.ipynb_checkpoints/app-checkpoint.py

import gradio as gr
from model_loader import load_model

import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader

import re
import numpy as np
import os
import pandas as pd
import copy

import transformers, datasets
from transformers import AutoTokenizer
from transformers import DataCollatorForTokenClassification

from datasets import Dataset

from scipy.special import expit

import requests

from gradio_molecule3d import Molecule3D

# Biopython imports
from Bio.PDB import PDBParser, Select, PDBIO
from Bio.PDB.DSSP import DSSP
from Bio.PDB import PDBList

from matplotlib import cm  # For color mapping
from matplotlib.colors import Normalize

# Load model and move to device
checkpoint = 'ThorbenF/prot_t5_xl_uniref50'
max_length = 1500
model, tokenizer = load_model(checkpoint, max_length)
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
model.to(device)
model.eval()

# Function to fetch a PDB file
def fetch_pdb(pdb_id):
    pdb_url = f'https://files.rcsb.org/download/{pdb_id}.pdb'
    pdb_path = f'pdb_files/{pdb_id}.pdb'
    os.makedirs('pdb_files', exist_ok=True)
    response = requests.get(pdb_url)
    if response.status_code == 200:
        with open(pdb_path, 'wb') as f:
            f.write(response.content)
        return pdb_path
    return None


def normalize_scores(scores):
    min_score = np.min(scores)
    max_score = np.max(scores)
    return (scores - min_score) / (max_score - min_score) if max_score > min_score else scores

def process_pdb(pdb_id, segment):
    pdb_path = fetch_pdb(pdb_id)
    if not pdb_path:
        return "Failed to fetch PDB file", None, None
    
    parser = PDBParser(QUIET=1)
    structure = parser.get_structure('protein', pdb_path)
    chain = structure[0][segment]
    
    # Comprehensive amino acid mapping
    aa_dict = {
        'ALA': 'A', 'CYS': 'C', 'ASP': 'D', 'GLU': 'E', 'PHE': 'F',
        'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LYS': 'K', 'LEU': 'L',
        'MET': 'M', 'ASN': 'N', 'PRO': 'P', 'GLN': 'Q', 'ARG': 'R',
        'SER': 'S', 'THR': 'T', 'VAL': 'V', 'TRP': 'W', 'TYR': 'Y',
        'MSE': 'M', 'SEP': 'S', 'TPO': 'T', 'CSO': 'C', 'PTR': 'Y', 'HYP': 'P'
    }
    
    # Exclude non-amino acid residues
    sequence = "".join(
        aa_dict[residue.get_resname().strip()] 
        for residue in chain 
        if residue.get_resname().strip() in aa_dict
    )
    
    # Prepare input for model prediction
    input_ids = tokenizer(" ".join(sequence), return_tensors="pt").input_ids.to(device)
    with torch.no_grad():
        outputs = model(input_ids).logits.detach().cpu().numpy().squeeze()

    # Calculate scores and normalize them
    scores = expit(outputs[:, 1] - outputs[:, 0])
    normalized_scores = normalize_scores(scores)
    
    # Prepare the result string, including only amino acid residues
    result_str = "\n".join([
        f"{res.get_resname()} {res.id[1]} {sequence[i]} {normalized_scores[i]:.2f}" 
        for i, res in enumerate(chain) if res.get_resname().strip() in aa_dict
    ])
    
    # Save predictions to file
    with open(f"{pdb_id}_predictions.txt", "w") as f:
        f.write(result_str)
    
    return result_str, pdb_path, f"{pdb_id}_predictions.txt"

reps = [{"model": 0, "style": "cartoon", "color": "spectrum"}]

# Gradio UI
with gr.Blocks() as demo:
    gr.Markdown("# Protein Binding Site Prediction")

    with gr.Row():
        pdb_input = gr.Textbox(value="2IWI",
                label="PDB ID",
                placeholder="Enter PDB ID here...")
        segment_input = gr.Textbox(value="A",
                label="Chain ID (Segment)",
                placeholder="Enter Chain ID here...")
        visualize_btn = gr.Button("Visualize Sructure")
        prediction_btn = gr.Button("Predict Ligand Binding Site")

    molecule_output = Molecule3D(label="Protein Structure", reps=reps)
    predictions_output = gr.Textbox(label="Binding Site Predictions")
    download_output = gr.File(label="Download Predictions")

    visualize_btn.click(fetch_pdb, inputs=[pdb_input], outputs=molecule_output)
    prediction_btn.click(
        process_pdb, 
        inputs=[pdb_input, segment_input], 
        outputs=[predictions_output, molecule_output, download_output]
    )

    gr.Markdown("## Examples")
    gr.Examples(
        examples=[
            ["2IWI"],
            ["7RPZ"],
            ["3TJN"]
        ],
        inputs=[pdb_input, segment_input], 
        outputs=[predictions_output, molecule_output, download_output]
    )

demo.launch(share=True)