drugforge.spectrum.calculate_rmsd.get_binding_site_rmsd

drugforge.spectrum.calculate_rmsd.get_binding_site_rmsd(file_mob: Path | str, file_ref: Path | str, bsite_dist: float = 4.5, rmsd_mode: str = 'CA', chain_mob: str = 'A', chain_ref: str = 'A', ligres: str = 'LIG', lig_ref_pdb: str = None, chain_ref2: str = 'A', aligned_temp: str = None) → float[source]

Calculate RMSD for the Binding Site residues between file_mob and file_ref The binding site is defined as all residues protein within bsite_dist Angs of the ligand in the reference protein. If the ligand is missing in the reference, an auxiliary reference (lig_ref_pdb) may be provided to define the binding site.

Parameters:

  • file_mob (Union[Path, str]) – Path to target file

  • file_ref (Union[Path, str]) – Path to reference file

  • bsite_dist (float, optional) – Cutoff distance to ligand in Angs, by default 4.5

  • rmsd_mode (str, optional) – Type of RMSD to compute: ‘CA’ for alpha carbons or ‘heavy’ for all heavy atoms, by default “CA”.

  • chain_mob (str, optional) – Chain ID of target to compare, by default “1”

  • chain_ref (str, optional) – Chain ID of reference to compare, by default “1”

  • ligres (str, optional) – Resname of ligand residue, by default “UNK”

  • lig_ref_pdb (Path, optional) – Optional Reference PDB to define binding site, in case ref doesn’t have a ligand, by default None

  • chain_ref2 (str, optional) – Optional reference Chain ID, used when the main reference doesn’t have a ligand, by default “A”

  • aligned_temp (Path, optional) – Optional folder to store alignment PDB when calculating bsite with additional PDB ref, by default None

Returns:

RMSD of binding site, or -1 if RMSD could not be calculated.

Return type:

float

Raises:

ValueError – No ligand found in reference, and not second reference provided.