app.py

import os
import time
import requests
import numpy as np
from flask import Flask, render_template, request, send_file
from rdkit import Chem
from transformers import AutoModelForMaskedLM, AutoTokenizer
from modelstrc import CVanilla_RNN_Builder, get_mol_from_graph_list
from transformers import AutoModel, AutoTokenizer
import torch
import re
import torch.nn as nn



# DIRECTORIES
bio_model_dir = "/app/modelsBioembedSmall"  
cvn_model_dir = "/app/models_folder"
UPLOAD_FOLDER = "/app/Samples"
UF="/tmp/"

os.makedirs(bio_model_dir, exist_ok=True)
os.makedirs(cvn_model_dir, exist_ok=True)
os.makedirs(UPLOAD_FOLDER, exist_ok=True)

# ENV VARIABLES
os.environ["TMPDIR"] = bio_model_dir
os.environ["TEMP"] = bio_model_dir
os.environ["TMP"] = bio_model_dir
os.environ['NUMBA_CACHE_DIR'] = '/app/numba_cache'
os.environ['TRANSFORMERS_CACHE'] = '/app/hf_cache'


# ESM2 MODEL AND TOKENIZER
try:
    print("Loading ESM2 model...")
    model_name = "facebook/esm2_t6_8M_UR50D"  # Smaller model with 320-dim embedding

    tokenizer = AutoTokenizer.from_pretrained(bio_model_dir)
    model = AutoModel.from_pretrained(bio_model_dir)
    model.eval()
    print("ESM2 model loaded.")
except Exception as e:
    print(f"Error loading ESM2 model: {e}")
    model = None
    tokenizer = None

# linear transformation to map 320D embeddings to 1024D
class EmbeddingTransformer(nn.Module):
    def __init__(self, input_dim, output_dim):
        super(EmbeddingTransformer, self).__init__()
        self.linear = nn.Linear(input_dim, output_dim)

    def forward(self, x):
        return self.linear(x)

transformer = EmbeddingTransformer(input_dim=320, output_dim=1024)

# UDF TO GENERATE EMBEDDINGS
def generate_bio_embeddings(sequence):
    """
    Generate protein sequence embeddings using ESM2 model.
    Maps the 320-dimensional embedding to 1024 dimensions.
    """
    if model is None or tokenizer is None:
        print("Model or tokenizer not loaded.")
        return None

    if not sequence:
        print("Sequence is empty after cleaning.")
        return None

    try:
        
        inputs = tokenizer(sequence, return_tensors="pt", add_special_tokens=True)
        
    
        with torch.no_grad():
            outputs = model(**inputs)

        embeddings = outputs.last_hidden_state  
        mean_embedding = embeddings.mean(dim=1).squeeze()  

    
        transformed_embedding = transformer(mean_embedding)

        
        transformed_embedding = transformed_embedding.detach().numpy()
        
        return transformed_embedding.reshape(1, -1)
    
    except Exception as e:
        print(f"Embedding Error: {e}")
        return None


# UDF FOR SMILES GENERATION
def generate_smiles(sequence, n_samples=100):
    start_time = time.time()

    protein_embedding = generate_bio_embeddings(sequence)
    if protein_embedding is None:
        return None, "Embedding generation failed!"

    model = CVanilla_RNN_Builder(cvn_model_dir, gpu_id=None)
    samples = model.sample(n_samples, c=protein_embedding[0], output_type='graph')
    valid_samples = [sample for sample in samples if sample is not None]

    smiles_list = [
        Chem.MolToSmiles(mol) for mol in get_mol_from_graph_list(valid_samples, sanitize=True) if mol is not None
    ]

    if not smiles_list:
        return None, "No valid SMILES generated!"

    filename = os.path.join(UF, "SMILES_GENERATED.txt")
    with open(filename, "w") as file:
        file.write("\n".join(smiles_list))

    elapsed_time = time.time() - start_time
    return filename, elapsed_time


app = Flask(__name__)

@app.route("/", methods=["GET", "POST"])
def index():
    if request.method == "POST":
        sequence = request.form["sequence"].strip()
        if not sequence:
            return render_template("index.html", message="Please enter a valid sequence.")

        file_path, result = generate_smiles(sequence)
        if file_path is None:
            return render_template("index.html", message=f"Error: {result}")

        return render_template("index.html", message="SMILES generated successfully!", file_path=file_path, time_taken=result)

    return render_template("index.html")

@app.route("/download")
def download_file():
    file_path = os.path.join(UF, "SMILES_GENERATED.txt")
    return send_file(file_path, as_attachment=True)


if __name__ == "__main__":
    app.run(host="0.0.0.0", port=7860)