        if j == 0:
            if k.isupper() and smiles[j + 1].islower() and smiles[j + 1] != "c":
                splitted_smiles.append(k + smiles[j + 1])
            else:
                splitted_smiles.append(k)
        elif j != 0 and j < len(smiles) - 1:
            if k.isupper() and smiles[j + 1].islower() and smiles[j + 1] != "c":
                splitted_smiles.append(k + smiles[j + 1])
            elif k.islower() and smiles[j - 1].isupper() and k != "c":
                pass
            else:
                splitted_smiles.append(k)

        elif j == len(smiles) - 1:
            if k.islower() and smiles[j - 1].isupper() and k != "c":
                pass
            else:
                splitted_smiles.append(k)
    return splitted_smiles

def get_maxlen(all_smiles, kekuleSmiles=True):
    maxlen = 0
    for smi in tqdm(all_smiles):
        spt = split_smiles(smi, kekuleSmiles=kekuleSmiles)
        if spt is None:
            continue
        maxlen = max(maxlen, len(spt))
    return maxlen
def get_dict(all_smiles, save_path, kekuleSmiles=True):
    words = [' ']
    for smi in tqdm(all_smiles):
        spt = split_smiles(smi, kekuleSmiles=kekuleSmiles)
        if spt is None:
            continue
        for w in spt:
            if w in words:
                continue
            else:
                words.append(w)
    with open(save_path, 'w') as js:
        json.dump(words, js)
    return words

def one_hot_coding(smi, words, kekuleSmiles=True, max_len=1000):
    coord_j = []
    coord_k = []
    spt = split_smiles(smi, kekuleSmiles=kekuleSmiles)
    if spt is None:
        return None
    for j,w in enumerate(spt):
        if j >= max_len:
            break
        try:
            k = words.index(w)
        except:
            continue
        coord_j.append(j)
        coord_k.append(k)
    data = np.repeat(1, len(coord_j))
    output = sparse.csr_matrix((data, (coord_j, coord_k)), shape=(max_len, len(words)))
    return output
def split_dataset(dataset, ratio):
    """Shuffle and split a dataset."""
   # np.random.seed(111)  # fix the seed for shuffle.
    #np.random.shuffle(dataset)
    n = int(ratio * len(dataset))
    return dataset[:n], dataset[n:]
def plot_confusion_matrix(cm, savename, title='Confusion Matrix'):

    plt.figure(figsize=(12, 8), dpi=100)
    np.set_printoptions(precision=2)
 
    ind_array = [np.arange(3)]
    x, y = np.meshgrid(ind_array, ind_array)
    for x_val, y_val in zip(x.flatten(), y.flatten()):
        c = cm[y_val][x_val]
        if c > 0.001:
            plt.text(x_val, y_val, "%0.2f" % (c,), color='red', fontsize=15, va='center', ha='center')
    
    plt.imshow(cm, interpolation='nearest', cmap=plt.cm.binary)
    plt.title(title)
    plt.colorbar()
    xlocations = np.array(range(len(classes)))
    plt.xticks(xlocations, classes, rotation=90)
    plt.yticks(xlocations, classes)
    plt.ylabel('Actual label')
    plt.xlabel('Predict label')
    
    # offset the tick
    tick_marks = np.array(range(len(classes))) + 0.5
    plt.gca().set_xticks(tick_marks, minor=True)
    plt.gca().set_yticks(tick_marks, minor=True)
    plt.gca().xaxis.set_ticks_position('none')
    plt.gca().yaxis.set_ticks_position('none')
    plt.grid(True, which='minor', linestyle='-')
    plt.gcf().subplots_adjust(bottom=0.15)
    
    # show confusion matrix
    plt.savefig(savename, format='png')
    plt.show()
def main(sm):
        with open("dict.json", "r", encoding="utf-8") as f:
            words = json.load(f)
 
        inchis = list([sm])
        rts = list([0])
        
        smiles, targets = [], []
        for i, inc in enumerate(tqdm(inchis)):
            mol = Chem.MolFromSmiles(inc)
            if mol is None:
                continue
            else:
                smi = Chem.MolToSmiles(mol)
                smiles.append(smi)
                targets.append(rts[i])
                
       
        
        features = []
        for i, smi in enumerate(tqdm(smiles)):
            xi = one_hot_coding(smi, words, max_len=600)
            if xi is not None:
                features.append(xi.todense())
        features = np.asarray(features)
        targets = np.asarray(targets)
        X_test=features
        Y_test=targets
        n_features=10
        
        model = RandomForestRegressor(n_estimators=100,  criterion='friedman_mse', max_depth=None, min_samples_split=2, min_samples_leaf=1, min_weight_fraction_leaf=0.0, max_features=1.0, max_leaf_nodes=None, min_impurity_decrease=0.0, bootstrap=True, oob_score=False, n_jobs=None, random_state=None, verbose=0, warm_start=False, ccp_alpha=0.0, max_samples=None)
       
        from tensorflow.keras import backend as K
        
        load_model = pickle.load(open(r"predict.dat","rb"))

     #   model = load_model('C:/Users/sunjinyu/Desktop/FingerID Reference/drug-likeness/CNN/single_model.h5')
        Y_predict = load_model.predict(K.cast_to_floatx(X_test).reshape((np.size(X_test,0),np.size(X_test,1)*np.size(X_test,2))))
         #Y_predict = model.predict(X_test) 
        x = list(Y_test)
        y = list(Y_predict)
       
        return Y_predict
        
def edit_dataset(drug,non_drug,task):
  #  np.random.seed(111)  # fix the seed for shuffle.

#    np.random.shuffle(non_drug)
    non_drug=non_drug[0:len(drug)]
       

      #  np.random.shuffle(non_drug)
   # np.random.shuffle(drug)
    dataset_train_drug, dataset_test_drug = split_dataset(drug, 0.9)
   # dataset_train_drug,dataset_dev_drug =  split_dataset(dataset_train_drug, 0.9)
    dataset_train_no, dataset_test_no = split_dataset(non_drug, 0.9)
   # dataset_train_no,dataset_dev_no =  split_dataset(dataset_train_no, 0.9)
    dataset_train =  pd.concat([dataset_train_drug,dataset_train_no], axis=0)
    dataset_test=pd.concat([ dataset_test_drug,dataset_test_no], axis=0)
  #  dataset_dev = dataset_dev_drug+dataset_dev_no
    return dataset_train, dataset_test