Index

A

AbsoluteScoreModifier (class in tdc.chem_utils.oracle.oracle) ADME (class in tdc.single_pred.adme) admet_group (class in tdc.benchmark_group.admet_group) amlodipine_mpo() (in module tdc.chem_utils.oracle.oracle) AntibodyAff (class in tdc.multi_pred.antibodyaff) askcos() (in module tdc.chem_utils.oracle.oracle)

assign_evaluator() (tdc.evaluator.Evaluator method) (tdc.oracles.Oracle method) atom2onehot() (in module tdc.chem_utils.featurize.molconvert) atom_to_one_hot() (in module tdc.utils.load) AtomCounter (class in tdc.chem_utils.oracle.oracle) atomstring2atomfeature() (in module tdc.chem_utils.featurize.molconvert) avg_auc() (in module tdc.evaluator)

B

balanced() (tdc.base_dataset.DataLoader method) BenchmarkGroup (class in tdc.benchmark_group.base_group) bi_distribution_dataset_load() (in module tdc.utils.load) binarize() (in module tdc.utils.label) (tdc.base_dataset.DataLoader method)

bm_download_wrapper() (in module tdc.utils.load) bm_group_load() (in module tdc.utils.load) bondtype2idx() (in module tdc.chem_utils.featurize.molconvert)

C

calculate_internal_pairwise_similarities() (in module tdc.chem_utils.evaluator) calculate_pc_descriptors() (in module tdc.chem_utils.evaluator) calculateScore() (in module tdc.chem_utils.oracle.oracle) canonicalize() (in module tdc.chem_utils.evaluator) (in module tdc.chem_utils.featurize.molconvert) (in module tdc.chem_utils.oracle.oracle) Catalyst (class in tdc.multi_pred.catalyst) centroid() (in module tdc.evaluator) ChainedModifier (class in tdc.chem_utils.oracle.oracle) cid2smiles() (in module tdc.utils.query) ClippedScoreModifier (class in tdc.chem_utils.oracle.oracle) continuous_kldiv() (in module tdc.chem_utils.evaluator) convert_back_log() (in module tdc.utils.label) convert_format (tdc.single_pred.single_pred_dataset.DataLoader attribute)

convert_from_log() (tdc.base_dataset.DataLoader method) convert_result (tdc.single_pred.single_pred_dataset.DataLoader attribute) convert_to_log() (in module tdc.utils.label) (tdc.base_dataset.DataLoader method) convert_y_unit() (in module tdc.utils.label) create_combination_generation_split() (in module tdc.utils.split) create_combination_split() (in module tdc.utils.split) create_fold() (in module tdc.utils.split) create_fold_setting_cold() (in module tdc.utils.split) create_fold_time() (in module tdc.utils.split) create_group_split() (in module tdc.utils.split) create_scaffold_split() (in module tdc.utils.split) CRISPROutcome (class in tdc.single_pred.crispr_outcome) cyp3a4_veith() (in module tdc.chem_utils.oracle.oracle)

D

DataLoader (class in tdc.base_dataset) (class in tdc.generation.generation_dataset) (class in tdc.multi_pred.bi_pred_dataset) (class in tdc.multi_pred.multi_pred_dataset) (class in tdc.single_pred.single_pred_dataset) DataLoader3D (class in tdc.generation.generation_dataset) dataset_names (tdc.generation.generation_dataset.DataLoader attribute) (tdc.generation.generation_dataset.PairedDataLoader attribute) dataverse_download() (in module tdc.utils.load) DDI (class in tdc.multi_pred.ddi) deco_hop() (in module tdc.chem_utils.oracle.oracle) Develop (class in tdc.single_pred.develop)

df (tdc.generation.generation_dataset.DataLoader3D attribute) discrete_kldiv() (in module tdc.chem_utils.evaluator) distance3d() (in module tdc.chem_utils.featurize.molconvert) distribution_dataset_load() (in module tdc.utils.load) diversity() (in module tdc.chem_utils.evaluator) docking_group (class in tdc.benchmark_group.docking_group) download_wrapper() (in module tdc.utils.load) drd2() (in module tdc.chem_utils.oracle.oracle) drugcombo_group (class in tdc.benchmark_group.drugcombo_group) DrugRes (class in tdc.multi_pred.drugres) DrugSyn (class in tdc.multi_pred.drugsyn) DTI (class in tdc.multi_pred.dti) dti_dg_group (class in tdc.benchmark_group.dti_dg_group)

E

eligible_format() (tdc.chem_utils.featurize.molconvert.MolConvert static method) entity1 (tdc.single_pred.single_pred_dataset.DataLoader attribute) entity1_idx (tdc.single_pred.single_pred_dataset.DataLoader attribute) entity1_name (tdc.multi_pred.test_multi_pred.TestMultiPred attribute) (tdc.single_pred.single_pred_dataset.DataLoader attribute) entity2_name (tdc.multi_pred.test_multi_pred.TestMultiPred attribute) Epitope (class in tdc.single_pred.epitope)

evaluate() (tdc.benchmark_group.base_group.BenchmarkGroup method) (tdc.benchmark_group.docking_group.docking_group method) evaluate_many() (tdc.benchmark_group.base_group.BenchmarkGroup method) (tdc.benchmark_group.docking_group.docking_group method) Evaluator (class in tdc.evaluator) extract_atom_from_mol() (in module tdc.utils.load) extract_atom_from_protein() (in module tdc.utils.load)

F

fcd_distance() (in module tdc.chem_utils.evaluator) fcd_distance_tf() (in module tdc.chem_utils.evaluator) fcd_distance_torch() (in module tdc.chem_utils.evaluator)

fexofenadine_mpo() (in module tdc.chem_utils.oracle.oracle) file_format (tdc.single_pred.single_pred_dataset.DataLoader attribute) fingerprints_from_mol() (in module tdc.chem_utils.oracle.oracle) fuzzy_search() (in module tdc.utils.misc)

G

GaussianModifier (class in tdc.chem_utils.oracle.oracle) GDA (class in tdc.multi_pred.gda) general_load() (in module tdc.utils.load) generation_dataset_load() (in module tdc.utils.load) generation_paired_dataset_load() (in module tdc.utils.load) get() (tdc.benchmark_group.base_group.BenchmarkGroup method) (tdc.benchmark_group.docking_group.docking_group method) get_approved_set() (tdc.single_pred.adme.ADME method) get_atom_features() (in module tdc.chem_utils.featurize.molconvert) get_cell_line_meta_data() (tdc.benchmark_group.drugcombo_group.drugcombo_group method) get_closet_match() (in module tdc.utils.misc) get_data() (tdc.base_dataset.DataLoader method) (tdc.generation.generation_dataset.DataLoader method) (tdc.generation.generation_dataset.DataLoader3D method) (tdc.generation.generation_dataset.PairedDataLoader method) (tdc.multi_pred.bi_pred_dataset.DataLoader method) (tdc.multi_pred.multi_pred_dataset.DataLoader method) (tdc.single_pred.single_pred_dataset.DataLoader method) get_fingerprints() (in module tdc.chem_utils.evaluator) get_gene_symbols() (tdc.multi_pred.drugres.DrugRes method)

get_label_map() (in module tdc.utils.retrieve) get_label_meaning() (tdc.base_dataset.DataLoader method) get_mol() (in module tdc.chem_utils.featurize.molconvert) get_mols() (in module tdc.chem_utils.evaluator) get_other_species() (tdc.single_pred.adme.ADME method) get_PHCO_fingerprint() (in module tdc.chem_utils.oracle.oracle) get_reaction_type() (in module tdc.utils.retrieve) get_split() (tdc.base_dataset.DataLoader method) (tdc.generation.generation_dataset.DataLoader method) (tdc.generation.generation_dataset.DataLoader3D method) (tdc.generation.generation_dataset.PairedDataLoader method) (tdc.generation.retrosyn.RetroSyn method) (tdc.multi_pred.bi_pred_dataset.DataLoader method) (tdc.multi_pred.multi_pred_dataset.DataLoader method) (tdc.single_pred.single_pred_dataset.DataLoader method) get_task2category() (in module tdc.metadata) get_train_valid_split() (tdc.benchmark_group.base_group.BenchmarkGroup method) (tdc.benchmark_group.docking_group.docking_group method) graphein() (tdc.single_pred.develop.Develop method) gsk3b() (in module tdc.chem_utils.oracle.oracle)

H

harmonize() (tdc.single_pred.adme.ADME method)

harmonize_affinities() (tdc.multi_pred.dti.DTI method) HTS (class in tdc.single_pred.hts)

I

ibm_rxn() (in module tdc.chem_utils.oracle.oracle) install() (in module tdc.utils.misc) interaction_dataset_load() (in module tdc.utils.load)

isomer_meta() (in module tdc.chem_utils.oracle.oracle) isomer_meta_prev() (in module tdc.chem_utils.oracle.oracle) Isomer_scoring (class in tdc.chem_utils.oracle.oracle) Isomer_scoring_prev (class in tdc.chem_utils.oracle.oracle)

J

jnk3 (class in tdc.chem_utils.oracle.oracle)

K

kabsch() (in module tdc.evaluator) kabsch_rmsd() (in module tdc.evaluator) kabsch_rotate() (in module tdc.evaluator)

kabsch_weighted() (in module tdc.evaluator) kabsch_weighted_rmsd() (in module tdc.evaluator) kl_divergence() (in module tdc.chem_utils.evaluator)

L

label_dist() (in module tdc.utils.label) label_distribution() (tdc.base_dataset.DataLoader method) label_name (tdc.single_pred.single_pred_dataset.DataLoader attribute) label_transform() (in module tdc.utils.label) LinearModifier (class in tdc.chem_utils.oracle.oracle)

load_cyp3a4_veith() (in module tdc.chem_utils.oracle.oracle) load_dict() (in module tdc.utils.misc) load_drd2_model() (in module tdc.chem_utils.oracle.oracle) load_gsk3b_model() (in module tdc.chem_utils.oracle.oracle) load_pickled_model() (in module tdc.chem_utils.oracle.oracle)

M

median_meta (class in tdc.chem_utils.oracle.oracle) MinMaxGaussianModifier (class in tdc.chem_utils.oracle.oracle) module tdc.base_dataset tdc.benchmark_group.admet_group tdc.benchmark_group.base_group tdc.benchmark_group.docking_group tdc.benchmark_group.drugcombo_group tdc.benchmark_group.dti_dg_group tdc.chem_utils.evaluator tdc.chem_utils.featurize.molconvert tdc.chem_utils.oracle.filter tdc.chem_utils.oracle.oracle tdc.evaluator tdc.generation.generation_dataset tdc.generation.molgen tdc.generation.reaction tdc.generation.retrosyn tdc.metadata tdc.multi_pred.antibodyaff tdc.multi_pred.bi_pred_dataset tdc.multi_pred.catalyst tdc.multi_pred.ddi tdc.multi_pred.drugres tdc.multi_pred.drugsyn tdc.multi_pred.dti tdc.multi_pred.gda tdc.multi_pred.mti tdc.multi_pred.multi_pred_dataset tdc.multi_pred.peptidemhc tdc.multi_pred.ppi tdc.multi_pred.test_multi_pred tdc.oracles tdc.single_pred.adme tdc.single_pred.crispr_outcome tdc.single_pred.develop tdc.single_pred.epitope tdc.single_pred.hts tdc.single_pred.paratope tdc.single_pred.qm tdc.single_pred.single_pred_dataset tdc.single_pred.test_single_pred tdc.single_pred.tox tdc.single_pred.yields tdc.utils.label tdc.utils.label_name_list tdc.utils.load tdc.utils.misc tdc.utils.query tdc.utils.retrieve tdc.utils.split

mol2file2smiles() (in module tdc.chem_utils.featurize.molconvert) mol2smiles() (in module tdc.chem_utils.featurize.molconvert) mol_conformer2graph3d() (in module tdc.chem_utils.featurize.molconvert) MolConvert (class in tdc.chem_utils.featurize.molconvert) molecule_one_retro (class in tdc.chem_utils.oracle.oracle) MoleculeFingerprint (class in tdc.chem_utils.featurize.molconvert) molfile2PyG() (in module tdc.chem_utils.featurize.molconvert) molfile2smiles() (in module tdc.chem_utils.featurize.molconvert) MolFilter (class in tdc.chem_utils.oracle.filter) MolGen (class in tdc.generation.molgen) MPO_meta (class in tdc.chem_utils.oracle.oracle) MTI (class in tdc.multi_pred.mti) multi_dataset_load() (in module tdc.utils.load)

N

name (tdc.generation.generation_dataset.DataLoader attribute) (tdc.generation.generation_dataset.DataLoader3D attribute) (tdc.generation.generation_dataset.PairedDataLoader attribute) (tdc.single_pred.single_pred_dataset.DataLoader attribute)

neg_sample() (tdc.multi_pred.bi_pred_dataset.DataLoader method) NegSample() (in module tdc.utils.label) novelty() (in module tdc.chem_utils.evaluator) numBridgeheadsAndSpiro() (in module tdc.chem_utils.oracle.oracle)

O

onek_encoding_unk() (in module tdc.chem_utils.featurize.molconvert) Oracle (class in tdc.oracles)

oracle_download_wrapper() (in module tdc.utils.load) oracle_load() (in module tdc.utils.load) osimertinib_mpo() (in module tdc.chem_utils.oracle.oracle)

P

PairedDataLoader (class in tdc.generation.generation_dataset) Paratope (class in tdc.single_pred.paratope) parse_molecular_formula() (in module tdc.chem_utils.oracle.oracle) path (tdc.generation.generation_dataset.DataLoader attribute) (tdc.generation.generation_dataset.DataLoader3D attribute) (tdc.generation.generation_dataset.PairedDataLoader attribute) (tdc.single_pred.single_pred_dataset.DataLoader attribute) pcc() (in module tdc.evaluator) pd_load() (in module tdc.utils.load) penalized_logp() (in module tdc.chem_utils.oracle.oracle) PeptideMHC (class in tdc.multi_pred.peptidemhc) perindopril_mpo() (in module tdc.chem_utils.oracle.oracle) PPI (class in tdc.multi_pred.ppi) precision_at_recall_k() (in module tdc.evaluator) print_stats() (tdc.base_dataset.DataLoader method) (tdc.generation.generation_dataset.DataLoader method) (tdc.generation.generation_dataset.DataLoader3D method) (tdc.generation.generation_dataset.PairedDataLoader method) (tdc.multi_pred.bi_pred_dataset.DataLoader method) (tdc.multi_pred.ddi.DDI method) (tdc.multi_pred.multi_pred_dataset.DataLoader method) (tdc.multi_pred.ppi.PPI method) (tdc.single_pred.single_pred_dataset.DataLoader method)

print_sys() (in module tdc.utils.misc) process_crossdock() (in module tdc.utils.load) process_dude() (in module tdc.utils.load) process_pdbbind() (in module tdc.utils.load) process_scpdb() (in module tdc.utils.load) property_dataset_load() (in module tdc.utils.load) PyScreener_meta (class in tdc.chem_utils.oracle.oracle)

Q

qed() (in module tdc.chem_utils.oracle.oracle)

QM (class in tdc.single_pred.qm)

R

range_logAUC() (in module tdc.evaluator) ranolazine_mpo() (in module tdc.chem_utils.oracle.oracle) raw3D2pyg() (in module tdc.chem_utils.featurize.molconvert) Reaction (class in tdc.generation.reaction) readFragmentScores() (in module tdc.chem_utils.oracle.oracle) recall_at_precision_k() (in module tdc.evaluator) receptor_download_wrapper() (in module tdc.utils.load) receptor_load() (in module tdc.utils.load)

rediscovery_meta (class in tdc.chem_utils.oracle.oracle) request() (in module tdc.utils.query) retrieve_all_benchmarks() (in module tdc.utils.retrieve) retrieve_benchmark_names() (in module tdc.utils.retrieve) retrieve_dataset_names() (in module tdc.utils.retrieve) retrieve_label_name_list() (in module tdc.utils.retrieve) RetroSyn (class in tdc.generation.retrosyn) rmsd() (in module tdc.evaluator) rmse() (in module tdc.evaluator)

S

SA() (in module tdc.chem_utils.oracle.oracle) save_dict() (in module tdc.utils.misc) scaffold_hop() (in module tdc.chem_utils.oracle.oracle) Score_3d (class in tdc.chem_utils.oracle.oracle) ScoreModifier (class in tdc.chem_utils.oracle.oracle) sdffile2coulomb() (in module tdc.chem_utils.featurize.molconvert) sdffile2graph3d_lst() (in module tdc.chem_utils.featurize.molconvert) sdffile2mol_conformer() (in module tdc.chem_utils.featurize.molconvert) sdffile2selfies_lst() (in module tdc.chem_utils.featurize.molconvert) sdffile2smiles_lst() (in module tdc.chem_utils.featurize.molconvert) selfies2smiles() (in module tdc.chem_utils.featurize.molconvert) similarity() (in module tdc.chem_utils.oracle.oracle) similarity_meta (class in tdc.chem_utils.oracle.oracle) single_molecule_validity() (in module tdc.chem_utils.evaluator) sitagliptin_mpo() (in module tdc.chem_utils.oracle.oracle) sitagliptin_mpo_prev() (in module tdc.chem_utils.oracle.oracle) SMARTS_scoring (class in tdc.chem_utils.oracle.oracle) smiles2daylight() (in module tdc.chem_utils.featurize.molconvert) smiles2DGL() (in module tdc.chem_utils.featurize.molconvert) smiles2ECFP2() (in module tdc.chem_utils.featurize.molconvert)

smiles2ECFP4() (in module tdc.chem_utils.featurize.molconvert) smiles2ECFP6() (in module tdc.chem_utils.featurize.molconvert) smiles2formula() (in module tdc.chem_utils.oracle.oracle) smiles2graph2D() (in module tdc.chem_utils.featurize.molconvert) smiles2maccs() (in module tdc.chem_utils.featurize.molconvert) smiles2mol() (in module tdc.chem_utils.featurize.molconvert) smiles2morgan() (in module tdc.chem_utils.featurize.molconvert) smiles2PyG() (in module tdc.chem_utils.featurize.molconvert) smiles2rdkit2d() (in module tdc.chem_utils.featurize.molconvert) smiles2selfies() (in module tdc.chem_utils.featurize.molconvert) smiles_2_fingerprint_AP() (in module tdc.chem_utils.oracle.oracle) smiles_2_fingerprint_ECFP4() (in module tdc.chem_utils.oracle.oracle) smiles_2_fingerprint_ECFP6() (in module tdc.chem_utils.oracle.oracle) smiles_2_fingerprint_FCFP4() (in module tdc.chem_utils.oracle.oracle) smiles_lst (tdc.generation.generation_dataset.DataLoader attribute) smiles_lst2coulomb() (in module tdc.chem_utils.featurize.molconvert) smiles_to_rdkit_mol() (in module tdc.chem_utils.oracle.oracle) smina() (in module tdc.chem_utils.oracle.oracle) SmoothClippedScoreModifier (class in tdc.chem_utils.oracle.oracle) SquaredModifier (class in tdc.chem_utils.oracle.oracle)

T

tdc.base_dataset module tdc.benchmark_group.admet_group module tdc.benchmark_group.base_group module tdc.benchmark_group.docking_group module tdc.benchmark_group.drugcombo_group module tdc.benchmark_group.dti_dg_group module tdc.chem_utils.evaluator module tdc.chem_utils.featurize.molconvert module tdc.chem_utils.oracle.filter module tdc.chem_utils.oracle.oracle module tdc.evaluator module tdc.generation.generation_dataset module tdc.generation.molgen module tdc.generation.reaction module tdc.generation.retrosyn module tdc.metadata module tdc.multi_pred.antibodyaff module tdc.multi_pred.bi_pred_dataset module tdc.multi_pred.catalyst module tdc.multi_pred.ddi module tdc.multi_pred.drugres module tdc.multi_pred.drugsyn module tdc.multi_pred.dti module tdc.multi_pred.gda module tdc.multi_pred.mti module tdc.multi_pred.multi_pred_dataset module

tdc.multi_pred.peptidemhc module tdc.multi_pred.ppi module tdc.multi_pred.test_multi_pred module tdc.oracles module tdc.single_pred.adme module tdc.single_pred.crispr_outcome module tdc.single_pred.develop module tdc.single_pred.epitope module tdc.single_pred.hts module tdc.single_pred.paratope module tdc.single_pred.qm module tdc.single_pred.single_pred_dataset module tdc.single_pred.test_single_pred module tdc.single_pred.tox module tdc.single_pred.yields module tdc.utils.label module tdc.utils.label_name_list module tdc.utils.load module tdc.utils.misc module tdc.utils.query module tdc.utils.retrieve module tdc.utils.split module TestMultiPred (class in tdc.multi_pred.test_multi_pred) TestSinglePred (class in tdc.single_pred.test_single_pred) three_dim_dataset_load() (in module tdc.utils.load) ThresholdedLinearModifier (class in tdc.chem_utils.oracle.oracle) to_graph() (tdc.multi_pred.bi_pred_dataset.DataLoader method) to_submission_format() (in module tdc.utils.misc) Tox (class in tdc.single_pred.tox) tree_analysis() (in module tdc.chem_utils.oracle.oracle) two_types (tdc.multi_pred.test_multi_pred.TestMultiPred attribute)

U

uniprot2seq() (in module tdc.utils.query) unique_lst_of_smiles() (in module tdc.chem_utils.evaluator)

uniqueness() (in module tdc.chem_utils.evaluator) upper_atom() (in module tdc.chem_utils.featurize.molconvert)

V

validity() (in module tdc.chem_utils.evaluator) valsartan_smarts() (in module tdc.chem_utils.oracle.oracle)

Vina_3d (class in tdc.chem_utils.oracle.oracle) Vina_smiles (class in tdc.chem_utils.oracle.oracle)

X

xyzfile2coulomb() (in module tdc.chem_utils.featurize.molconvert) xyzfile2graph3d() (in module tdc.chem_utils.featurize.molconvert)

xyzfile2selfies() (in module tdc.chem_utils.featurize.molconvert) xyzfile2smiles() (in module tdc.chem_utils.featurize.molconvert)

Y

y (tdc.single_pred.single_pred_dataset.DataLoader attribute)

Yields (class in tdc.single_pred.yields)

Z

zaleplon_mpo() (in module tdc.chem_utils.oracle.oracle)

zaleplon_mpo_prev() (in module tdc.chem_utils.oracle.oracle) zip_data_download_wrapper() (in module tdc.utils.load)