drugforge.spectrum.calculate_rmsd.find_bsite_resids

drugforge.spectrum.calculate_rmsd.find_bsite_resids(pdb: str, pdb_ref: str, aligned_temp: str, ligres: str = 'UNK', chain_m: str = 'A', chain_r: str = 'A', bsite_dist: float = 4.5, res_threshold: int = 5)[source]

Find binding site residues in a protein-ligand complex based on ligand proximity.

Parameters:

  • pdb (str) – Path to PDB of protein to align.

  • pdb_ref (str) – Path to reference PDB to align target against.

  • aligned_temp (str) – Path to save aligned PDB.

  • ligres (str, optional) – Residue name of ligand, by default “UNK”

  • chain_m (str, optional) – Chain ID of mobile, by default “A”

  • chain_r (str, optional) – Chain ID of ref, by default “A”

  • bsite_dist (float, optional) – Distance to ligand in angstroms defining binding site, by default 4.5

  • res_threshold (int, optional) – Threshold of residue IDs that can be assigned to binding site. Avoids asigning terminal atoms. By default 5

Returns:

Arrays of binding site residue IDs in mobile and reference structures.

Return type:

tuple[np.ndarray, np.ndarray]

Raises:

ValueError – No binding site residues have an idx above res_threshold