scripts/generate.py

import torch
import numpy as np
from transformers import AutoTokenizer, AutoModel
from diffusion import Diffusion
import config
from esm_utils import load_esm2_model, get_latents

def mask_sequence(sequence, mask_char='X'):
    """Masks parts of the sequence based on the mask_char."""
    mask_indices = [i for i, char in enumerate(sequence) if char == mask_char]
    masked_sequence = sequence.replace(mask_char, '[MASK]')
    return masked_sequence, mask_indices

def generate_filled_sequence(model, tokenizer, esm_model, masked_sequence, mask_indices):
    """Generates the filled sequence for the masked regions."""
    inputs = tokenizer(masked_sequence, return_tensors="pt")
    with torch.no_grad():
        outputs = esm_model(**inputs)
    latents = outputs.last_hidden_state.squeeze(0)
    
    sigma = torch.rand(1, device=latents.device)
    noisy_latents = model.forward(latents, sigma)
    denoised_latents = model.reverse_diffusion(noisy_latents, sigma)
    
    filled_sequence = list(masked_sequence)
    for idx in mask_indices:
        token_id = torch.argmax(denoised_latents[idx]).item()
        filled_sequence[idx] = tokenizer.decode([token_id])
    
    return ''.join(filled_sequence)

def generate_scaffold_sequence(model, tokenizer, esm_model, peptides, final_length):
    """Generates a scaffold sequence to connect multiple peptides."""
    total_peptide_length = sum(len(peptide) for peptide in peptides)
    scaffold_length = final_length - total_peptide_length
    if scaffold_length <= 0:
        raise ValueError("Final length must be greater than the combined length of the peptides.")
    
    scaffold = "[MASK]" * scaffold_length
    masked_sequence = "".join(peptides[:1] + [scaffold] + peptides[1:])
    
    inputs = tokenizer(masked_sequence, return_tensors="pt")
    with torch.no_grad():
        outputs = esm_model(**inputs)
    latents = outputs.last_hidden_state.squeeze(0)
    
    sigma = torch.rand(1, device=latents.device)
    noisy_latents = model.forward(latents, sigma)
    denoised_latents = model.reverse_diffusion(noisy_latents, sigma)
    
    filled_sequence = list(masked_sequence)
    scaffold_start = len(peptides[0])
    scaffold_end = scaffold_start + scaffold_length
    for idx in range(scaffold_start, scaffold_end):
        token_id = torch.argmax(denoised_latents[idx]).item()
        filled_sequence[idx] = tokenizer.decode([token_id])
    
    return ''.join(filled_sequence)

def generate_de_novo_sequence(model, tokenizer, esm_model, sequence_length):
    """Generates a de novo protein sequence of the specified length."""
    scaffold = "[MASK]" * sequence_length
    masked_sequence = scaffold
    
    inputs = tokenizer(masked_sequence, return_tensors="pt")
    with torch.no_grad():
        outputs = esm_model(**inputs)
    latents = outputs.last_hidden_state.squeeze(0)
    
    sigma = torch.rand(1, device=latents.device)
    noisy_latents = model.forward(latents, sigma)
    denoised_latents = model.reverse_diffusion(noisy_latents, sigma)
    
    filled_sequence = list(masked_sequence)
    for idx in range(sequence_length):
        token_id = torch.argmax(denoised_latents[idx]).item()
        filled_sequence[idx] = tokenizer.decode([token_id])
    
    return ''.join(filled_sequence)

if __name__ == "__main__":
    import argparse

    # Argument parsing
    parser = argparse.ArgumentParser(description="Generate protein sequences using latent diffusion model.")
    subparsers = parser.add_subparsers(dest="mode")

    # Subparser for the first strategy (multiple peptides to scaffold)
    parser_scaffold = subparsers.add_parser("scaffold", help="Generate scaffold to connect multiple peptides.")
    parser_scaffold.add_argument("peptides", nargs='+', help="Peptides to connect.")
    parser_scaffold.add_argument("final_length", type=int, help="Final length of the protein sequence.")

    # Subparser for the second strategy (fill in regions)
    parser_fill = subparsers.add_parser("fill", help="Fill in specified regions in a given protein sequence.")
    parser_fill.add_argument("sequence", help="Protein sequence with regions to fill specified by 'X'.")

    # Subparser for the third strategy (de novo generation)
    parser_de_novo = subparsers.add_parser("de_novo", help="Generate a de novo protein sequence.")
    parser_de_novo.add_argument("sequence_length", type=int, help="Length of the de novo generated protein sequence.")

    args = parser.parse_args()

    # Load models
    tokenizer, esm_model = load_esm2_model(config.MODEL_NAME)
    diffusion_model = Diffusion.load_from_checkpoint(config.Training.SAVE_DIR + "best_model.ckpt", config=config, latent_dim=config.LATENT_DIM)
    diffusion_model.eval()

    if args.mode == "scaffold":
        peptides = args.peptides
        final_length = args.final_length
        filled_sequence = generate_scaffold_sequence(diffusion_model, tokenizer, esm_model, peptides, final_length)
        print(f"Peptides:          {' '.join(peptides)}")
        print(f"Final Length:      {final_length}")
        print(f"Generated Protein: {filled_sequence}")

    elif args.mode == "fill":
        sequence = args.sequence
        masked_sequence, mask_indices = mask_sequence(sequence)
        filled_sequence = generate_filled_sequence(diffusion_model, tokenizer, esm_model, masked_sequence, mask_indices)
        print(f"Original Sequence: {sequence}")
        print(f"Masked Sequence:   {masked_sequence}")
        print(f"Filled Sequence:   {filled_sequence}")

    elif args.mode == "de_novo":
        sequence_length = args.sequence_length
        filled_sequence = generate_de_novo_sequence(diffusion_model, tokenizer, esm_model, sequence_length)
        print(f"De Novo Sequence Length: {sequence_length}")
        print(f"Generated Protein: {filled_sequence}")