scripts/generator.py

import os
import json
import subprocess
import warnings
import sys
import shutil

def sync_protein_metadata(jsonl_path, dict_path):
    """
    Automated metadata sanitization to prevent KeyError (e.g., 'seq_chain_C').
    Prunes non-proteogenic chain IDs from the dictionary before the run.
    """
    if not os.path.exists(jsonl_path) or not os.path.exists(dict_path):
        return

    # 1. Identify chains that actually have proteogenic sequence data
    valid_chains_map = {}
    with open(jsonl_path, 'r') as f:
        for line in f:
            entry = json.loads(line)
            name = entry['name']
            # Only keep chains that have a 'seq_chain_X' entry in the JSONL
            valid = {k.split('_')[-1] for k in entry.keys() if k.startswith('seq_chain_')}
            valid_chains_map[name] = valid

    # 2. Clean the chain ID dictionary
    with open(dict_path, 'r') as f:
        chain_id_dict = json.load(f)

    for pdb_name, configs in chain_id_dict.items():
        if pdb_name in valid_chains_map:
            valid = valid_chains_map[pdb_name]
            # configs[0] = redesign list, configs[1] = fixed list
            original_chains = set(configs[0] + configs[1])
            
            chain_id_dict[pdb_name] = [
                [c for c in configs[0] if c in valid],
                [c for c in configs[1] if c in valid]
            ]
            
            # Diagnostic feedback
            removed = original_chains - valid
            if removed:
                print(f"🧹 Sanitizer: Pruned non-protein chains from metadata: {removed}")

    # 3. Overwrite with cleaned metadata for ProteinMPNN
    with open(dict_path, 'w') as f:
        json.dump(chain_id_dict, f)

def run_broteinshake_generator(pdb_path, fixed_chains, variable_chains, num_seqs=20, temp=0.1):
    # 1. Setup identifiers and directories
    pdb_name = os.path.basename(pdb_path).split('.')[0]
    output_dir = f"./generated/{pdb_name}" 
    os.makedirs(output_dir, exist_ok=True)
    
    script_dir = os.path.dirname(os.path.abspath(__file__))
    project_root = os.path.dirname(script_dir)
    proteinmpnn_dir = os.path.join(project_root, "ProteinMPNN")
    
    if not os.path.exists(proteinmpnn_dir):
        print("ProteinMPNN not found, cloning repository...")
        subprocess.run(["git", "clone", "https://github.com/dauparas/ProteinMPNN.git"], cwd=project_root, check=True)
    
    mpnn_script = os.path.join(proteinmpnn_dir, "protein_mpnn_run.py")
    
    # 2. Handle Single vs Multi-Chain Logic 
    if not fixed_chains or len(fixed_chains) == 0:
        chain_to_design = variable_chains[0] if variable_chains else "A"
        mpnn_cmd = (
            f"python -W ignore {mpnn_script} --pdb_path {pdb_path} --pdb_path_chains {chain_to_design} "
            f"--out_folder {output_dir} --num_seq_per_target {num_seqs} --sampling_temp {temp} --seed 42 --batch_size 1"
        )
        print(f"🚀 Designing {pdb_name} (Single-chain: {chain_to_design})...")
    else:
        # Multi-chain setup
        pdb_dir = os.path.dirname(os.path.abspath(pdb_path)) or "."
        jsonl_path = os.path.join(output_dir, "parsed_pdbs.jsonl")
        parse_script = os.path.join(proteinmpnn_dir, "helper_scripts", "parse_multiple_chains.py")
        
        # Step A: Parse PDB to JSONL
        subprocess.run(f"python -W ignore {parse_script} --input_path={pdb_dir}/ --output_path={jsonl_path}", shell=True, check=True)

        # Step B: Create initial Chain Dictionary
        pdb_name_clones = f"{pdb_name}_clones"
        # Fix: ensure the name in JSONL matches the dict key
        with open(jsonl_path, 'r') as f:
            jsonl_data = json.loads(f.readline())
        jsonl_data['name'] = pdb_name_clones
        with open(jsonl_path, 'w') as f:
            f.write(json.dumps(jsonl_data) + '\n')

        chain_id_json = os.path.join(output_dir, "chain_id_dict.json")
        chain_id_dict = {pdb_name_clones: [[c for c in variable_chains], [c for c in fixed_chains]]}
        with open(chain_id_json, 'w') as f:
            json.dump(chain_id_dict, f)

        # Step C: AUTOMATED CLEANING - Prunes ghost chains like 'C'
        sync_protein_metadata(jsonl_path, chain_id_json)

        # Step D: Final Execution Command
        mpnn_cmd = (
            f"python -W ignore {mpnn_script} --jsonl_path {jsonl_path} --chain_id_jsonl {chain_id_json} "
            f"--out_folder {output_dir} --num_seq_per_target {num_seqs} --sampling_temp {temp} --seed 42"
        )
        print(f"🚀 Designing {pdb_name}... (Fixed: {fixed_chains} | Redesign: {variable_chains})")
    
    # 3. Execute with suppressed warnings
    env = os.environ.copy()
    env['PYTHONWARNINGS'] = 'ignore'
    subprocess.run(mpnn_cmd, shell=True, check=True, env=env, stderr=subprocess.DEVNULL)
    
    print(f"✅ Success! Design complete for {pdb_name}.")

if __name__ == "__main__":
    if len(sys.argv) < 4:
        print("Usage: python scripts/generator.py <pdb_path> <fixed_chains> <variable_chains> [num_seqs] [temp]")
        sys.exit(1)
    run_broteinshake_generator(
        sys.argv[1], sys.argv[2], sys.argv[3], 
        int(sys.argv[4]) if len(sys.argv) > 4 else 20, 
        float(sys.argv[5]) if len(sys.argv) > 5 else 0.1
    )