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_postfix: str = '_aligned', atom_df_name: str = 'ATOM')

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_postfix – Postfix to append to the aligned files

• atom_df_name – Name of the atom dataframe in the PDB file

posebench.analysis.complex_alignment.main(cfg: DictConfig)

Align the predicted protein-ligand structures to the reference protein-ligand structures.

Parameters:

cfg – Configuration dictionary from the hydra YAML file.

posebench.analysis.complex_alignment.save_aligned_complex(predicted_protein_pdb: str, predicted_ligand_sdf: str | None, reference_protein_pdb: str, reference_ligand_sdf: str, save_protein: bool = True, save_ligand: bool = True, aligned_filename_postfix: str = '_aligned', atom_df_name: str = 'ATOM')

Align the predicted protein-ligand structures to the reference protein-ligand structures and save the aligned results.

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

• reference_ligand_sdf – Path to the reference ligand structure in SDF format

• save_protein – Whether to save the aligned protein structure

• save_ligand – Whether to save the aligned ligand structure

• aligned_filename_postfix – Postfix to append to the aligned files

• atom_df_name – Name of the atom dataframe in the PDB file