Index

A

accept_atom() (posebench.models.minimize_energy.NoHydrogen method) accept_residue() (posebench.data.binding_site_crop_preparation.BindingSiteSelect method) add_ligand_to_complex() (in module posebench.models.minimize_energy)

align_complex_to_protein_only() (in module posebench.analysis.complex_alignment) align_to_binding_site() (in module posebench.analysis.complex_alignment) assign_reference_residue_b_factors() (in module posebench.models.ensemble_generation)

B

BindingSiteSelect (class in posebench.data.binding_site_crop_preparation)

C

calculate_rmsd() (in module posebench.utils.model_utils) combine_molecules() (in module posebench.utils.data_utils) compute_ligand_local_geometry_violations() (in module posebench.models.minimize_energy) compute_protein_local_geometry_violations() (in module posebench.models.minimize_energy) consensus_rank_ensemble_predictions() (in module posebench.models.ensemble_generation) count_num_residues_in_pdb_file() (in module posebench.utils.data_utils) count_pdb_inter_residue_clashes() (in module posebench.utils.data_utils) create_chai_bash_script() (in module posebench.models.ensemble_generation)

create_diffdock_bash_script() (in module posebench.models.ensemble_generation) create_dynamicbind_bash_script() (in module posebench.models.ensemble_generation) create_flowdock_bash_script() (in module posebench.models.ensemble_generation) create_neuralplexer_bash_script() (in module posebench.models.ensemble_generation) create_rfaa_bash_script() (in module posebench.models.ensemble_generation) create_sdf_file_from_smiles() (in module posebench.utils.data_utils) create_temporary_fasta_file() (in module posebench.models.ensemble_generation) create_vina_bash_script() (in module posebench.models.ensemble_generation) crop_protein_binding_site() (in module posebench.data.binding_site_crop_preparation)

D

deserialize() (in module posebench.models.minimize_energy)

dynamically_build_rfaa_input_config() (in module posebench.models.ensemble_generation)

E

export_ligands_in_casp15_format() (in module posebench.models.ensemble_generation) export_proteins_in_casp_format() (in module posebench.models.ensemble_generation)

extract_protein_and_ligands_with_prody() (in module posebench.utils.data_utils) extract_remarks_from_pdb() (in module posebench.utils.data_utils) extract_sequences_from_protein_structure_file() (in module posebench.utils.data_utils)

F

ff_rank_ensemble_predictions() (in module posebench.models.ensemble_generation)

find_ligand_files() (in module posebench.utils.utils) find_protein_files() (in module posebench.utils.utils)

G

generate_conformer() (in module posebench.models.minimize_energy) generate_ensemble_predictions() (in module posebench.models.ensemble_generation) generate_method_prediction_script() (in module posebench.models.ensemble_generation) generate_system() (in module posebench.models.minimize_energy) get_all_ligand_non_hydrogen_atoms() (in module posebench.models.minimize_energy)

get_all_protein_atoms() (in module posebench.models.minimize_energy) get_binding_site_residue_indices() (in module posebench.data.binding_site_crop_preparation) get_fastest_platform() (in module posebench.models.minimize_energy) get_method_predictions() (in module posebench.models.ensemble_generation) get_pdb_components_with_prody() (in module posebench.utils.data_utils)

I

insert_hpc_headers() (in module posebench.models.ensemble_generation)

L

load_molecule() (in module posebench.models.minimize_energy)

M

main() (in module posebench.analysis.complex_alignment) (in module posebench.data.binding_site_crop_preparation) (in module posebench.models.ensemble_generation) (in module posebench.models.inference_relaxation) (in module posebench.models.minimize_energy) minimize_energy() (in module posebench.models.minimize_energy) module posebench.__init__ posebench.analysis.complex_alignment posebench.data.binding_site_crop_preparation posebench.models.ensemble_generation posebench.models.inference_relaxation posebench.models.minimize_energy posebench.utils.data_utils posebench.utils.model_utils posebench.utils.utils

N

NoHydrogen (class in posebench.models.minimize_energy)

O

optimize_ligand_in_pocket() (in module posebench.models.minimize_energy)

P

parse_fasta() (in module posebench.utils.data_utils) parse_inference_inputs_from_dir() (in module posebench.utils.data_utils) posebench.__init__ module posebench.analysis.complex_alignment module posebench.data.binding_site_crop_preparation module posebench.models.ensemble_generation module posebench.models.inference_relaxation module

posebench.models.minimize_energy module posebench.utils.data_utils module posebench.utils.model_utils module posebench.utils.utils module predict_protein_structure_from_sequence() (in module posebench.models.ensemble_generation) prep_ligand() (in module posebench.models.minimize_energy) prep_protein() (in module posebench.models.minimize_energy) process_ligand_with_prody() (in module posebench.utils.data_utils)

R

randomly_rotate_protein_side_chains() (in module posebench.models.minimize_energy) rank_ensemble_predictions() (in module posebench.models.ensemble_generation) rank_key() (in module posebench.models.ensemble_generation) read_ligand_expo() (in module posebench.utils.data_utils) register_custom_omegaconf_resolvers() (in module posebench.__init__) relax_inference_results() (in module posebench.models.inference_relaxation) relax_single_filepair() (in module posebench.models.inference_relaxation) remove_hydrogens_from_pdb() (in module posebench.models.minimize_energy) remove_mol_hydrogens_and_reorder() (in module posebench.models.minimize_energy)

renumber_biopython_structure_residues() (in module posebench.utils.data_utils) renumber_pdb_df_residues() (in module posebench.utils.data_utils) resolve_method_input_csv_path() (in module posebench.__init__) resolve_method_ligand_dir() (in module posebench.__init__) resolve_method_output_dir() (in module posebench.__init__) resolve_method_protein_dir() (in module posebench.__init__) resolve_method_title() (in module posebench.__init__) resolve_omegaconf_variable() (in module posebench.__init__) rfaa_get_chain_letter() (in module posebench.models.ensemble_generation) run_command_with_timeout() (in module posebench.utils.utils)

S

save_biopython_structure_to_pdb() (in module posebench.models.minimize_energy) save_cropped_protein_binding_site() (in module posebench.data.binding_site_crop_preparation) save_ranked_predictions() (in module posebench.models.ensemble_generation)

save_with_rdkit() (in module posebench.models.minimize_energy) serialize() (in module posebench.models.minimize_energy) setup_simulation() (in module posebench.models.minimize_energy)

W

will_restrain() (in module posebench.models.minimize_energy)

write_pdb_with_prody() (in module posebench.utils.data_utils) write_sdf() (in module posebench.utils.data_utils)