Index

A

accept_residue() (posebench.data.binding_site_crop_preparation.BindingSiteSelect method)

align_complex_to_protein_only() (in module posebench.analysis.complex_alignment) align_to_binding_site() (in module posebench.analysis.complex_alignment)

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) count_num_residues_in_pdb_file() (in module posebench.utils.data_utils)

count_pdb_inter_residue_clashes() (in module posebench.utils.data_utils) create_sdf_file_from_smiles() (in module posebench.utils.data_utils) crop_protein_binding_site() (in module posebench.data.binding_site_crop_preparation)

E

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

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

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

G

get_binding_site_residue_indices() (in module posebench.data.binding_site_crop_preparation)

get_pdb_components_with_prody() (in module posebench.utils.data_utils)

M

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

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.inference_relaxation module posebench.utils.data_utils module posebench.utils.model_utils module posebench.utils.utils module process_ligand_with_prody() (in module posebench.utils.data_utils)

R

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) 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__) run_command_with_timeout() (in module posebench.utils.utils)

S

save_cropped_protein_binding_site() (in module posebench.data.binding_site_crop_preparation)

W

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

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