Complex alignment

multicom_ligand.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')[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_postfix – Postfix to append to the aligned files

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

multicom_ligand.analysis.complex_alignment.main(cfg: DictConfig)[source]

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

Parameters:

cfg – Configuration dictionary from the hydra YAML file.

multicom_ligand.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')[source]

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