import streamlit as st import torch import torch.nn as nn import pickle import numpy as np import pandas as pd from typing import List, Dict, Tuple, Optional # RDKit for molecule handling from rdkit import Chem from rdkit.Chem import Draw, Descriptors from rdkit import RDLogger RDLogger.DisableLog('rdApp.*') # Visualization libraries import matplotlib.pyplot as plt import seaborn as sns # For generating images in Streamlit from PIL import Image # Suppress warnings in RDKit import warnings warnings.filterwarnings('ignore') # Set Seaborn style sns.set_style('whitegrid') # Additional imports for GNN import torch.nn.functional as F from torch.nn import Linear, Sequential, BatchNorm1d, ReLU from torch_geometric.data import Data from torch_geometric.nn import GCNConv, GINConv from torch_geometric.nn import global_mean_pool, global_add_pool # Function to load the VAE model @st.cache_resource def load_vae_model(device): # Load the vocabulary with open('vae_vocab.pkl', 'rb') as f: vocab = pickle.load(f) vocab_size = len(vocab) # Initialize the model with the same parameters hidden_dim = 256 # Ensure this matches your trained model latent_dim = 64 # Ensure this matches your trained model # Define the VAE class (same as in your training script) class VAE(nn.Module): def __init__(self, vocab_size: int, hidden_dim: int, latent_dim: int): super(VAE, self).__init__() self.vocab_size = vocab_size self.hidden_dim = hidden_dim self.latent_dim = latent_dim self.encoder = nn.GRU(vocab_size, hidden_dim, batch_first=True) self.fc_mu = nn.Linear(hidden_dim, latent_dim) self.fc_logvar = nn.Linear(hidden_dim, latent_dim) self.decoder = nn.GRU(vocab_size + latent_dim, hidden_dim, batch_first=True) self.fc_output = nn.Linear(hidden_dim, vocab_size) def encode(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]: _, h = self.encoder(x) h = h.squeeze(0) return self.fc_mu(h), self.fc_logvar(h) def reparameterize(self, mu: torch.Tensor, logvar: torch.Tensor) -> torch.Tensor: std = torch.exp(0.5 * logvar) eps = torch.randn_like(std) return mu + eps * std def decode(self, z: torch.Tensor, max_length: int) -> torch.Tensor: batch_size = z.size(0) h = torch.zeros(1, batch_size, self.hidden_dim).to(z.device) x = torch.zeros(batch_size, 1, self.vocab_size).to(z.device) x[:, 0, vocab['<']] = 1 # Start token outputs = [] for _ in range(max_length): z_input = z.unsqueeze(1) decoder_input = torch.cat([x, z_input], dim=2) output, h = self.decoder(decoder_input, h) output = self.fc_output(output) outputs.append(output) x = torch.softmax(output, dim=-1) return torch.cat(outputs, dim=1) def forward(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor, torch.Tensor]: mu, logvar = self.encode(x) z = self.reparameterize(mu, logvar) return self.decode(z, x.size(1)), mu, logvar model = VAE(vocab_size, hidden_dim, latent_dim) model.load_state_dict(torch.load('vae_model.pth', map_location=device)) model.to(device) model.eval() return model, vocab # Function to generate molecules using VAE def generate_smiles_vae(model, vocab, num_samples=10, max_length=100): model.eval() inv_vocab = {v: k for k, v in vocab.items()} generated_smiles = [] device = next(model.parameters()).device with torch.no_grad(): for _ in range(num_samples): z = torch.randn(1, model.latent_dim).to(device) x = torch.zeros(1, 1, model.vocab_size).to(device) x[0, 0, vocab['<']] = 1 h = torch.zeros(1, 1, model.hidden_dim).to(device) smiles = '' for _ in range(max_length): z_input = z.unsqueeze(1) decoder_input = torch.cat([x, z_input], dim=2) output, h = model.decoder(decoder_input, h) output = model.fc_output(output) probs = torch.softmax(output.squeeze(0), dim=-1) next_char = torch.multinomial(probs, 1).item() if next_char == vocab['>']: break smiles += inv_vocab.get(next_char, '') x = torch.zeros(1, 1, model.vocab_size).to(device) x[0, 0, next_char] = 1 generated_smiles.append(smiles) return generated_smiles # Function to post-process and validate SMILES strings def enhanced_post_process_smiles(smiles: str) -> str: smiles = smiles.replace('<', '').replace('>', '') allowed_chars = set('CNOPSFIBrClcnops()[]=@+-#0123456789') smiles = ''.join(c for c in smiles if c in allowed_chars) # Balance parentheses open_count = smiles.count('(') close_count = smiles.count(')') if open_count > close_count: smiles += ')' * (open_count - close_count) elif close_count > open_count: smiles = '(' * (close_count - open_count) + smiles # Replace invalid double bonds smiles = smiles.replace('==', '=') # Attempt to close unclosed rings for i in range(1, 10): if smiles.count(str(i)) % 2 != 0: smiles += str(i) return smiles def validate_and_correct_smiles(smiles: str) -> Tuple[bool, str]: mol = Chem.MolFromSmiles(smiles) if mol is not None: try: Chem.SanitizeMol(mol) return True, Chem.MolToSmiles(mol, isomericSmiles=True) except: pass return False, smiles # Function to analyze molecules def analyze_molecules(smiles_list: List[str], training_smiles_set: set) -> Dict: results = { 'total': len(smiles_list), 'valid': 0, 'invalid': 0, 'unique': 0, 'corrected': 0, 'novel': 0, 'valid_properties': [], 'novel_properties': [], 'invalid_smiles': [] } unique_smiles = set() novel_smiles = set() for smiles in smiles_list: processed_smiles = enhanced_post_process_smiles(smiles) is_valid, corrected_smiles = validate_and_correct_smiles(processed_smiles) if is_valid: results['valid'] += 1 unique_smiles.add(corrected_smiles) if corrected_smiles != processed_smiles: results['corrected'] += 1 mol = Chem.MolFromSmiles(corrected_smiles) if mol: props = { 'smiles': corrected_smiles, 'MolWt': Descriptors.ExactMolWt(mol), 'LogP': Descriptors.MolLogP(mol), 'NumHDonors': Descriptors.NumHDonors(mol), 'NumHAcceptors': Descriptors.NumHAcceptors(mol) } if corrected_smiles not in training_smiles_set: novel_smiles.add(corrected_smiles) results['novel'] += 1 results['novel_properties'].append(props) else: results['valid_properties'].append(props) else: results['invalid'] += 1 results['invalid_smiles'].append(smiles) results['unique'] = len(unique_smiles) return results # Function to visualize molecules def visualize_molecules(smiles_list: List[str], n: int = 5) -> Optional[Image.Image]: valid_mols = [] for smiles in smiles_list: smiles = smiles.strip().strip('<>').strip() if not smiles: continue try: mol = Chem.MolFromSmiles(smiles) if mol is not None: valid_mols.append(mol) if len(valid_mols) == n: break except Exception: continue if not valid_mols: return None try: img = Draw.MolsToGridImage( valid_mols, molsPerRow=min(3, len(valid_mols)), subImgSize=(200, 200), legends=[f"Mol {i+1}" for i in range(len(valid_mols))] ) return img except Exception: return None # GCN and GIN model definitions class GCN(torch.nn.Module): """Graph Convolutional Network class with 3 convolutional layers and a linear layer""" def __init__(self, dim_h): """init method for GCN Args: dim_h (int): the dimension of hidden layers """ super().__init__() self.conv1 = GCNConv(11, dim_h) self.conv2 = GCNConv(dim_h, dim_h) self.conv3 = GCNConv(dim_h, dim_h) self.lin = torch.nn.Linear(dim_h, 1) def forward(self, data): e = data.edge_index x = data.x x = self.conv1(x, e) x = x.relu() x = self.conv2(x, e) x = x.relu() x = self.conv3(x, e) x = global_mean_pool(x, data.batch) x = F.dropout(x, p=0.5, training=self.training) x = self.lin(x) return x class GIN(torch.nn.Module): """Graph Isomorphism Network class with 3 GINConv layers and 2 linear layers""" def __init__(self, dim_h): """Initializing GIN class Args: dim_h (int): the dimension of hidden layers """ super(GIN, self).__init__() nn1 = Sequential(Linear(11, dim_h), BatchNorm1d(dim_h), ReLU(), Linear(dim_h, dim_h), ReLU()) self.conv1 = GINConv(nn1) nn2 = Sequential(Linear(dim_h, dim_h), BatchNorm1d(dim_h), ReLU(), Linear(dim_h, dim_h), ReLU()) self.conv2 = GINConv(nn2) nn3 = Sequential(Linear(dim_h, dim_h), BatchNorm1d(dim_h), ReLU(), Linear(dim_h, dim_h), ReLU()) self.conv3 = GINConv(nn3) self.lin1 = Linear(dim_h, dim_h) self.lin2 = Linear(dim_h, 1) def forward(self, data): x = data.x edge_index = data.edge_index batch = data.batch # Node embeddings h = self.conv1(x, edge_index) h = h.relu() h = self.conv2(h, edge_index) h = h.relu() h = self.conv3(h, edge_index) # Graph-level readout h = global_add_pool(h, batch) h = self.lin1(h) h = h.relu() h = F.dropout(h, p=0.5, training=self.training) h = self.lin2(h) return h # Function to load GNN models @st.cache_resource def load_gnn_models(device): # Load GCN model gcn_model = GCN(dim_h=128) gcn_model.load_state_dict(torch.load("GCN_model.pth", map_location=device)) gcn_model.to(device) gcn_model.eval() # Load GIN model gin_model = GIN(dim_h=64) gin_model.load_state_dict(torch.load("GIN_model.pth", map_location=device)) gin_model.to(device) gin_model.eval() return gcn_model, gin_model # Function to load normalization parameters @st.cache_resource def load_data_norm(device): data_norm = torch.load('data_norm.pth', map_location=device) data_mean = data_norm['mean'] data_std = data_norm['std'] return data_mean, data_std # Function to convert SMILES to Data object def smiles_to_data(smiles): mol = Chem.MolFromSmiles(smiles) if mol is None: return None atoms = mol.GetAtoms() num_atoms = len(atoms) atom_type_list = ['H', 'C', 'N', 'O', 'F'] hybridization_list = [Chem.rdchem.HybridizationType.SP, Chem.rdchem.HybridizationType.SP2, Chem.rdchem.HybridizationType.SP3] x = [] for atom in atoms: atom_type = atom.GetSymbol() atom_type_feature = [int(atom_type == s) for s in atom_type_list] # 5 features # Atom degree (scalar between 0 and 4) degree = atom.GetDegree() degree_feature = [degree / 4] # Normalize degree to [0,1] # 1 feature # Formal charge formal_charge = atom.GetFormalCharge() formal_charge_feature = [formal_charge / 4] # Assume max formal charge is 4 # 1 feature # Aromaticity is_aromatic = atom.GetIsAromatic() aromatic_feature = [int(is_aromatic)] # 1 feature # Hybridization hybridization = atom.GetHybridization() hybridization_feature = [int(hybridization == hyb) for hyb in hybridization_list] # 3 features # Total features: 5 + 1 +1 +1 +3 = 11 atom_feature = atom_type_feature + degree_feature + formal_charge_feature + aromatic_feature + hybridization_feature x.append(atom_feature) x = torch.tensor(x, dtype=torch.float) # Build edge indices edge_index = [] for bond in mol.GetBonds(): i = bond.GetBeginAtomIdx() j = bond.GetEndAtomIdx() edge_index.append([i, j]) edge_index.append([j, i]) # Since it's undirected edge_index = torch.tensor(edge_index, dtype=torch.long).t().contiguous() # Build batch tensor (since batch size is 1) batch = torch.zeros(num_atoms, dtype=torch.long) # Build Data object data = Data(x=x, edge_index=edge_index, batch=batch) return data # Streamlit app def main(): st.set_page_config( page_title="๐Ÿงช Molecule Generator and Property Predictor", page_icon="๐Ÿงช", layout="wide", initial_sidebar_state="expanded", ) # Main Title and Description st.title("๐Ÿงช Molecular Generation and Analysis using VAE and GNN") st.markdown(""" SMILES (Simplified Molecular Input Line Entry System) is a widely-used notation that encodes chemical structures into short, linear strings of characters. This representation allows for the easy storage, transmission, and manipulation of molecular information in computational applications. This application allows you to generate novel molecular SMILES structures using a Variational Autoencoder (VAE) model trained on the QM9 dataset. You can also predict molecular properties using Graph Neural Network (GNN) models (GCN and GIN). """) # Initialize session state variables if 'analysis' not in st.session_state: st.session_state.analysis = None if 'generated_smiles' not in st.session_state: st.session_state.generated_smiles = [] if 'vae_generated' not in st.session_state: st.session_state.vae_generated = False # Sidebar configuration st.sidebar.title("๐Ÿ”ง Configuration") st.sidebar.markdown("Adjust the settings below to generate molecules or predict properties.") # Load training data and canonicalize SMILES @st.cache_data def load_training_data(): df = pd.read_csv("qm9.csv") smiles_list_raw = df['smiles'].tolist() # Canonicalize SMILES for accurate comparison smiles_list = [Chem.MolToSmiles(Chem.MolFromSmiles(s), isomericSmiles=True) for s in smiles_list_raw] return set(smiles_list) training_smiles_set = load_training_data() # Device selection device = torch.device("cuda" if torch.cuda.is_available() else "cpu") # Model selection st.sidebar.title("๐Ÿ“Œ Model Selection") model_option = st.sidebar.selectbox("Choose a functionality", ("Generate Molecules (VAE)", "Predict Property (GNN)")) if model_option == "Generate Molecules (VAE)": # Number of samples num_samples = st.sidebar.slider("Number of Molecules to Generate", min_value=5, max_value=500, value=50, step=5) # Random seed seed = st.sidebar.number_input("Random Seed", value=42, step=1) torch.manual_seed(seed) np.random.seed(seed) if st.sidebar.button("๐Ÿš€ Generate Molecules"): with st.spinner("Generating molecules..."): # Load VAE model model, vocab = load_vae_model(device) generated_smiles = generate_smiles_vae(model, vocab, num_samples=num_samples) # Analyze molecules analysis = analyze_molecules(generated_smiles, training_smiles_set) # Store results in session state st.session_state.generated_smiles = generated_smiles st.session_state.analysis = analysis st.session_state.vae_generated = True # Display summary st.success("โœ… Molecule generation completed!") st.subheader("Summary of Generated Molecules") col1, col2, col3, col4 = st.columns(4) col1.metric("Total Generated", analysis['total']) col2.metric("Valid Molecules", f"{analysis['valid']} ({(analysis['valid']/analysis['total'])*100:.2f}%)") col3.metric("Unique Molecules", f"{analysis['unique']} ({(analysis['unique']/analysis['total'])*100:.2f}%)") col4.metric("Corrected Molecules", f"{analysis['corrected']} ({(analysis['corrected']/analysis['total'])*100:.2f}%)") col1, col2 = st.columns(2) col1.metric("Novel Molecules", f"{analysis['novel']} ({(analysis['novel']/analysis['total'])*100:.2f}%)") col2.metric("Invalid Molecules", f"{analysis['invalid']} ({(analysis['invalid']/analysis['total'])*100:.2f}%)") # Display properties if analysis['valid_properties'] or analysis['novel_properties']: st.subheader("Properties of Generated Molecules") tab1, tab2 = st.tabs(["โœ… Valid Molecules", "๐ŸŒŸ Novel Molecules"]) with tab1: if analysis['valid_properties']: df_valid = pd.DataFrame(analysis['valid_properties']) st.dataframe(df_valid) # Visualize valid molecules (limit to 9 for performance) st.subheader("Sample Valid Molecules") mol_image_valid = visualize_molecules([prop['smiles'] for prop in analysis['valid_properties']], n=9) if mol_image_valid: st.image(mol_image_valid) 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) # Visualize novel molecules (limit to 9 for performance) st.subheader("Sample Novel Molecules") mol_image_novel = visualize_molecules([prop['smiles'] for prop in analysis['novel_properties']], n=9) if mol_image_novel: st.image(mol_image_novel) else: st.write("No novel molecules to display.") else: st.write("No novel molecules found.") # Property distributions 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) # Download options 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="๐Ÿ’พ Download Valid Molecules CSV", data=csv_valid, file_name='valid_molecules.csv', mime='text/csv' ) with col2: st.download_button( label="๐Ÿ’พ 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)": # Load GNN models with st.spinner("Loading GNN models..."): gcn_model, gin_model = load_gnn_models(device) # Load normalization parameters data_mean, data_std = load_data_norm(device) # GNN Model selection gnn_model_option = st.sidebar.selectbox("Choose a GNN model", ("GCN", "GIN")) st.subheader("๐Ÿ” Predict Molecular Property using GNN") st.markdown(""" Input a SMILES string to predict the dipole moment using the selected GNN model. """) # User inputs a SMILES string 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() # Unnormalize the prediction prediction = prediction * data_std.item() + data_mean.item() st.success(f"**Predicted Dipole Moment ({gnn_model_option}):** {prediction:.4f}") # Display molecule mol = Chem.MolFromSmiles(user_smiles) if mol: st.subheader("Molecular Structure") st.image(Draw.MolToImage(mol, size=(300, 300))) else: st.error("โŒ Invalid SMILES string.") st.markdown("---") st.markdown("### Or select a molecule from the generated molecules (if any).") # Check if molecules have been generated if st.session_state.vae_generated and st.session_state.analysis is not None: # Combine valid and novel properties 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() # Unnormalize the prediction prediction = prediction * data_std.item() + data_mean.item() st.success(f"**Predicted Dipole Moment ({gnn_model_option}):** {prediction:.4f}") # Display molecule mol = Chem.MolFromSmiles(selected_smiles) if mol: st.subheader("Molecular Structure") st.image(Draw.MolToImage(mol, size=(300, 300))) else: st.error("โŒ Invalid SMILES string.") else: st.info("๐Ÿ” No valid or novel molecules available.") else: st.info("๐Ÿ” No generated molecules available. Generate molecules using the VAE first.") # About section st.sidebar.title("โ„น๏ธ 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 footer and header hide_streamlit_style = """ """ st.markdown(hide_streamlit_style, unsafe_allow_html=True) # Run the app if __name__ == "__main__": main()