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import streamlit as st |
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import torch |
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import torch.nn as nn |
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import pickle |
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import numpy as np |
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import pandas as pd |
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from typing import List, Dict, Tuple, Optional |
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from rdkit import Chem |
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from rdkit.Chem import Draw, Descriptors |
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from rdkit import RDLogger |
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RDLogger.DisableLog('rdApp.*') |
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import matplotlib.pyplot as plt |
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import seaborn as sns |
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from PIL import Image |
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import warnings |
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warnings.filterwarnings('ignore') |
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sns.set_style('whitegrid') |
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import torch.nn.functional as F |
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from torch.nn import Linear, Sequential, BatchNorm1d, ReLU |
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from torch_geometric.data import Data |
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from torch_geometric.nn import GCNConv, GINConv |
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from torch_geometric.nn import global_mean_pool, global_add_pool |
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@st.cache_resource |
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def load_vae_model(device): |
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with open('vae_vocab.pkl', 'rb') as f: |
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vocab = pickle.load(f) |
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vocab_size = len(vocab) |
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hidden_dim = 256 |
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latent_dim = 64 |
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class VAE(nn.Module): |
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def __init__(self, vocab_size: int, hidden_dim: int, latent_dim: int): |
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super(VAE, self).__init__() |
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self.vocab_size = vocab_size |
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self.hidden_dim = hidden_dim |
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self.latent_dim = latent_dim |
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self.encoder = nn.GRU(vocab_size, hidden_dim, batch_first=True) |
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self.fc_mu = nn.Linear(hidden_dim, latent_dim) |
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self.fc_logvar = nn.Linear(hidden_dim, latent_dim) |
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self.decoder = nn.GRU(vocab_size + latent_dim, hidden_dim, batch_first=True) |
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self.fc_output = nn.Linear(hidden_dim, vocab_size) |
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def encode(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]: |
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_, h = self.encoder(x) |
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h = h.squeeze(0) |
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return self.fc_mu(h), self.fc_logvar(h) |
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def reparameterize(self, mu: torch.Tensor, logvar: torch.Tensor) -> torch.Tensor: |
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std = torch.exp(0.5 * logvar) |
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eps = torch.randn_like(std) |
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return mu + eps * std |
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def decode(self, z: torch.Tensor, max_length: int) -> torch.Tensor: |
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batch_size = z.size(0) |
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h = torch.zeros(1, batch_size, self.hidden_dim).to(z.device) |
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x = torch.zeros(batch_size, 1, self.vocab_size).to(z.device) |
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x[:, 0, vocab['<']] = 1 |
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outputs = [] |
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for _ in range(max_length): |
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z_input = z.unsqueeze(1) |
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decoder_input = torch.cat([x, z_input], dim=2) |
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output, h = self.decoder(decoder_input, h) |
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output = self.fc_output(output) |
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outputs.append(output) |
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x = torch.softmax(output, dim=-1) |
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return torch.cat(outputs, dim=1) |
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def forward(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]: |
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mu, logvar = self.encode(x) |
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z = self.reparameterize(mu, logvar) |
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return self.decode(z, x.size(1)), mu, logvar |
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model = VAE(vocab_size, hidden_dim, latent_dim) |
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model.load_state_dict(torch.load('vae_model.pth', map_location=device)) |
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model.to(device) |
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model.eval() |
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return model, vocab |
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def generate_smiles_vae(model, vocab, num_samples=10, max_length=100): |
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model.eval() |
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inv_vocab = {v: k for k, v in vocab.items()} |
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generated_smiles = [] |
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device = next(model.parameters()).device |
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with torch.no_grad(): |
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for _ in range(num_samples): |
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z = torch.randn(1, model.latent_dim).to(device) |
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x = torch.zeros(1, 1, model.vocab_size).to(device) |
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x[0, 0, vocab['<']] = 1 |
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h = torch.zeros(1, 1, model.hidden_dim).to(device) |
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smiles = '' |
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for _ in range(max_length): |
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z_input = z.unsqueeze(1) |
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decoder_input = torch.cat([x, z_input], dim=2) |
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output, h = model.decoder(decoder_input, h) |
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output = model.fc_output(output) |
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probs = torch.softmax(output.squeeze(0), dim=-1) |
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next_char = torch.multinomial(probs, 1).item() |
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if next_char == vocab['>']: |
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break |
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smiles += inv_vocab.get(next_char, '') |
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x = torch.zeros(1, 1, model.vocab_size).to(device) |
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x[0, 0, next_char] = 1 |
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generated_smiles.append(smiles) |
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return generated_smiles |
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def enhanced_post_process_smiles(smiles: str) -> str: |
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smiles = smiles.replace('<', '').replace('>', '') |
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allowed_chars = set('CNOPSFIBrClcnops()[]=@+-#0123456789') |
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smiles = ''.join(c for c in smiles if c in allowed_chars) |
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open_count = smiles.count('(') |
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close_count = smiles.count(')') |
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if open_count > close_count: |
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smiles += ')' * (open_count - close_count) |
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elif close_count > open_count: |
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smiles = '(' * (close_count - open_count) + smiles |
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smiles = smiles.replace('==', '=') |
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for i in range(1, 10): |
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if smiles.count(str(i)) % 2 != 0: |
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smiles += str(i) |
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return smiles |
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def validate_and_correct_smiles(smiles: str) -> Tuple[bool, str]: |
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mol = Chem.MolFromSmiles(smiles) |
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if mol is not None: |
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try: |
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Chem.SanitizeMol(mol) |
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return True, Chem.MolToSmiles(mol, isomericSmiles=True) |
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except: |
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pass |
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return False, smiles |
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def analyze_molecules(smiles_list: List[str], training_smiles_set: set) -> Dict: |
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results = { |
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'total': len(smiles_list), |
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'valid': 0, |
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'invalid': 0, |
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'unique': 0, |
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'corrected': 0, |
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'novel': 0, |
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'valid_properties': [], |
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'novel_properties': [], |
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'invalid_smiles': [] |
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} |
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unique_smiles = set() |
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novel_smiles = set() |
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for smiles in smiles_list: |
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processed_smiles = enhanced_post_process_smiles(smiles) |
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is_valid, corrected_smiles = validate_and_correct_smiles(processed_smiles) |
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if is_valid: |
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results['valid'] += 1 |
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unique_smiles.add(corrected_smiles) |
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if corrected_smiles != processed_smiles: |
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results['corrected'] += 1 |
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mol = Chem.MolFromSmiles(corrected_smiles) |
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if mol: |
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props = { |
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'smiles': corrected_smiles, |
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'MolWt': Descriptors.ExactMolWt(mol), |
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'LogP': Descriptors.MolLogP(mol), |
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'NumHDonors': Descriptors.NumHDonors(mol), |
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'NumHAcceptors': Descriptors.NumHAcceptors(mol) |
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} |
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if corrected_smiles not in training_smiles_set: |
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novel_smiles.add(corrected_smiles) |
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results['novel'] += 1 |
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results['novel_properties'].append(props) |
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else: |
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results['valid_properties'].append(props) |
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else: |
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results['invalid'] += 1 |
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results['invalid_smiles'].append(smiles) |
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results['unique'] = len(unique_smiles) |
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return results |
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def visualize_molecules(smiles_list: List[str], n: int = 5) -> Optional[Image.Image]: |
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valid_mols = [] |
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for smiles in smiles_list: |
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smiles = smiles.strip().strip('<>').strip() |
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if not smiles: |
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continue |
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try: |
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mol = Chem.MolFromSmiles(smiles) |
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if mol is not None: |
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valid_mols.append(mol) |
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if len(valid_mols) == n: |
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break |
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except Exception: |
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continue |
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if not valid_mols: |
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return None |
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try: |
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img = Draw.MolsToGridImage( |
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valid_mols, |
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molsPerRow=min(3, len(valid_mols)), |
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subImgSize=(200, 200), |
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legends=[f"Mol {i+1}" for i in range(len(valid_mols))] |
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) |
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return img |
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except Exception: |
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return None |
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class GCN(torch.nn.Module): |
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"""Graph Convolutional Network class with 3 convolutional layers and a linear layer""" |
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def __init__(self, dim_h): |
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"""init method for GCN |
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Args: |
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dim_h (int): the dimension of hidden layers |
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""" |
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super().__init__() |
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self.conv1 = GCNConv(11, dim_h) |
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self.conv2 = GCNConv(dim_h, dim_h) |
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self.conv3 = GCNConv(dim_h, dim_h) |
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self.lin = torch.nn.Linear(dim_h, 1) |
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def forward(self, data): |
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e = data.edge_index |
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x = data.x |
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x = self.conv1(x, e) |
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x = x.relu() |
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x = self.conv2(x, e) |
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x = x.relu() |
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x = self.conv3(x, e) |
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x = global_mean_pool(x, data.batch) |
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x = F.dropout(x, p=0.5, training=self.training) |
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x = self.lin(x) |
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return x |
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class GIN(torch.nn.Module): |
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"""Graph Isomorphism Network class with 3 GINConv layers and 2 linear layers""" |
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def __init__(self, dim_h): |
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"""Initializing GIN class |
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Args: |
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dim_h (int): the dimension of hidden layers |
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""" |
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super(GIN, self).__init__() |
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nn1 = Sequential(Linear(11, dim_h), BatchNorm1d(dim_h), ReLU(), Linear(dim_h, dim_h), ReLU()) |
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self.conv1 = GINConv(nn1) |
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nn2 = Sequential(Linear(dim_h, dim_h), BatchNorm1d(dim_h), ReLU(), Linear(dim_h, dim_h), ReLU()) |
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self.conv2 = GINConv(nn2) |
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nn3 = Sequential(Linear(dim_h, dim_h), BatchNorm1d(dim_h), ReLU(), Linear(dim_h, dim_h), ReLU()) |
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self.conv3 = GINConv(nn3) |
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self.lin1 = Linear(dim_h, dim_h) |
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self.lin2 = Linear(dim_h, 1) |
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def forward(self, data): |
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x = data.x |
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edge_index = data.edge_index |
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batch = data.batch |
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h = self.conv1(x, edge_index) |
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h = h.relu() |
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h = self.conv2(h, edge_index) |
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h = h.relu() |
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h = self.conv3(h, edge_index) |
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h = global_add_pool(h, batch) |
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h = self.lin1(h) |
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h = h.relu() |
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h = F.dropout(h, p=0.5, training=self.training) |
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h = self.lin2(h) |
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return h |
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@st.cache_resource |
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def load_gnn_models(device): |
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gcn_model = GCN(dim_h=128) |
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gcn_model.load_state_dict(torch.load("GCN_model.pth", map_location=device)) |
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gcn_model.to(device) |
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gcn_model.eval() |
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gin_model = GIN(dim_h=64) |
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gin_model.load_state_dict(torch.load("GIN_model.pth", map_location=device)) |
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gin_model.to(device) |
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gin_model.eval() |
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return gcn_model, gin_model |
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@st.cache_resource |
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def load_data_norm(device): |
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data_norm = torch.load('data_norm.pth', map_location=device) |
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data_mean = data_norm['mean'] |
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data_std = data_norm['std'] |
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return data_mean, data_std |
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def smiles_to_data(smiles): |
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mol = Chem.MolFromSmiles(smiles) |
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if mol is None: |
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return None |
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atoms = mol.GetAtoms() |
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num_atoms = len(atoms) |
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atom_type_list = ['H', 'C', 'N', 'O', 'F'] |
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hybridization_list = [Chem.rdchem.HybridizationType.SP, Chem.rdchem.HybridizationType.SP2, Chem.rdchem.HybridizationType.SP3] |
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x = [] |
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for atom in atoms: |
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atom_type = atom.GetSymbol() |
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atom_type_feature = [int(atom_type == s) for s in atom_type_list] |
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degree = atom.GetDegree() |
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degree_feature = [degree / 4] |
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formal_charge = atom.GetFormalCharge() |
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formal_charge_feature = [formal_charge / 4] |
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is_aromatic = atom.GetIsAromatic() |
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aromatic_feature = [int(is_aromatic)] |
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hybridization = atom.GetHybridization() |
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hybridization_feature = [int(hybridization == hyb) for hyb in hybridization_list] |
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atom_feature = atom_type_feature + degree_feature + formal_charge_feature + aromatic_feature + hybridization_feature |
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x.append(atom_feature) |
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x = torch.tensor(x, dtype=torch.float) |
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edge_index = [] |
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for bond in mol.GetBonds(): |
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i = bond.GetBeginAtomIdx() |
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j = bond.GetEndAtomIdx() |
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edge_index.append([i, j]) |
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edge_index.append([j, i]) |
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edge_index = torch.tensor(edge_index, dtype=torch.long).t().contiguous() |
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batch = torch.zeros(num_atoms, dtype=torch.long) |
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data = Data(x=x, edge_index=edge_index, batch=batch) |
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return data |
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def main(): |
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st.set_page_config( |
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page_title="π§ͺ Molecule Generator and Property Predictor", |
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page_icon="π§ͺ", |
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layout="wide", |
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initial_sidebar_state="expanded", |
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) |
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st.title("π§ͺ Molecular Generation and Analysis using VAE and GNN") |
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st.markdown(""" |
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SMILES (Simplified Molecular Input Line Entry System) is a widely-used notation that encodes chemical structures into short, linear strings of characters. |
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This representation allows for the easy storage, transmission, and manipulation of molecular information in computational applications. |
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This application allows you to generate novel molecular SMILES structures using a Variational Autoencoder (VAE) model trained on the QM9 dataset. |
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You can also predict molecular properties using Graph Neural Network (GNN) models (GCN and GIN). |
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""") |
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if 'analysis' not in st.session_state: |
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st.session_state.analysis = None |
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if 'generated_smiles' not in st.session_state: |
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st.session_state.generated_smiles = [] |
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if 'vae_generated' not in st.session_state: |
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st.session_state.vae_generated = False |
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st.sidebar.title("π§ Configuration") |
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st.sidebar.markdown("Adjust the settings below to generate molecules or predict properties.") |
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@st.cache_data |
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def load_training_data(): |
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df = pd.read_csv("qm9.csv") |
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smiles_list_raw = df['smiles'].tolist() |
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smiles_list = [Chem.MolToSmiles(Chem.MolFromSmiles(s), isomericSmiles=True) for s in smiles_list_raw] |
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return set(smiles_list) |
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training_smiles_set = load_training_data() |
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device = torch.device("cuda" if torch.cuda.is_available() else "cpu") |
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st.sidebar.title("π Model Selection") |
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model_option = st.sidebar.selectbox("Choose a functionality", ("Generate Molecules (VAE)", "Predict Property (GNN)")) |
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if model_option == "Generate Molecules (VAE)": |
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num_samples = st.sidebar.slider("Number of Molecules to Generate", min_value=5, max_value=500, value=50, step=5) |
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seed = st.sidebar.number_input("Random Seed", value=42, step=1) |
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torch.manual_seed(seed) |
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np.random.seed(seed) |
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|
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if st.sidebar.button("π Generate Molecules"): |
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with st.spinner("Generating molecules..."): |
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model, vocab = load_vae_model(device) |
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generated_smiles = generate_smiles_vae(model, vocab, num_samples=num_samples) |
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analysis = analyze_molecules(generated_smiles, training_smiles_set) |
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st.session_state.generated_smiles = generated_smiles |
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st.session_state.analysis = analysis |
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st.session_state.vae_generated = True |
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|
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st.success("β
Molecule generation completed!") |
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st.subheader("Summary of Generated Molecules") |
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col1, col2, col3, col4 = st.columns(4) |
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col1.metric("Total Generated", analysis['total']) |
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col2.metric("Valid Molecules", f"{analysis['valid']} ({(analysis['valid']/analysis['total'])*100:.2f}%)") |
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col3.metric("Unique Molecules", f"{analysis['unique']} ({(analysis['unique']/analysis['total'])*100:.2f}%)") |
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col4.metric("Corrected Molecules", f"{analysis['corrected']} ({(analysis['corrected']/analysis['total'])*100:.2f}%)") |
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|
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col1, col2 = st.columns(2) |
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col1.metric("Novel Molecules", f"{analysis['novel']} ({(analysis['novel']/analysis['total'])*100:.2f}%)") |
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col2.metric("Invalid Molecules", f"{analysis['invalid']} ({(analysis['invalid']/analysis['total'])*100:.2f}%)") |
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|
|
|
|
if analysis['valid_properties'] or analysis['novel_properties']: |
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st.subheader("Properties of Generated Molecules") |
|
|
|
tab1, tab2 = st.tabs(["β
Valid Molecules", "π Novel Molecules"]) |
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with tab1: |
|
if analysis['valid_properties']: |
|
df_valid = pd.DataFrame(analysis['valid_properties']) |
|
st.dataframe(df_valid) |
|
|
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st.subheader("Sample Valid Molecules") |
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mol_image_valid = visualize_molecules([prop['smiles'] for prop in analysis['valid_properties']], n=9) |
|
if mol_image_valid: |
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st.image(mol_image_valid) |
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else: |
|
st.write("No valid molecules to display.") |
|
else: |
|
st.write("No valid molecules found.") |
|
|
|
with tab2: |
|
if analysis['novel_properties']: |
|
df_novel = pd.DataFrame(analysis['novel_properties']) |
|
st.dataframe(df_novel) |
|
|
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st.subheader("Sample Novel Molecules") |
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mol_image_novel = visualize_molecules([prop['smiles'] for prop in analysis['novel_properties']], n=9) |
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if mol_image_novel: |
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st.image(mol_image_novel) |
|
else: |
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st.write("No novel molecules to display.") |
|
else: |
|
st.write("No novel molecules found.") |
|
|
|
|
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st.subheader("Property Distributions") |
|
fig, axs = plt.subplots(2, 2, figsize=(14, 10)) |
|
if analysis['valid_properties']: |
|
sns.histplot(df_valid['MolWt'], bins=20, ax=axs[0, 0], kde=True, color='skyblue', label='Valid') |
|
if analysis['novel_properties']: |
|
sns.histplot(df_novel['MolWt'], bins=20, ax=axs[0, 0], kde=True, color='orange', label='Novel') |
|
axs[0, 0].set_title('Molecular Weight Distribution') |
|
axs[0, 0].legend() |
|
|
|
if analysis['valid_properties']: |
|
sns.histplot(df_valid['LogP'], bins=20, ax=axs[0, 1], kde=True, color='skyblue', label='Valid') |
|
if analysis['novel_properties']: |
|
sns.histplot(df_novel['LogP'], bins=20, ax=axs[0, 1], kde=True, color='orange', label='Novel') |
|
axs[0, 1].set_title('LogP Distribution') |
|
axs[0, 1].legend() |
|
|
|
if analysis['valid_properties']: |
|
sns.histplot(df_valid['NumHDonors'], bins=range(0, max(df_valid['NumHDonors'].max(), |
|
df_novel['NumHDonors'].max()) + 2), |
|
ax=axs[1, 0], kde=False, color='skyblue', label='Valid') |
|
if analysis['novel_properties']: |
|
sns.histplot(df_novel['NumHDonors'], bins=range(0, max(df_valid['NumHDonors'].max(), |
|
df_novel['NumHDonors'].max()) + 2), |
|
ax=axs[1, 0], kde=False, color='orange', label='Novel') |
|
axs[1, 0].set_title('Number of H Donors') |
|
axs[1, 0].legend() |
|
|
|
if analysis['valid_properties']: |
|
sns.histplot(df_valid['NumHAcceptors'], bins=range(0, max(df_valid['NumHAcceptors'].max(), |
|
df_novel['NumHAcceptors'].max()) + 2), |
|
ax=axs[1, 1], kde=False, color='skyblue', label='Valid') |
|
if analysis['novel_properties']: |
|
sns.histplot(df_novel['NumHAcceptors'], bins=range(0, max(df_valid['NumHAcceptors'].max(), |
|
df_novel['NumHAcceptors'].max()) + 2), |
|
ax=axs[1, 1], kde=False, color='orange', label='Novel') |
|
axs[1, 1].set_title('Number of H Acceptors') |
|
axs[1, 1].legend() |
|
|
|
plt.tight_layout() |
|
st.pyplot(fig) |
|
|
|
|
|
csv_valid = df_valid.to_csv(index=False).encode('utf-8') |
|
csv_novel = df_novel.to_csv(index=False).encode('utf-8') |
|
col1, col2 = st.columns(2) |
|
with col1: |
|
st.download_button( |
|
label="πΎ Download Valid Molecules CSV", |
|
data=csv_valid, |
|
file_name='valid_molecules.csv', |
|
mime='text/csv' |
|
) |
|
with col2: |
|
st.download_button( |
|
label="πΎ Download Novel Molecules CSV", |
|
data=csv_novel, |
|
file_name='novel_molecules.csv', |
|
mime='text/csv' |
|
) |
|
else: |
|
st.warning("No valid or novel molecules were generated.") |
|
|
|
elif model_option == "Predict Property (GNN)": |
|
|
|
with st.spinner("Loading GNN models..."): |
|
gcn_model, gin_model = load_gnn_models(device) |
|
|
|
data_mean, data_std = load_data_norm(device) |
|
|
|
|
|
gnn_model_option = st.sidebar.selectbox("Choose a GNN model", ("GCN", "GIN")) |
|
|
|
st.subheader("π Predict Molecular Property using GNN") |
|
st.markdown(""" |
|
Input a SMILES string to predict the dipole moment using the selected GNN model. |
|
""") |
|
|
|
|
|
user_smiles = st.text_input("Enter a SMILES string for property prediction:", "") |
|
|
|
if user_smiles: |
|
data = smiles_to_data(user_smiles) |
|
if data: |
|
data = data.to(device) |
|
if gnn_model_option == "GCN": |
|
prediction = gcn_model(data) |
|
prediction = prediction.item() |
|
elif gnn_model_option == "GIN": |
|
prediction = gin_model(data) |
|
prediction = prediction.item() |
|
|
|
prediction = prediction * data_std.item() + data_mean.item() |
|
st.success(f"**Predicted Dipole Moment ({gnn_model_option}):** {prediction:.4f}") |
|
|
|
mol = Chem.MolFromSmiles(user_smiles) |
|
if mol: |
|
st.subheader("Molecular Structure") |
|
st.image(Draw.MolToImage(mol, size=(300, 300))) |
|
else: |
|
st.error("β Invalid SMILES string.") |
|
|
|
st.markdown("---") |
|
st.markdown("### Or select a molecule from the generated molecules (if any).") |
|
|
|
|
|
if st.session_state.vae_generated and st.session_state.analysis is not None: |
|
|
|
all_properties = st.session_state.analysis['valid_properties'] + st.session_state.analysis['novel_properties'] |
|
if all_properties: |
|
smiles_options = [prop['smiles'] for prop in all_properties] |
|
selected_smiles = st.selectbox("Select a molecule", smiles_options) |
|
if selected_smiles: |
|
data = smiles_to_data(selected_smiles) |
|
if data: |
|
data = data.to(device) |
|
if gnn_model_option == "GCN": |
|
prediction = gcn_model(data) |
|
prediction = prediction.item() |
|
elif gnn_model_option == "GIN": |
|
prediction = gin_model(data) |
|
prediction = prediction.item() |
|
|
|
prediction = prediction * data_std.item() + data_mean.item() |
|
st.success(f"**Predicted Dipole Moment ({gnn_model_option}):** {prediction:.4f}") |
|
|
|
mol = Chem.MolFromSmiles(selected_smiles) |
|
if mol: |
|
st.subheader("Molecular Structure") |
|
st.image(Draw.MolToImage(mol, size=(300, 300))) |
|
else: |
|
st.error("β Invalid SMILES string.") |
|
else: |
|
st.info("π No valid or novel molecules available.") |
|
else: |
|
st.info("π No generated molecules available. Generate molecules using the VAE first.") |
|
|
|
|
|
st.sidebar.title("βΉοΈ About") |
|
st.sidebar.info(""" |
|
**Molecule Generator and Property Predictor App** |
|
|
|
This app uses a Variational Autoencoder (VAE) model and Graph Neural Networks (GNNs) to generate novel molecular structures and predict molecular properties. |
|
|
|
- **Developed by**: Arjun, Kaustubh, and Nachiket |
|
- **Hugging Face Repository**: https://huggingface.co/spaces/Raykarr/SMILES_Generation_and_Prediction |
|
""") |
|
|
|
|
|
hide_streamlit_style = """ |
|
<style> |
|
footer {visibility: hidden;} |
|
header {visibility: hidden;} |
|
</style> |
|
""" |
|
st.markdown(hide_streamlit_style, unsafe_allow_html=True) |
|
|
|
|
|
if __name__ == "__main__": |
|
main() |
|
|