Complex alignment¶
- posebench.analysis.complex_alignment.align_complex_to_protein_only(predicted_protein_pdb: str, predicted_ligand_sdf: str | None, reference_protein_pdb: str, save_protein: bool = True, save_ligand: bool = True, aligned_filename_suffix: str = '_aligned', atom_df_name: str = 'ATOM') int[source]¶
Align a predicted protein-ligand structure to a reference protein structure.
- Parameters:
predicted_protein_pdb – Path to the predicted protein structure in PDB format
predicted_ligand_sdf – Optional path to the predicted ligand structure in SDF format
reference_protein_pdb – Path to the reference protein structure in PDB format
save_protein – Whether to save the aligned protein structure
save_ligand – Whether to save the aligned ligand structure
aligned_filename_suffix – suffix to append to the aligned files
atom_df_name – Name of the atom dataframe in the PDB file
- Returns:
0 if successful, 1 if unsuccessful
- posebench.analysis.complex_alignment.align_to_binding_site(predicted_protein: str, predicted_ligand: str | None, reference_protein: str, reference_ligand: str | None, dataset: Literal['dockgen', 'casp15', 'posebusters_benchmark', 'astex_diverse'], aligned_filename_suffix: str = '_aligned', cutoff: float = 10.0, save_protein: bool = True, save_ligand: bool = True, verbose: bool = True)[source]¶
Align the predicted protein-ligand complex to the reference complex using the reference protein’s heavy atom ligand binding site residues.
- Parameters:
predicted_protein – File path to the predicted protein (PDB).
predicted_ligand – File path to the optional predicted ligand (SDF).
reference_protein – File path to the reference protein (PDB).
reference_ligand – File path to the optional reference ligand (SDF).
dataset – Dataset name (e.g., “dockgen”, “casp15”, “posebusters_benchmark”, or “astex_diverse”).
aligned_filename_suffix – Suffix to append to the aligned files (default “_aligned”).
cutoff – Distance cutoff in Å to define the binding site (default 10.0).
save_protein – Whether to save the aligned protein structure (default True).
save_ligand – Whether to save the aligned ligand structure (default True).
verbose – Whether to print the alignment RMSD and number of aligned atoms (default True).