drugforge.spectrum.calculate_rmsd.rmsd_alignment

drugforge.spectrum.calculate_rmsd.rmsd_alignment(target_pdb: str, ref_pdb: str, final_pdb: str, target_chain='A', ref_chain='A') → tuple[float, Path][source]

Calculate RMSD of a molecule against a reference

Parameters:

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

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

  • final_pdb (str) – Path to save PDB of aligned target.

  • target_chain (str, optional) – The chain of target which will be used for alignment, by default “A”

  • ref_chain (str, optional) – The chain of reference which will be used for alignment, by default “A”

Returns:

RMSD after alignment, Path to saved PDB

Return type:

float, str