code/scripts/pxdesign_guidance/convert_cif_to_pdb.py

"""
Convert PXDesign CIF outputs to PDB format for evaluation pipeline.

PXDesign outputs .cif files with:
- Chain IDs like A0/B0 (multi-char, not PDB-compatible)
- Non-standard residue name 'xpb' for designed binder residues

This script converts them to PDB format with:
- Single-char chain IDs (A, B)
- Preserved residue names (xpb is kept; eval tools handle it)

Usage:
    python code/scripts/pxdesign_guidance/convert_cif_to_pdb.py
"""
import os
import sys
from glob import glob

from Bio.PDB import MMCIFParser, PDBIO, Select

_SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
_PROJECT_DIR = os.path.abspath(os.path.join(_SCRIPT_DIR, '../../..'))


class ChainRenamer(Select):
    """Rename multi-char chain IDs to single-char for PDB format."""
    def __init__(self, chain_map):
        self.chain_map = chain_map

    def accept_chain(self, chain):
        return 1

    def accept_residue(self, residue):
        return 1

    def accept_atom(self, atom):
        return 1


def convert_cif_to_pdb(cif_path, pdb_path):
    """Convert a single CIF file to PDB format."""
    parser = MMCIFParser(QUIET=True)
    structure = parser.get_structure('s', cif_path)
    model = structure[0]

    # Build chain ID mapping (A0->A, B0->B, etc.)
    chain_map = {}
    used_ids = set()
    for chain in model.get_chains():
        old_id = chain.id
        # Use first character
        new_id = old_id[0] if old_id else 'A'
        # Avoid duplicates
        while new_id in used_ids:
            new_id = chr(ord(new_id) + 1)
        used_ids.add(new_id)
        chain_map[old_id] = new_id

    # Rename chains and fix non-standard residue names
    chains_to_rename = list(model.get_chains())
    for chain in chains_to_rename:
        old_id = chain.id
        new_id = chain_map.get(old_id, old_id)
        if old_id != new_id:
            chain.id = new_id
        # Rename 'xpb' residues to 'GLY' (backbone-only binder residues)
        for residue in chain.get_residues():
            if residue.resname.strip().lower() == 'xpb':
                residue.resname = 'GLY'

    # Write PDB
    io = PDBIO()
    io.set_structure(structure)
    io.save(pdb_path)
    return True


def convert_directory(src_dir, method_name):
    """Convert all CIF files in a directory tree to PDB."""
    cif_files = sorted(glob(os.path.join(src_dir, '**/*.cif'), recursive=True))
    cif_files = [f for f in cif_files if 'sample' in os.path.basename(f).lower()]

    if not cif_files:
        print(f"  No CIF files found in {src_dir}")
        return 0

    # Create converted_pdbs directory
    converted_dir = os.path.join(src_dir, 'converted_pdbs')
    os.makedirs(converted_dir, exist_ok=True)

    n_converted = 0
    for cif_path in cif_files:
        basename = os.path.basename(cif_path).replace('.cif', '.pdb')
        # For TDS/SMC with round subdirs, include round info
        rel_path = os.path.relpath(cif_path, src_dir)
        parts = rel_path.split(os.sep)
        if any(p.startswith('round_') for p in parts):
            round_part = [p for p in parts if p.startswith('round_')][0]
            basename = f"{round_part}_{basename}"

        pdb_path = os.path.join(converted_dir, basename)
        try:
            convert_cif_to_pdb(cif_path, pdb_path)
            n_converted += 1
        except Exception as e:
            print(f"  Failed {cif_path}: {e}")

    print(f"  Converted {n_converted}/{len(cif_files)} CIF -> PDB in {converted_dir}")
    return n_converted


def main():
    methods = {
        'pxdesign_guided': os.path.join(_PROJECT_DIR, 'results/pxdesign_guided'),
        'pxdesign_tds': os.path.join(_PROJECT_DIR, 'results/pxdesign_tds'),
        'pxdesign_smc': os.path.join(_PROJECT_DIR, 'results/pxdesign_smc'),
    }
    # Langevin outputs are already PDB (post-hoc refinement)

    total = 0
    for name, src_dir in methods.items():
        print(f"\n{name}:")
        if os.path.exists(src_dir):
            total += convert_directory(src_dir, name)
        else:
            print(f"  Directory not found: {src_dir}")

    print(f"\nTotal converted: {total}")


if __name__ == '__main__':
    main()