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preprocesses_version_0_3_highcv.py
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preprocesses_version_0_3_highcv.py
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# -*- coding: utf-8 -*-
"""Preprocesses_version_0.3.ipynb
Automatically generated by Colaboratory.
Original file is located at
https://colab.research.google.com/drive/1CZ6IzuoRDFqLJubXSCFoYaXjfikFBwIR
"""
# Task:
# Turn data into "images"
# Two networks
# GAN: generate atoms and bonds (adjacency) layers
# simple CNN: turning SMILES layer to atoms+bonds layers
import warnings
warnings.filterwarnings('ignore')
import numpy as np
import pandas as pd
from numpy import ndarray
from sklearn.feature_extraction.text import CountVectorizer, TfidfVectorizer
from tensorflow.keras.preprocessing.text import Tokenizer
from tensorflow.keras.preprocessing.sequence import pad_sequences
from tensorflow.keras.utils import to_categorical
import pickle
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.decomposition import PCA, TruncatedSVD
from sklearn.preprocessing import StandardScaler
# loading SMILES data using Chainer Chemistry
from chainer_chemistry.datasets.molnet import get_molnet_dataset
from chainer_chemistry.datasets.numpy_tuple_dataset import NumpyTupleDataset
from chainer_chemistry.dataset.preprocessors import GGNNPreprocessor
from rdkit import Chem
"""Chem.MolFromSmiles('CC1CC(O)C2(CC2)O1')"""
preprocessor = GGNNPreprocessor()
"""
data = get_molnet_dataset('qm9',
labels = 'cv',
preprocessor = preprocessor,
return_smiles = True,
frac_train = 1.0,
frac_valid = 0.0,
frac_test = 0.0
)
"""
with open('./../data/trainingsets/Data.pickle', 'rb') as f:
data = pickle.load (f)
X_smiles = []
SMILES = []
X_atoms = []
X_bonds = []
y = []
atom_lengths = []
atom_max = []
bonds_lengths = []
for smiles in data['smiles'][0]:
SMILES.append(smiles)
smiles += '.'
X_smiles.append(smiles)
for d in data['dataset'][0]:
X_atoms.append(d[0])
X_bonds.append(d[1])
atom_lengths.append(len(d[0]))
atom_max.append(np.max(d[0]))
bonds_lengths.append(d[1].shape[1])
y.append(d[2])
with open('database_SMILES.pickle', 'wb') as f:
pickle.dump((X_smiles, X_atoms, X_bonds, y), f)
MAX_NB_WORDS = 23
MAX_SEQUENCE_LENGTH = 35
tokenizer = Tokenizer(num_words = MAX_NB_WORDS,
char_level = True,
filters = '',
lower = False)
tokenizer.fit_on_texts(X_smiles)
X_smiles = tokenizer.texts_to_sequences(X_smiles)
X_smiles = pad_sequences(X_smiles,
maxlen = MAX_SEQUENCE_LENGTH,
padding = 'post')
X_smiles = to_categorical(X_smiles)
atom_max = np.max(atom_max)
bonds_max = np.max(bonds_lengths)
X_atoms_ = []
for atom in X_atoms:
if len(atom) < atom_max:
pad_len = atom_max - len(atom)
atom = np.pad(atom, (0, pad_len))
X_atoms_.append(atom)
X_atoms = np.asarray(X_atoms_)
X_atoms = to_categorical(X_atoms)
X_bonds_ = []
for bond in X_bonds:
if bond.shape[1] < bonds_max:
pad_len = bonds_max - bond.shape[1]
bond = np.pad(bond, ((0,0),(0,pad_len),(0,pad_len)))
X_bonds_.append(bond)
X_bonds = np.asarray(X_bonds_)
SHAPE = list(X_smiles.shape) + [1]
X_smiles = X_smiles.reshape(SHAPE)
y = np.asarray(y).reshape([-1])
SHAPE = list(X_atoms.shape) + [1]
X_atoms = X_atoms.reshape(SHAPE)
X_bonds = X_bonds.transpose([0,2,3,1])
####
# ANALYSIS
sns.distplot(y);
####
SMILES = np.asarray(SMILES)
# TRAIN/VAL split
np.random.seed(0)
idx = np.random.choice(len(y), int(len(y) * 0.2), replace = False)
train_idx = np.setdiff1d(np.arange(len(y)), idx)
X_smiles_test, SMILES_test, X_atoms_test, X_bonds_test, y_test = X_smiles[idx], SMILES[idx],X_atoms[idx], X_bonds[idx], y[idx]
X_smiles_train, SMILES_train, X_atoms_train, X_bonds_train, y_train = X_smiles[train_idx], SMILES[train_idx],X_atoms[train_idx], X_bonds[train_idx], y[train_idx]
####
# ANALYSIS
X_atoms_train_ = X_atoms_train.reshape([X_atoms_train.shape[0],
9 * 10])
X_bonds_train_ = X_bonds_train.reshape([X_bonds_train.shape[0],
9 * 9 * 4])
X_atoms_test_ = X_atoms_test.reshape([X_atoms_test.shape[0],
9 * 10])
X_bonds_test_ = X_bonds_test.reshape([X_bonds_test.shape[0],
9 * 9 * 4])
pca_1 = PCA()
X_atoms_train_ = pca_1.fit_transform(X_atoms_train_)
X_atoms_test_ = pca_1.transform(X_atoms_test_)
pca_2 = PCA()
X_bonds_train_ = pca_2.fit_transform(X_bonds_train_)
X_bonds_test_ = pca_2.transform(X_bonds_test_)
# Atoms Distribution
plt.scatter(X_atoms_train_[:,0], X_atoms_train_[:,1], alpha = 0.3, c = 'blue');
plt.scatter(X_atoms_test_[:,0], X_atoms_test_[:,1], alpha = 0.3, c = 'red');
####
# Bonds Distribution
plt.scatter(X_bonds_train_[:,0], X_bonds_train_[:,1], alpha = 0.3, c = 'blue');
plt.scatter(X_bonds_test_[:,0], X_bonds_test_[:,1], alpha = 0.3, c = 'red');
print ('length of general samples', len(y_train))
idx = np.where(y_train > 42)[0]
X_smiles_train, X_atoms_train, X_bonds_train, y_train = (X_smiles_train[idx],
X_atoms_train[idx],
X_bonds_train[idx],
y_train[idx])
idx = np.where(y_test > 42)[0]
X_smiles_test, X_atoms_test, X_bonds_test, y_test = (X_smiles_test[idx],
X_atoms_test[idx],
X_bonds_test[idx],
y_test[idx])
idx = np.where(y > 42)[0]
X_smiles, X_atoms, X_bonds, y = (X_smiles[idx],
X_atoms[idx],
X_bonds[idx],
y[idx])
"""
# subsampling
idx = np.random.choice(len(y_train), int(len(y_train) * 0.6), replace = False)
X_smiles_train, SMILES_train, X_atoms_train, X_bonds_train, y_train = (X_smiles_train[idx], SMILES_train[idx],
X_atoms_train[idx],
X_bonds_train[idx],
y_train[idx])
idx = np.random.choice(len(y_test), int(len(y_test) * 0.35), replace = False)
X_smiles_test, SMILES_test, X_atoms_test, X_bonds_test, y_test = (X_smiles_test[idx], SMILES_test[idx],
X_atoms_test[idx],
X_bonds_test[idx],
y_test[idx])
"""
print (len(y_train))
print (len(y_test))
print (len(y))
with open('./../data/trainingsets/highcv_qm9/image_train.pickle', 'wb') as f:
pickle.dump((X_smiles_train, SMILES_train, X_atoms_train, X_bonds_train, y_train), f)
with open('./../data/trainingsets/highcv_qm9/image_test.pickle', 'wb') as f:
pickle.dump((X_smiles_test, SMILES_test, X_atoms_test, X_bonds_test, y_test), f)
with open('./../data/trainingsets/highcv_qm9/train_GAN.pickle', 'wb') as f:
pickle.dump((X_smiles, SMILES, X_atoms, X_bonds, y), f)
with open('tokenizer.pickle', 'wb') as f:
pickle.dump(tokenizer.index_word, f)
"""
with open('database.pickle', 'wb') as f:
pickle.dump((X_smiles, X_atoms, X_bonds, y), f)
"""