Index

_

__call__() (AlphaDropoutCP method) (CProfileFuncProfile method) (FuncProfile method) (FuncTimer method) (NanMaskingLayer method), [1] (TraceFuncCoverage method) __getitem__() (char method) (clus method) (DataSignature method) (Default method) (Molset method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) __iter__() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method)

__repr__() (BaseSignature method) (char method) (clus method) (Dataset method) (DatasetHasDatasource method) (Datasource method) (Default method) (Molrepo method) (MolrepoHasDatasource method) (MolrepoHasMolecule method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) __str__() (FuncSource method)

A

AbsErrorErrFunc (class in chemicalchecker.tool.targetmate.nonconformist.nc) across_coverage() (Diagnosis method) across_roc() (Diagnosis method) activity_regularizer (AlphaDropoutCP property) (NanMaskingLayer property), [1] AdaNetWrapper (class in chemicalchecker.tool.adanet.adanet_wrap) add() (Dataset static method) (DatasetHasDatasource static method) (Datasource static method) (Molecule static method) (Molrepo static method) (MolrepoHasDatasource static method) (Pubchem static method) add_attr() (char method) add_bulk() (Molecule static method) (Pubchem static method) add_datasets() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) add_loss() (AlphaDropoutCP method) (NanMaskingLayer method), [1] add_metric() (AlphaDropoutCP method) (NanMaskingLayer method), [1] add_missing_only() (Molecule static method) add_model_metadata() (ChemicalChecker method) add_sign_metadata() (ChemicalChecker method) add_task() (Pipeline method) add_update() (AlphaDropoutCP method) (NanMaskingLayer method), [1] add_variable() (AlphaDropoutCP method) (NanMaskingLayer method), [1] add_weight() (AlphaDropoutCP method) (NanMaskingLayer method), [1] AdditionalValidationSets (class in chemicalchecker.tool.siamese.siamese) (class in chemicalchecker.tool.siamese.siamese_triplets) AdriaTripletSampler (class in chemicalchecker.util.splitter.neighbortriplet) AE_SiameseTraintest (class in chemicalchecker.util.splitter.ae_siam_traintest) Aggregate (class in chemicalchecker.util.aggregate.aggregate) AggregateAsMatrix (class in chemicalchecker.util.aggregate.aggregate)

AggregateAsPairs (class in chemicalchecker.util.aggregate.aggregate) AggregatedCp (class in chemicalchecker.tool.targetmate.nonconformist.acp) AlphaDropoutCP (class in chemicalchecker.tool.siamese.siamese_triplets) annotate() (Molset method) ApplicabilityPredictor (class in chemicalchecker.tool.smilespred.apppred) apply() (AbsErrorErrFunc method) (ClassificationErrFunc method) (InverseProbabilityErrFunc method) (MarginErrFunc method) (RegressionErrFunc method) (SignErrorErrFunc method) apply_inverse() (AbsErrorErrFunc method) (RegressionErrFunc method) (SignErrorErrFunc method) apply_mappings() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) architecture() (AdaNetWrapper method) as_indices() (Pairs method) as_keys() (Pairs method) as_pipeline() (HyperoptClassifierConfigs method) atexit() (CProfileFuncProfile method) (FuncProfile method) (TraceFuncCoverage method) available (Datasource property) available() (BaseSignature method) (CCStatsPlot method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method)

B

bacc_score() (in module chemicalchecker.tool.targetmate.utils.metrics) background_distances() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) BaseExample (class in chemicalchecker.core.examples) BaseIcp (class in chemicalchecker.tool.targetmate.nonconformist.icp) BaseIcpCvHelper (class in chemicalchecker.tool.targetmate.nonconformist.evaluation) BaseModelAdapter (class in chemicalchecker.tool.targetmate.nonconformist.base) BaseModelNc (class in chemicalchecker.tool.targetmate.nonconformist.nc) BaseScorer (class in chemicalchecker.tool.targetmate.nonconformist.nc) BaseSignature (class in chemicalchecker.core.signature_base)

BaseSignaturizer (class in chemicalchecker.tool.targetmate.signaturizer) BaseTask (class in chemicalchecker.util.pipeline.task_base) BaseTransform (class in chemicalchecker.util.transform.base) BaseTripletSampler (class in chemicalchecker.util.splitter.neighbortriplet) BaseValidation (class in chemicalchecker.tool.targetmate.evaluation.validation) batch_size_heuristic() (in module chemicalchecker.core.sign3) batcher() (in module chemicalchecker.util.decomposition.correlation) bedroc_score() (in module chemicalchecker.tool.targetmate.utils.metrics) BootstrapConformalClassifier (class in chemicalchecker.tool.targetmate.nonconformist.acp) BootstrapSampler (class in chemicalchecker.tool.targetmate.nonconformist.acp) build() (AlphaDropoutCP method) (NanMaskingLayer method), [1] build_mixture_weights_train_op() (ExtendDNNBuilder method) (StackDNNBuilder method) build_model() (Siamese method) (SiameseTriplets method) build_subnetwork() (ExtendDNNBuilder method) (StackDNNBuilder method) build_subnetwork_report() (ExtendDNNBuilder method) (StackDNNBuilder method) build_subnetwork_train_op() (ExtendDNNBuilder method) (StackDNNBuilder method)

C

cached_property (class in chemicalchecker.util.decorator.property) calc_fn() (DataCalculator static method) calc_p() (in module chemicalchecker.tool.targetmate.nonconformist.util) Calcdata() (in module chemicalchecker.database.calcdata) calculate() (thOpt method) calibrate() (BaseIcp method) (IcpClassifier method) (IcpRegressor method) (OobCpClassifier method) (OobCpRegressor method) call() (AlphaDropoutCP method) (NanMaskingLayer method), [1] call_preprocess() (Preprocess method) canvas() (in module chemicalchecker.util.plot.util) canvas_hpc() (Diagnosis method) cc_colors() (in module chemicalchecker.util.plot.util) cc_coords() (in module chemicalchecker.util.plot.util) cc_coords_name() (in module chemicalchecker.util.plot.util) cc_grid() (in module chemicalchecker.util.plot.util) cc_palette() (in module chemicalchecker.util.plot.util) (MultiCCPlot method) (MultiPlot method) CCFit (class in chemicalchecker.util.pipeline.tasks.task_cc_fit) CCPredict (class in chemicalchecker.util.pipeline.tasks.task_cc_predict) CCStatsPlot (class in chemicalchecker.util.plot.ccstatsplot) cell_sensitivity() (Example method) char (class in chemicalchecker.core.char) check_dir_existance_create() (ChemicalChecker method) (FileSystem method) check_errors() (HPC method) (local method) (sge method) (slurm method) (slurmGPU method) check_file_existance_create() (ChemicalChecker method) (FileSystem method) Chembl (class in chemicalchecker.tool.targetmate.datasets.chembl.fetch_chembl) ChemblDb (class in chemicalchecker.tool.targetmate.datasets.chembl.fetch_chembl) chemical_name_to_inchi() (Converter static method) chemical_name_to_smiles() (Converter static method) chemicalchecker module ChemicalChecker (class in chemicalchecker.core.chemcheck) chemicalchecker.core module chemicalchecker.core.char module chemicalchecker.core.chemcheck module chemicalchecker.core.clus module chemicalchecker.core.data module chemicalchecker.core.diagnostics module chemicalchecker.core.examples module chemicalchecker.core.molkit module chemicalchecker.core.neig module chemicalchecker.core.preprocess module chemicalchecker.core.proj module chemicalchecker.core.projector module chemicalchecker.core.projector.default module chemicalchecker.core.projector.pca module chemicalchecker.core.projector.tsne module chemicalchecker.core.projector.umap_ module chemicalchecker.core.sign0 module chemicalchecker.core.sign1 module chemicalchecker.core.sign2 module chemicalchecker.core.sign3 module chemicalchecker.core.sign4 module chemicalchecker.core.signature_base module chemicalchecker.core.signature_data module chemicalchecker.core.validation module chemicalchecker.database module chemicalchecker.database.calcdata module chemicalchecker.database.database module chemicalchecker.database.dataset module chemicalchecker.database.datasource module chemicalchecker.database.molecule module chemicalchecker.database.molrepo module chemicalchecker.database.pubchem module chemicalchecker.database.uniprotkb module chemicalchecker.tool module chemicalchecker.tool.adanet module chemicalchecker.tool.adanet.adanet_wrap module chemicalchecker.tool.adanet.dnn_extend_generator module chemicalchecker.tool.adanet.dnn_stack_generator module chemicalchecker.tool.hotnet module chemicalchecker.tool.hotnet.hotnet module chemicalchecker.tool.node2vec module chemicalchecker.tool.node2vec.node2vec module chemicalchecker.tool.node2vec.word2vec module chemicalchecker.tool.siamese module chemicalchecker.tool.siamese.callbacks module chemicalchecker.tool.siamese.siamese module chemicalchecker.tool.siamese.siamese_triplets module chemicalchecker.tool.smilespred module chemicalchecker.tool.smilespred.apppred module chemicalchecker.tool.smilespred.smilespred module chemicalchecker.tool.targetmate module chemicalchecker.tool.targetmate.base module chemicalchecker.tool.targetmate.datasets module chemicalchecker.tool.targetmate.datasets.chembl module chemicalchecker.tool.targetmate.datasets.chembl.fetch_chembl module chemicalchecker.tool.targetmate.datasets.drugbank module chemicalchecker.tool.targetmate.datasets.drugbank.fetch_drugbank module chemicalchecker.tool.targetmate.datasets.moleculenet module chemicalchecker.tool.targetmate.datasets.moleculenet.fetch_moleculenet module chemicalchecker.tool.targetmate.evaluation module chemicalchecker.tool.targetmate.evaluation.prediction module chemicalchecker.tool.targetmate.evaluation.score module chemicalchecker.tool.targetmate.evaluation.validation module chemicalchecker.tool.targetmate.examples module chemicalchecker.tool.targetmate.io module chemicalchecker.tool.targetmate.ml module chemicalchecker.tool.targetmate.models module chemicalchecker.tool.targetmate.models.hyperoptconfigs module chemicalchecker.tool.targetmate.models.vanillaconfigs module chemicalchecker.tool.targetmate.multi module chemicalchecker.tool.targetmate.nonconformist module chemicalchecker.tool.targetmate.nonconformist.acp module chemicalchecker.tool.targetmate.nonconformist.base module chemicalchecker.tool.targetmate.nonconformist.cp module chemicalchecker.tool.targetmate.nonconformist.evaluation module chemicalchecker.tool.targetmate.nonconformist.icp module chemicalchecker.tool.targetmate.nonconformist.nc module chemicalchecker.tool.targetmate.nonconformist.util module chemicalchecker.tool.targetmate.run module chemicalchecker.tool.targetmate.signaturizer module chemicalchecker.tool.targetmate.tmsetup module chemicalchecker.tool.targetmate.universes module chemicalchecker.tool.targetmate.universes.univs module chemicalchecker.tool.targetmate.utils module chemicalchecker.tool.targetmate.utils.chemistry module chemicalchecker.tool.targetmate.utils.conformal module chemicalchecker.tool.targetmate.utils.hpc module chemicalchecker.tool.targetmate.utils.log module chemicalchecker.tool.targetmate.utils.metrics module chemicalchecker.tool.targetmate.utils.pairs module chemicalchecker.tool.targetmate.utils.splitters module chemicalchecker.tool.targetmate.utils.tasks module chemicalchecker.tool.targetmate.utils.topped module chemicalchecker.util module chemicalchecker.util.aggregate module chemicalchecker.util.aggregate.aggregate module chemicalchecker.util.config module chemicalchecker.util.config.config module chemicalchecker.util.decomposition module chemicalchecker.util.decomposition.correlation module chemicalchecker.util.decorator module chemicalchecker.util.decorator.profilehooks module chemicalchecker.util.decorator.property module chemicalchecker.util.decorator.safe module chemicalchecker.util.decorator.timeout module chemicalchecker.util.download module chemicalchecker.util.download.download module chemicalchecker.util.filesystem module chemicalchecker.util.filesystem.filesystem module chemicalchecker.util.hpc module chemicalchecker.util.hpc.hpc module chemicalchecker.util.hpc.local module chemicalchecker.util.hpc.sge module chemicalchecker.util.hpc.slurm module chemicalchecker.util.hpc.slurm_gpu module chemicalchecker.util.hpc.test_script module chemicalchecker.util.keytype module chemicalchecker.util.keytype.detect module chemicalchecker.util.logging module chemicalchecker.util.logging.our_logging module chemicalchecker.util.mol2svg module chemicalchecker.util.mol2svg.mol2svg module chemicalchecker.util.network module chemicalchecker.util.network.network module chemicalchecker.util.parser module chemicalchecker.util.parser.converter module chemicalchecker.util.parser.data_calculator module chemicalchecker.util.parser.parser module chemicalchecker.util.performance module chemicalchecker.util.performance.linkprediction module

chemicalchecker.util.performance.performance module chemicalchecker.util.pipeline module chemicalchecker.util.pipeline.pipeline module chemicalchecker.util.pipeline.task_base module chemicalchecker.util.pipeline.tasks module chemicalchecker.util.pipeline.tasks.python_callable_task module chemicalchecker.util.pipeline.tasks.task_cc_fit module chemicalchecker.util.pipeline.tasks.task_cc_predict module chemicalchecker.util.pipeline.tasks_web module chemicalchecker.util.pipeline.tasks_web.task_web_coordinates module chemicalchecker.util.pipeline.tasks_web.task_web_libraries module chemicalchecker.util.pipeline.tasks_web.task_web_molinfo module chemicalchecker.util.pipeline.tasks_web.task_web_plots module chemicalchecker.util.pipeline.tasks_web.task_web_projections module chemicalchecker.util.pipeline.tasks_web.task_web_pubchem module chemicalchecker.util.pipeline.tasks_web.task_web_showtargets module chemicalchecker.util.pipeline.tasks_web.task_web_similars module chemicalchecker.util.pipeline.tasks_web.task_web_statsplots module chemicalchecker.util.plot module chemicalchecker.util.plot.ccstatsplot module chemicalchecker.util.plot.diagnosticsplot module chemicalchecker.util.plot.multiccplot module chemicalchecker.util.plot.multiplot module chemicalchecker.util.plot.plot module chemicalchecker.util.plot.util module chemicalchecker.util.psql module chemicalchecker.util.psql.psql module chemicalchecker.util.remove_near_duplicates module chemicalchecker.util.remove_near_duplicates.remove_near_duplicates module chemicalchecker.util.sampler module chemicalchecker.util.sampler.triplets module chemicalchecker.util.sanitize module chemicalchecker.util.sanitize.sanitizer module chemicalchecker.util.splitter module chemicalchecker.util.splitter.ae_siam_traintest module chemicalchecker.util.splitter.globalneighbortriplets module chemicalchecker.util.splitter.neighborerror module chemicalchecker.util.splitter.neighborpair module chemicalchecker.util.splitter.neighbortriplet module chemicalchecker.util.splitter.pairtraintest module chemicalchecker.util.splitter.traintest module chemicalchecker.util.transform module chemicalchecker.util.transform.base module chemicalchecker.util.transform.gaussian_scale_impute module chemicalchecker.util.transform.gaussianize module chemicalchecker.util.transform.lsi module chemicalchecker.util.transform.metric_learn module chemicalchecker.util.transform.pca module chemicalchecker.util.transform.scale module choice() (TripletSampler method) choose_beta() (Hotnet method) chunk_iter() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) chunker() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) class_avg_c() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_empty() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_mean_errors() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_mean_errors_one_class() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_mean_p_val() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_n_correct() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_one_c() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_one_err() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) class_one_err_one_class() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) ClassIcpCvHelper (class in chemicalchecker.tool.targetmate.nonconformist.evaluation) ClassificationErrFunc (class in chemicalchecker.tool.targetmate.nonconformist.nc) classifier_performances() (Performances method) ClassifierAdapter (class in chemicalchecker.tool.targetmate.nonconformist.base) ClassifierMixin (class in chemicalchecker.tool.targetmate.nonconformist.base) ClassifierNc (class in chemicalchecker.tool.targetmate.nonconformist.nc) clean() (BaseTask method) (CCFit method) (CCPredict method) (Coordinates method) (Libraries method) (MolecularInfo method) (Pipeline method) (Plots method) (Projections method) (Pubchem method) (PythonCallable method) (ShowTargets method) (Similars method) (StatsPlots method) clear() (BaseSignature method) (char method) (clus method) (CProfileFuncProfile.Profile method) (Default method) (Diagnosis method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) clear_all() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) close() (AE_SiameseTraintest method) (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (Traintest method) (TripletIterator method) clus (class in chemicalchecker.core.clus) cm2inch() (in module chemicalchecker.util.plot.util) cmap_discretize() (MultiCCPlot method) (MultiPlot method) cohen_kappa_score() (in module chemicalchecker.tool.targetmate.utils.metrics) col_wise_correlation() (in module chemicalchecker.core.sign3) complete_sign2_universe() (sign3 method) CompleteModel (class in chemicalchecker.tool.targetmate.run) compress() (HPC method) (local method) (sge method) (slurm method) (slurmGPU method) compress_models() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) compute_distance_pvalues() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) compute_dtype (AlphaDropoutCP property) (NanMaskingLayer property), [1] compute_mask() (AlphaDropoutCP method) (NanMaskingLayer method), [1] compute_output_shape() (AlphaDropoutCP method) (NanMaskingLayer method), [1] compute_output_signature() (AlphaDropoutCP method) (NanMaskingLayer method), [1] condition() (in module chemicalchecker.tool.targetmate.utils.conformal) Config (class in chemicalchecker.util.config.config) consistency_check() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) ConversionError Converter (class in chemicalchecker.util.parser.converter) coord_color() (in module chemicalchecker.util.plot.plot) (in module chemicalchecker.util.plot.util) coordinates (ChemicalChecker property) Coordinates (class in chemicalchecker.util.pipeline.tasks_web.task_web_coordinates) copy_from() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) copy_sign0_to_sign1() (sign1 method) copy_signature_from() (ChemicalChecker method) Corpus (class in chemicalchecker.util.transform.lsi) cosine_distances() (Diagnosis method) count() (Molrepo static method) count_never_executed() (FuncSource method) count_params() (AlphaDropoutCP method) (NanMaskingLayer method), [1] coverage() (in module chemicalchecker.util.decorator.profilehooks) coverage_with_hotshot() (in module chemicalchecker.util.decorator.profilehooks) CProfileFuncProfile (class in chemicalchecker.util.decorator.profilehooks) CProfileFuncProfile.Profile (class in chemicalchecker.util.decorator.profilehooks) create() (NeighborErrorTraintest static method) (NeighborPairTraintest static method) (PairTraintest static method) (Traintest static method) create_signature_file() (Traintest static method) create_similarity_matrix() (Hotnet method) cross_coverage() (Diagnosis method) cross_roc() (Diagnosis method) cross_val_score() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) cross_validate() (in module chemicalchecker.util.decomposition.correlation) CrossConformalClassifier (class in chemicalchecker.tool.targetmate.nonconformist.acp) CrossSampler (class in chemicalchecker.tool.targetmate.nonconformist.acp) ctd_to_smiles() (Converter static method) CyclicLR (class in chemicalchecker.tool.siamese.callbacks)

D

data_from_disk() (in module chemicalchecker.tool.targetmate.io) data_path (Datasource property) data_to_disk() (in module chemicalchecker.tool.targetmate.io) DataCalculator (class in chemicalchecker.util.parser.data_calculator) DataFactory (class in chemicalchecker.core.data) dataloader() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) Dataset (class in chemicalchecker.database.dataset) dataset_correlation() (in module chemicalchecker.util.decomposition.correlation) DatasetHasDatasource (class in chemicalchecker.database.dataset) datasets (ChemicalChecker property) datasets_exemplary() (ChemicalChecker method)

DataSignature (class in chemicalchecker.core.signature_data) Datasource (class in chemicalchecker.database.datasource) DBConfig (class in chemicalchecker.database.database) DeepchemScaffoldSplit (class in chemicalchecker.tool.targetmate.utils.splitters) Default (class in chemicalchecker.core.projector.default) delta_gmm() (in module chemicalchecker.util.transform.gaussianize) delta_init() (in module chemicalchecker.util.transform.gaussianize) Diagnosis (class in chemicalchecker.core.diagnostics) DiagnosisPlot (class in chemicalchecker.util.plot.diagnosticsplot) diagnostics_hpc() (Diagnosis static method) dimensions() (Diagnosis method) disable() (CProfileFuncProfile.Profile method) download() (Datasource method) (Downloader method) download_hpc() (Datasource static method) Downloader (class in chemicalchecker.util.download.download) drug_targets() (Example method) DrugBank (class in chemicalchecker.tool.targetmate.datasets.drugbank.fetch_drugbank) DrugBankDb (class in chemicalchecker.tool.targetmate.datasets.drugbank.fetch_drugbank) dtype (AlphaDropoutCP property) (NanMaskingLayer property), [1] dtype_policy (AlphaDropoutCP property) (NanMaskingLayer property), [1] dynamic (AlphaDropoutCP property) (NanMaskingLayer property), [1]

E

emb_to_h5() (Node2Vec method) enable() (CProfileFuncProfile.Profile method) epoch_per_iteration_heuristic() (in module chemicalchecker.core.sign3) euclidean_distances() (Diagnosis method) eval_node2vec() (sign2 method) Example (class in chemicalchecker.core.examples) execute() (CCFit method) (CCPredict method) (Coordinates method) (Libraries method) (MolecularInfo method) (Plots method) (Projections method) (Pubchem method) (ShowTargets method) (Similars method) (StatsPlots method)

Explanation (class in chemicalchecker.tool.targetmate.io) export() (ChemicalChecker method) export_cc() (ChemicalChecker method) export_symlinks() (ChemicalChecker method) ExtendDNNBuilder (class in chemicalchecker.tool.adanet.dnn_extend_generator) ExtendDNNGenerator (class in chemicalchecker.tool.adanet.dnn_extend_generator)

F

FileSystem (class in chemicalchecker.util.filesystem.filesystem) filter_h5_dataset() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) filter_validity() (in module chemicalchecker.tool.targetmate.io) finalize_state() (AlphaDropoutCP method) (NanMaskingLayer method), [1] find_base_mod() (Model method) (SignaturedModel method) (StackedModel method) (TargetMateStackedClassifier method) find_class() (UniverseLoader method) find_source_lines() (FuncSource method) find_thr() (char method) Fingerprinter (class in chemicalchecker.tool.targetmate.signaturizer) fingerprints() (Example method) fit() (AggregatedCp method) (BaseIcp method) (BaseModelAdapter method) (BaseModelNc method) (BaseSignature method) (BootstrapConformalClassifier method) (char method) (ClassifierAdapter method) (ClassifierNc method) (clus method) (CrossConformalClassifier method) (Default method) (Gaussianize method) (IcpClassifier method) (IcpRegressor method) (neig method) (OobClassifierAdapter method) (OobCpClassifier method) (OobCpRegressor method) (OobRegressorAdapter method) (PCA method) (Preprocess method) (proj method) (RegressorAdapter method) (RegressorNc method) (Siamese method) (SiameseTriplets method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (StackedModel method) (TargetMateStackedClassifier method) (TSNE method) (UMAP method) fit_end() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method)

fit_hpc() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) fit_transform() (Gaussianize method) from_config() (AlphaDropoutCP class method) (NanMaskingLayer class method), [1] from_csv() (Dataset static method) (DatasetHasDatasource static method) (Datasource static method) (Molrepo static method) (MolrepoHasDatasource static method) from_molrepo_name() (Molrepo static method) func_hpc() (BaseSignature method) (BaseSignaturizer method) (char method) (clus method) (Default method) (Fingerprinter method) (HPCUtils method) (Model method) (ModelSetup method) (Molset method) (neig method) (PCA method) (Prediction method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) (TSNE method) (UMAP method) (Validation method) FuncProfile (class in chemicalchecker.util.decorator.profilehooks) FuncProfile.Profile (class in chemicalchecker.util.decorator.profilehooks) FuncSource (class in chemicalchecker.util.decorator.profilehooks) FuncTimer (class in chemicalchecker.util.decorator.profilehooks)

G

Gatherer (class in chemicalchecker.tool.targetmate.evaluation.validation) Gaussianize (class in chemicalchecker.util.transform.gaussianize) generate_candidates() (ExtendDNNGenerator method) (StackDNNGenerator method) generate_scaffold() (in module chemicalchecker.tool.targetmate.utils.chemistry) generate_scaffolds() (in module chemicalchecker.tool.targetmate.utils.splitters) generate_triplets() (AdriaTripletSampler method) (OldTripletSampler method) generator_fn() (AE_SiameseTraintest static method) (char method) (clus method) (DataSignature method) (Default method) (neig method) (NeighborErrorTraintest static method) (NeighborPairTraintest static method) (PairTraintest static method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (Traintest static method) (TripletIterator static method) (TSNE method) (UMAP method) get() (Dataset static method) (Datasource static method) (Molecule static method) (Molrepo static method) (MolrepoHasMolecule static method) (Pubchem static method) get_agg_func() (AggregateAsMatrix method) (AggregateAsPairs method) get_all_p() (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (TripletIterator method) get_all_x() (NeighborErrorTraintest method) (NeighborPairTraintest method) (Traintest method) (TripletIterator method) get_all_x1() (PairTraintest method) get_all_x2() (PairTraintest method) get_all_x_columns() (Traintest method) get_all_y() (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (Traintest method) (TripletIterator method) get_by_molrepo_name() (Molrepo static method) get_cc() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_chebi() (Molset static method) get_chembl_hierarchy() (Molset static method) get_chembl_protein_classes() (Molset static method) get_config() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_connection() (in module chemicalchecker.util.psql.psql) get_coordinates() (Dataset static method) get_cross_conformal_classifier() (in module chemicalchecker.tool.targetmate.utils.conformal) get_cross_conformal_regressor() (in module chemicalchecker.tool.targetmate.utils.conformal) get_data() (sign0 method) get_data_signature() (ChemicalChecker method) get_dict() (char method) get_engine() (in module chemicalchecker.database.database) get_fields_by_molrepo_name() (Molrepo static method) get_global_signature() (ChemicalChecker method) get_h5_attr() (char method) get_h5_dataset() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_h5_metadata() (ChemicalChecker static method) get_input_at() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_input_mask_at() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_input_shape_at() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_intersection() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_kth_nearest() (neig method) get_losses_for() (NanMaskingLayer method), [1] get_metadatas() (ChemicalChecker static method) get_model_metadata() (ChemicalChecker static method) get_molecule() (ChemicalChecker method) get_molset() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_neig() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_non_redundant_intersection() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method)

get_output_at() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_output_mask_at() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_output_shape_at() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_p() (NeighborPairTraintest method) (PairTraintest method) get_params() (AggregatedCp method) (BaseIcp method) (BaseIcpCvHelper method) (BaseModelAdapter method) (BaseModelNc method) (BaseScorer method) (BootstrapConformalClassifier method) (ClassIcpCvHelper method) (ClassifierAdapter method) (ClassifierNc method) (CrossConformalClassifier method) (IcpClassifier method) (IcpRegressor method) (OobClassifierAdapter method) (OobCpClassifier method) (OobCpRegressor method) (OobRegressorAdapter method) (RegIcpCvHelper method) (RegressorAdapter method) (RegressorNc method) (RegressorNormalizer method) (TcpClassifier method) get_protein() (UniprotKB method) get_proteins() (UniprotKB method) get_py() (NeighborPairTraintest method) (PairTraintest method) get_py_shapes() (NeighborPairTraintest method) (PairTraintest method) get_random_hash() (in module chemicalchecker.database.uniprotkb) get_reference_proteome() (UniprotKB method) get_same_different() (Plot method) get_sample_actual_pred() (LinkPrediction method) get_self_triplets() (sign1 method) get_session() (in module chemicalchecker.database.database) get_sign() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_signature() (ChemicalChecker method) get_signature_path() (ChemicalChecker method) get_split_indeces() (AdriaTripletSampler method) (AE_SiameseTraintest static method) (BaseTripletSampler method) (NeighborErrorTraintest static method) (NeighborPairTraintest static method) (OldTripletSampler method) (PairTraintest static method) (PrecomputedTripletSampler method) (Traintest static method) get_split_names() (AE_SiameseTraintest method) (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (Traintest method) (TripletIterator method) get_sw() (AE_SiameseTraintest method) (Traintest method) get_t() (NeighborErrorTraintest method) (TripletIterator method) get_trainable_variables() (AdaNetWrapper static method) get_triplets() (sign1 method) get_ty_shapes() (NeighborErrorTraintest method) (TripletIterator method) get_uniprot_annotation() (Molset static method) get_universe_molrepos() (Molrepo static method) get_updates_for() (NanMaskingLayer method), [1] get_vectors() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_vectors_lite() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) get_weights() (AlphaDropoutCP method) (NanMaskingLayer method), [1] get_x() (AE_SiameseTraintest method) (Traintest method) get_x_columns() (TripletIterator method) get_x_shapes() (AE_SiameseTraintest method) (Traintest method) get_xy() (AE_SiameseTraintest method) (Traintest method) get_Xy_from_data() (SignaturedModel method) (StackedModel method) (TargetMateStackedClassifier method) get_xy_shapes() (AE_SiameseTraintest method) (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (Traintest method) (TripletIterator method) get_y() (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (Traintest method) (TripletIterator method) GetSplitter() (in module chemicalchecker.tool.targetmate.utils.splitters) getstats() (CProfileFuncProfile.Profile method) global_ranks_agreement() (Diagnosis method) GlobalNeighborTripletTraintest (class in chemicalchecker.util.splitter.globalneighbortriplets) grid_search_adanet() (sign2 method) grid_search_node2vec() (sign2 method)

H

heuristic_max_degree() (Node2Vec static method) homogenous_ticks() (in module chemicalchecker.util.plot.util) Hotnet (class in chemicalchecker.tool.hotnet.hotnet) HotnetNetwork (class in chemicalchecker.util.network.network) HPC (class in chemicalchecker.util.hpc.hpc) HPCUtils (class in chemicalchecker.tool.targetmate.utils.hpc) hstack_signatures() (char static method) (clus static method) (DataSignature static method) (Default static method) (neig static method) (PCA static method) (proj static method) (sign0 static method) (sign1 static method) (sign2 static method) (sign3 static method) (sign4 static method) (TSNE static method) (UMAP static method)

HyperOpt (class in chemicalchecker.tool.targetmate.models.hyperoptconfigs) HyperoptClassifierConfigs (class in chemicalchecker.tool.targetmate.models.hyperoptconfigs)

I

IcpClassifier (class in chemicalchecker.tool.targetmate.nonconformist.icp) IcpRegressor (class in chemicalchecker.tool.targetmate.nonconformist.icp) igmm() (in module chemicalchecker.util.transform.gaussianize) inbound_nodes (AlphaDropoutCP property) (NanMaskingLayer property), [1] inchi_to_inchikey() (Converter method) inchi_to_mol() (Converter method) inchi_to_smiles() (Converter method) InchiData (class in chemicalchecker.tool.targetmate.io) inchikey_to_inchi() (Converter static method) index() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) info_h5 (char property) (clus property) (DataSignature property) (Default property) (neig property) (PCA property) (proj property) (sign0 property) (sign1 property) (sign2 property) (sign3 property) (sign4 property) (TSNE property) (UMAP property)

input (AlphaDropoutCP property) (NanMaskingLayer property), [1] input_fn() (AdaNetWrapper method) input_mask (AlphaDropoutCP property) (NanMaskingLayer property), [1] input_shape (AlphaDropoutCP property) (NanMaskingLayer property), [1] input_spec (AlphaDropoutCP property) (NanMaskingLayer property), [1] InputData (class in chemicalchecker.tool.targetmate.io) insert_task() (Pipeline method) inverse() (in module chemicalchecker.util.transform.gaussianize) inverse_linear_pow2() (in module chemicalchecker.core.sign3) inverse_transform() (Gaussianize method) InverseProbabilityErrFunc (class in chemicalchecker.tool.targetmate.nonconformist.nc) is_inchi() (KeyTypeDetector static method) is_inchikey() (KeyTypeDetector static method) is_ready() (BaseTask method) (CCFit method) (CCPredict method) (Coordinates method) (Libraries method) (MolecularInfo method) (Plots method) (Projections method) (Pubchem method) (PythonCallable method) (ShowTargets method) (Similars method) (StatsPlots method) is_smiles() (KeyTypeDetector static method) isin() (Mol method)

J

jaccard_similarity() (neig static method)

K

KeyTypeDetector (class in chemicalchecker.util.keytype.detect)

L

layer_size_heuristic() (in module chemicalchecker.core.sign3) learn_sign0() (sign4 method) learn_sign0_conf() (sign4 method) LearningRateFinder (class in chemicalchecker.tool.siamese.callbacks) left_right_split() (Pairs method) left_split() (Pairs method) Libraries (class in chemicalchecker.util.pipeline.tasks_web.task_web_libraries) lighten_color() (in module chemicalchecker.util.plot.plot) (in module chemicalchecker.util.plot.util) linear_pow2() (in module chemicalchecker.core.sign3) link() (ChemicalChecker method) LinkPrediction (class in chemicalchecker.util.performance.linkprediction) load() (BaseSignaturizer static method) (Fingerprinter static method) (Model static method) (ModelSetup static method) (Molset class method) (SignaturedModel static method) (Signaturizer static method) (SignaturizerSetup static method) (StackedModel static method) (TargetMateClassifierSetup static method) (TargetMateRegressorSetup static method) (TargetMateSetup static method) (TargetMateStackedClassifier static method) (UniverseLoader method)

load_base_mod() (Model method) (SignaturedModel method) (StackedModel method) (TargetMateStackedClassifier method) load_base_model() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) load_morgan_arena() (in module chemicalchecker.tool.targetmate.utils.chemistry) load_validation() (in module chemicalchecker.tool.targetmate.evaluation.validation) local (class in chemicalchecker.util.hpc.local) losses (AlphaDropoutCP property) (NanMaskingLayer property), [1] Lsi (class in chemicalchecker.util.transform.lsi)

M

maccs_matrix() (in module chemicalchecker.tool.targetmate.utils.chemistry) make_cbar_ax() (in module chemicalchecker.util.plot.util) make_cmap() (in module chemicalchecker.util.plot.util) make_data() (DataFactory static method) make_filtered_copy() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) map_names_to_uniprot_acs() (UniprotKB method) map_protein_to_uniref100_representative() (UniprotKB method) map_secondary_to_primary() (UniprotKB method) map_triplets_to_reference() (TripletSampler method) map_xrefs_to_uniprot_acs() (UniprotKB method) MarginErrFunc (class in chemicalchecker.tool.targetmate.nonconformist.nc) mark() (FuncSource method) mark_ready() (BaseTask method) (CCFit method) (CCPredict method) (Coordinates method) (Libraries method) (MolecularInfo method) (Plots method) (Projections method) (Pubchem method) (PythonCallable method) (ShowTargets method) (Similars method) (StatsPlots method) mask_exclude() (in module chemicalchecker.core.sign3) mask_keep() (in module chemicalchecker.core.sign3) master_key_type() (BaseSignaturizer method) (Fingerprinter method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateStackedClassifier method) merge_edgelists() (Node2Vec method) metadata (ChemicalChecker property) metapredict() (Prediction method) Metric() (in module chemicalchecker.tool.targetmate.utils.metrics) metric_calc() (Model method) (SignaturedModel method) (StackedModel method) (TargetMateStackedClassifier method) MetricLearn (class in chemicalchecker.util.transform.metric_learn) metrics (AlphaDropoutCP property) (NanMaskingLayer property), [1] Model (class in chemicalchecker.tool.targetmate.base) ModelSetup (class in chemicalchecker.tool.targetmate.tmsetup) module chemicalchecker chemicalchecker.core chemicalchecker.core.char chemicalchecker.core.chemcheck chemicalchecker.core.clus chemicalchecker.core.data chemicalchecker.core.diagnostics chemicalchecker.core.examples chemicalchecker.core.molkit chemicalchecker.core.neig chemicalchecker.core.preprocess chemicalchecker.core.proj chemicalchecker.core.projector chemicalchecker.core.projector.default chemicalchecker.core.projector.pca chemicalchecker.core.projector.tsne chemicalchecker.core.projector.umap_ chemicalchecker.core.sign0 chemicalchecker.core.sign1 chemicalchecker.core.sign2 chemicalchecker.core.sign3 chemicalchecker.core.sign4 chemicalchecker.core.signature_base chemicalchecker.core.signature_data chemicalchecker.core.validation chemicalchecker.database chemicalchecker.database.calcdata chemicalchecker.database.database chemicalchecker.database.dataset chemicalchecker.database.datasource chemicalchecker.database.molecule chemicalchecker.database.molrepo chemicalchecker.database.pubchem chemicalchecker.database.uniprotkb chemicalchecker.tool chemicalchecker.tool.adanet chemicalchecker.tool.adanet.adanet_wrap chemicalchecker.tool.adanet.dnn_extend_generator chemicalchecker.tool.adanet.dnn_stack_generator chemicalchecker.tool.hotnet chemicalchecker.tool.hotnet.hotnet chemicalchecker.tool.node2vec chemicalchecker.tool.node2vec.node2vec chemicalchecker.tool.node2vec.word2vec chemicalchecker.tool.siamese chemicalchecker.tool.siamese.callbacks chemicalchecker.tool.siamese.siamese chemicalchecker.tool.siamese.siamese_triplets chemicalchecker.tool.smilespred chemicalchecker.tool.smilespred.apppred chemicalchecker.tool.smilespred.smilespred chemicalchecker.tool.targetmate chemicalchecker.tool.targetmate.base chemicalchecker.tool.targetmate.datasets chemicalchecker.tool.targetmate.datasets.chembl chemicalchecker.tool.targetmate.datasets.chembl.fetch_chembl chemicalchecker.tool.targetmate.datasets.drugbank chemicalchecker.tool.targetmate.datasets.drugbank.fetch_drugbank chemicalchecker.tool.targetmate.datasets.moleculenet chemicalchecker.tool.targetmate.datasets.moleculenet.fetch_moleculenet chemicalchecker.tool.targetmate.evaluation chemicalchecker.tool.targetmate.evaluation.prediction chemicalchecker.tool.targetmate.evaluation.score chemicalchecker.tool.targetmate.evaluation.validation chemicalchecker.tool.targetmate.examples chemicalchecker.tool.targetmate.io chemicalchecker.tool.targetmate.ml chemicalchecker.tool.targetmate.models chemicalchecker.tool.targetmate.models.hyperoptconfigs chemicalchecker.tool.targetmate.models.vanillaconfigs chemicalchecker.tool.targetmate.multi chemicalchecker.tool.targetmate.nonconformist chemicalchecker.tool.targetmate.nonconformist.acp chemicalchecker.tool.targetmate.nonconformist.base chemicalchecker.tool.targetmate.nonconformist.cp chemicalchecker.tool.targetmate.nonconformist.evaluation chemicalchecker.tool.targetmate.nonconformist.icp chemicalchecker.tool.targetmate.nonconformist.nc chemicalchecker.tool.targetmate.nonconformist.util chemicalchecker.tool.targetmate.run chemicalchecker.tool.targetmate.signaturizer chemicalchecker.tool.targetmate.tmsetup chemicalchecker.tool.targetmate.universes chemicalchecker.tool.targetmate.universes.univs chemicalchecker.tool.targetmate.utils chemicalchecker.tool.targetmate.utils.chemistry chemicalchecker.tool.targetmate.utils.conformal chemicalchecker.tool.targetmate.utils.hpc chemicalchecker.tool.targetmate.utils.log chemicalchecker.tool.targetmate.utils.metrics chemicalchecker.tool.targetmate.utils.pairs chemicalchecker.tool.targetmate.utils.splitters chemicalchecker.tool.targetmate.utils.tasks chemicalchecker.tool.targetmate.utils.topped chemicalchecker.util chemicalchecker.util.aggregate chemicalchecker.util.aggregate.aggregate chemicalchecker.util.config chemicalchecker.util.config.config chemicalchecker.util.decomposition chemicalchecker.util.decomposition.correlation chemicalchecker.util.decorator chemicalchecker.util.decorator.profilehooks chemicalchecker.util.decorator.property chemicalchecker.util.decorator.safe chemicalchecker.util.decorator.timeout chemicalchecker.util.download chemicalchecker.util.download.download chemicalchecker.util.filesystem chemicalchecker.util.filesystem.filesystem chemicalchecker.util.hpc chemicalchecker.util.hpc.hpc chemicalchecker.util.hpc.local chemicalchecker.util.hpc.sge chemicalchecker.util.hpc.slurm chemicalchecker.util.hpc.slurm_gpu chemicalchecker.util.hpc.test_script chemicalchecker.util.keytype chemicalchecker.util.keytype.detect chemicalchecker.util.logging chemicalchecker.util.logging.our_logging chemicalchecker.util.mol2svg chemicalchecker.util.mol2svg.mol2svg chemicalchecker.util.network chemicalchecker.util.network.network chemicalchecker.util.parser chemicalchecker.util.parser.converter chemicalchecker.util.parser.data_calculator chemicalchecker.util.parser.parser chemicalchecker.util.performance chemicalchecker.util.performance.linkprediction chemicalchecker.util.performance.performance chemicalchecker.util.pipeline chemicalchecker.util.pipeline.pipeline chemicalchecker.util.pipeline.task_base chemicalchecker.util.pipeline.tasks chemicalchecker.util.pipeline.tasks.python_callable_task chemicalchecker.util.pipeline.tasks.task_cc_fit chemicalchecker.util.pipeline.tasks.task_cc_predict chemicalchecker.util.pipeline.tasks_web chemicalchecker.util.pipeline.tasks_web.task_web_coordinates chemicalchecker.util.pipeline.tasks_web.task_web_libraries chemicalchecker.util.pipeline.tasks_web.task_web_molinfo chemicalchecker.util.pipeline.tasks_web.task_web_plots chemicalchecker.util.pipeline.tasks_web.task_web_projections chemicalchecker.util.pipeline.tasks_web.task_web_pubchem chemicalchecker.util.pipeline.tasks_web.task_web_showtargets chemicalchecker.util.pipeline.tasks_web.task_web_similars chemicalchecker.util.pipeline.tasks_web.task_web_statsplots chemicalchecker.util.plot chemicalchecker.util.plot.ccstatsplot chemicalchecker.util.plot.diagnosticsplot chemicalchecker.util.plot.multiccplot chemicalchecker.util.plot.multiplot chemicalchecker.util.plot.plot chemicalchecker.util.plot.util chemicalchecker.util.psql chemicalchecker.util.psql.psql chemicalchecker.util.remove_near_duplicates chemicalchecker.util.remove_near_duplicates.remove_near_duplicates chemicalchecker.util.sampler chemicalchecker.util.sampler.triplets chemicalchecker.util.sanitize chemicalchecker.util.sanitize.sanitizer chemicalchecker.util.splitter chemicalchecker.util.splitter.ae_siam_traintest chemicalchecker.util.splitter.globalneighbortriplets chemicalchecker.util.splitter.neighborerror chemicalchecker.util.splitter.neighborpair chemicalchecker.util.splitter.neighbortriplet chemicalchecker.util.splitter.pairtraintest chemicalchecker.util.splitter.traintest chemicalchecker.util.transform chemicalchecker.util.transform.base chemicalchecker.util.transform.gaussian_scale_impute chemicalchecker.util.transform.gaussianize chemicalchecker.util.transform.lsi chemicalchecker.util.transform.metric_learn chemicalchecker.util.transform.pca chemicalchecker.util.transform.scale

Mol (class in chemicalchecker.core.molkit) Mol2svg (class in chemicalchecker.util.mol2svg.mol2svg) mol2svg() (Mol2svg method) MolecularInfo (class in chemicalchecker.util.pipeline.tasks_web.task_web_molinfo) Molecule (class in chemicalchecker.database.molecule) MoleculeData (class in chemicalchecker.tool.targetmate.io) MoleculeNet (class in chemicalchecker.tool.targetmate.datasets.moleculenet.fetch_moleculenet) Molrepo (class in chemicalchecker.database.molrepo) molrepo_hpc() (Molrepo static method) MolrepoHasDatasource (class in chemicalchecker.database.molrepo) MolrepoHasMolecule (class in chemicalchecker.database.molrepo) Molset (class in chemicalchecker.core.molkit) morgan_arena() (in module chemicalchecker.tool.targetmate.utils.chemistry) morgan_matrix() (in module chemicalchecker.tool.targetmate.utils.chemistry) MultiCCPlot (class in chemicalchecker.util.plot.multiccplot) MultiEdgeNetwork (class in chemicalchecker.util.network.network) MultiFit (class in chemicalchecker.tool.targetmate.run) MultiPlot (class in chemicalchecker.util.plot.multiplot) MultiPredict (class in chemicalchecker.tool.targetmate.run) MultiSetup (class in chemicalchecker.tool.targetmate.multi) MultiValidation (class in chemicalchecker.tool.targetmate.run)

N

n_test() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) naive_split() (Pairs method) name (AlphaDropoutCP property) (ChemicalChecker property) (ExtendDNNBuilder property) (NanMaskingLayer property), [1] (StackDNNBuilder property) name_scope (AlphaDropoutCP property) (NanMaskingLayer property), [1] NanMaskingLayer (class in chemicalchecker.tool.adanet.dnn_extend_generator) (class in chemicalchecker.tool.adanet.dnn_stack_generator)

NcFactory (class in chemicalchecker.tool.targetmate.nonconformist.nc) neig (class in chemicalchecker.core.neig) neigh_roc() (Diagnosis method) NeighborErrorTraintest (class in chemicalchecker.util.splitter.neighborerror) NeighborPairTraintest (class in chemicalchecker.util.splitter.neighborpair) neighbors() (sign1 method) NetworkxNetwork (class in chemicalchecker.util.network.network) Node2Vec (class in chemicalchecker.tool.node2vec.node2vec) non_trainable_variables (AlphaDropoutCP property) (NanMaskingLayer property), [1] non_trainable_weights (AlphaDropoutCP property) (NanMaskingLayer property), [1]

O

OldTripletSampler (class in chemicalchecker.util.splitter.neighbortriplet) on_batch_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_batch_end() (AdditionalValidationSets method), [1] (CyclicLR method) on_epoch_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_epoch_end() (AdditionalValidationSets method), [1] (CyclicLR method) on_predict_batch_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_predict_batch_end() (AdditionalValidationSets method), [1] (CyclicLR method) on_predict_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_predict_end() (AdditionalValidationSets method), [1] (CyclicLR method) on_test_batch_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_test_batch_end() (AdditionalValidationSets method), [1] (CyclicLR method) on_test_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_test_end() (AdditionalValidationSets method), [1] (CyclicLR method) on_train_batch_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_train_batch_end() (AdditionalValidationSets method), [1] (CyclicLR method)

on_train_begin() (AdditionalValidationSets method), [1] (CyclicLR method) on_train_end() (AdditionalValidationSets method), [1] (CyclicLR method) onehot_proteins_signature() (in module chemicalchecker.tool.targetmate.utils.pairs) OobClassifierAdapter (class in chemicalchecker.tool.targetmate.nonconformist.base) OobCpClassifier (class in chemicalchecker.tool.targetmate.nonconformist.icp) OobCpRegressor (class in chemicalchecker.tool.targetmate.nonconformist.icp) OobMixin (class in chemicalchecker.tool.targetmate.nonconformist.base) OobRegressorAdapter (class in chemicalchecker.tool.targetmate.nonconformist.base) open() (AE_SiameseTraintest method) (NeighborErrorTraintest method) (NeighborPairTraintest method) (PairTraintest method) (Traintest method) (TripletIterator method) optimal_t() (sign1 method) outbound_nodes (AlphaDropoutCP property) (NanMaskingLayer property), [1] outliers() (Diagnosis method) OutOfUniverseStratified (class in chemicalchecker.tool.targetmate.utils.splitters) output (AlphaDropoutCP property) (NanMaskingLayer property), [1] output_mask (AlphaDropoutCP property) (NanMaskingLayer property), [1] output_shape (AlphaDropoutCP property) (NanMaskingLayer property), [1]

P

Pairs (class in chemicalchecker.tool.targetmate.utils.pairs) PairTraintest (class in chemicalchecker.util.splitter.pairtraintest) parse_fn() (Parser static method) Parser (class in chemicalchecker.util.parser.parser) PCA (class in chemicalchecker.core.projector.pca) Pca (class in chemicalchecker.util.transform.pca) PerformanceBinary (class in chemicalchecker.util.performance.performance) PerformanceCluster (class in chemicalchecker.util.performance.performance) Performances (class in chemicalchecker.tool.targetmate.evaluation.validation) pick_colors() (in module chemicalchecker.core.char) pick_reference() (UniprotKB method) Pipeline (class in chemicalchecker.util.pipeline.pipeline) Plot (class in chemicalchecker.util.plot.plot) plot() (proj method) plot_all() (CCStatsPlot method) plot_category() (proj method) plot_over() (proj method) plot_projection() (char method) plot_subsample() (in module chemicalchecker.core.sign3) Plots (class in chemicalchecker.util.pipeline.tasks_web.task_web_plots) pls() (in module chemicalchecker.util.decomposition.correlation) pls_single() (in module chemicalchecker.util.decomposition.correlation) pr_score() (in module chemicalchecker.tool.targetmate.utils.metrics) pre_fit_transform() (proj method) pre_predict() (proj method) PrecomputedSplitter (class in chemicalchecker.tool.targetmate.evaluation.validation) PrecomputedTripletSampler (class in chemicalchecker.util.splitter.neighbortriplet) predefined_cc_colors() (in module chemicalchecker.util.plot.util) predict() (AdaNetWrapper static method) (AggregatedCp method) (BaseModelAdapter method) (BaseSignature method) (BootstrapConformalClassifier method) (char method) (ClassifierAdapter method) (clus method) (CrossConformalClassifier method) (Default method) (IcpClassifier method) (IcpRegressor method) (Molset method) (neig method) (OobClassifierAdapter method) (OobCpClassifier method) (OobCpRegressor method) (OobRegressorAdapter method) (PCA method) (Preprocess method) (proj method) (RegressorAdapter method) (RegressorNc method) (Siamese method) (SiameseTriplets method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TcpClassifier method) (TSNE method) (UMAP method) (Universe method)

predict_adanet() (sign2 static method) predict_conf() (IcpClassifier method) (OobCpClassifier method) (TcpClassifier method) predict_feat() (char method) predict_fn() (AdaNetWrapper static method) predict_from_string() (sign4 method) predict_linear_regression() (sign2 static method) predict_nearest_neighbor() (sign2 static method) predict_novelty() (sign3 method) predict_online() (AdaNetWrapper static method) Prediction (class in chemicalchecker.tool.targetmate.evaluation.prediction) (class in chemicalchecker.tool.targetmate.io) Preprocess (class in chemicalchecker.core.preprocess) preprocess() (Preprocess class method) preprocess_predict() (Preprocess class method) print_model_architechture() (AdaNetWrapper static method) print_stats() (CProfileFuncProfile method) (FuncProfile method) process_features() (sign0 method) process_keys() (sign0 method) profile() (in module chemicalchecker.util.decorator.profilehooks) proj (class in chemicalchecker.core.proj) project() (Molset method) project_scores() (char method) projection() (Diagnosis method) (in module chemicalchecker.util.plot.util) Projections (class in chemicalchecker.util.pipeline.tasks_web.task_web_projections) Pubchem (class in chemicalchecker.database.pubchem) (class in chemicalchecker.util.pipeline.tasks_web.task_web_pubchem) PythonCallable (class in chemicalchecker.util.pipeline.tasks.python_callable_task)

Q

qqplot() (Gaussianize method) qstring() (in module chemicalchecker.util.psql.psql) qstring_cur() (in module chemicalchecker.util.psql.psql) qualified_name (BaseSignature property) (char property) (clus property) (Default property) (neig property) (PCA property) (proj property) (sign0 property) (sign1 property) (sign2 property) (sign3 property) (sign4 property) (TSNE property) (UMAP property)

query() (in module chemicalchecker.util.psql.psql)

R

RandomBatchSampler (class in chemicalchecker.core.signature_data) RandomSubSampler (class in chemicalchecker.tool.targetmate.nonconformist.acp) ranks_agreement() (Diagnosis method) read_data() (in module chemicalchecker.tool.targetmate.io) read_inchi_from_multiple_data() (in module chemicalchecker.tool.targetmate.io) read_molecule() (in module chemicalchecker.tool.targetmate.utils.chemistry) read_molecules_from_multiple_data() (in module chemicalchecker.tool.targetmate.io) read_signatures() (Fingerprinter method) (SignaturedModel method) (SignaturizerSetup method) (StackedModel method) (TargetMateStackedClassifier method) read_signatures_ensemble() (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateStackedClassifier method) read_signatures_prestacked() (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateStackedClassifier method) read_signatures_stacked() (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateStackedClassifier method) read_smiles() (in module chemicalchecker.tool.targetmate.utils.chemistry) read_smiles_from_multiple_data() (in module chemicalchecker.tool.targetmate.io) reader() (in module chemicalchecker.tool.targetmate.io) reassemble_activity_sets() (in module chemicalchecker.tool.targetmate.io) refresh() (char method) (clus method) (DataSignature method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) reg_max_size() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_mean_errors() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_mean_size() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_median_size() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_min_size() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_n_correct() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_q1_size() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) reg_q3_size() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) RegIcpCvHelper (class in chemicalchecker.tool.targetmate.nonconformist.evaluation) RegressionErrFunc (class in chemicalchecker.tool.targetmate.nonconformist.nc) regressor_performances() (Performances method) RegressorAdapter (class in chemicalchecker.tool.targetmate.nonconformist.base) RegressorMixin (class in chemicalchecker.tool.targetmate.nonconformist.base) RegressorNc (class in chemicalchecker.tool.targetmate.nonconformist.nc) RegressorNormalizer (class in chemicalchecker.tool.targetmate.nonconformist.nc) remove() (RNDuplicates method) repath_bases_by_fold() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method)

repath_predictions_by_fold() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) repath_predictions_by_set() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) report_available() (ChemicalChecker method) (Mol method) report_dimensions() (ChemicalChecker method) report_keys() (ChemicalChecker method) report_status() (ChemicalChecker method) rerun_confidence() (sign3 method) reset_path_predictions() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) reset_stats() (CProfileFuncProfile method) (FuncProfile method) restrict_to_universe() (sign0 method) rgb2hex() (in module chemicalchecker.util.plot.util) right_split() (Pairs method) RNDuplicates (class in chemicalchecker.util.remove_near_duplicates.remove_near_duplicates) roc_curve() (in module chemicalchecker.tool.targetmate.utils.metrics) roc_score() (in module chemicalchecker.tool.targetmate.utils.metrics) row_wise_correlation() (in module chemicalchecker.core.sign3) run() (BaseTask method) (CCFit method) (CCPredict method) (Coordinates method) (Libraries method) (MolecularInfo method) (MultiValidation method) (Node2Vec method) (Pipeline method) (Plots method) (Projections method) (Pubchem method) (PythonCallable method) (ShowTargets method) (Similars method) (StatsPlots method) (Validation method) run_experiment() (in module chemicalchecker.tool.targetmate.nonconformist.evaluation) run_SAFE() (char method)

S

safe_create() (in module chemicalchecker.core.sign3) safe_return() (in module chemicalchecker.util.decorator.safe) sample() (ToppedSampler method) (TripletSampler method) sample_balanced() (Pairs method) sample_triplets() (TripletSampler method) Sanitizer (class in chemicalchecker.util.sanitize.sanitizer) save() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (Molset method) (RNDuplicates method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) save_full() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) save_model() (AdaNetWrapper method) save_output() (Preprocess static method) save_performances() (AdaNetWrapper method) save_reference() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) save_sign2_coverage() (sign3 static method) save_sign2_matrix() (sign3 method) save_sign2_universe() (sign3 static method) save_triplets() (AdriaTripletSampler method) (BaseTripletSampler method) (OldTripletSampler method) (PrecomputedTripletSampler method) (TripletSampler method) Scale (class in chemicalchecker.util.transform.scale) score() (BaseModelNc method) (ClassifierNc method) (RegressorNc method) (sign1 method) Scorer (class in chemicalchecker.tool.targetmate.evaluation.validation) SemiSupervisedMetricLearn (class in chemicalchecker.util.transform.metric_learn) set_db_config() (in module chemicalchecker.database.database) set_logging() (in module chemicalchecker.tool.targetmate.utils.log) set_params() (AggregatedCp method) (BaseIcp method) (BaseIcpCvHelper method) (BaseModelAdapter method) (BaseModelNc method) (BaseScorer method) (BootstrapConformalClassifier method) (ClassIcpCvHelper method) (ClassifierAdapter method) (ClassifierNc method) (CrossConformalClassifier method) (IcpClassifier method) (IcpRegressor method) (OobClassifierAdapter method) (OobCpClassifier method) (OobCpRegressor method) (OobRegressorAdapter method) (RegIcpCvHelper method) (RegressorAdapter method) (RegressorNc method) (RegressorNormalizer method) (TcpClassifier method) set_style() (in module chemicalchecker.util.plot.util) set_verbosity() (ChemicalChecker static method) set_weights() (AlphaDropoutCP method) (NanMaskingLayer method), [1] sge (class in chemicalchecker.util.hpc.sge) shape (char property) (clus property) (DataSignature property) (Default property) (neig property) (PCA property) (proj property) (sign0 property) (sign1 property) (sign2 property) (sign3 property) (sign4 property) (TSNE property) (UMAP property)

ShowTargets (class in chemicalchecker.util.pipeline.tasks_web.task_web_showtargets) shuffle() (InputData method) ShuffleScaffoldSplit (class in chemicalchecker.tool.targetmate.utils.splitters) Siamese (class in chemicalchecker.tool.siamese.siamese) SiameseTriplets (class in chemicalchecker.tool.siamese.siamese_triplets) sign0 (class in chemicalchecker.core.sign0) sign1 (class in chemicalchecker.core.sign1) sign2 (class in chemicalchecker.core.sign2) sign2_node2vec_stats() (MultiCCPlot method) (MultiPlot method) sign3 (class in chemicalchecker.core.sign3) sign4 (class in chemicalchecker.core.sign4) sign_metadata() (ChemicalChecker method) signature() (Mol method) SignaturedModel (class in chemicalchecker.tool.targetmate.base) signaturize() (DataFactory static method) (Molset method) Signaturizer (class in chemicalchecker.tool.targetmate.signaturizer) SignaturizerSetup (class in chemicalchecker.tool.targetmate.signaturizer) SignErrorErrFunc (class in chemicalchecker.tool.targetmate.nonconformist.nc) similarity_matrix() (in module chemicalchecker.tool.targetmate.utils.chemistry) Similars (class in chemicalchecker.util.pipeline.tasks_web.task_web_similars) size (char property) (clus property) (DataSignature property) (Default property) (neig property) (PCA property) (proj property) (sign0 property) (sign1 property) (sign2 property) (sign3 property) (sign4 property) (TSNE property) (UMAP property) skip_on_exception() (in module chemicalchecker.util.plot.plot) slurm (class in chemicalchecker.util.hpc.slurm) slurmGPU (class in chemicalchecker.util.hpc.slurm_gpu) smiles_to_inchi() (Converter method) smiles_to_scaffold() (Converter method) SmilesData (class in chemicalchecker.tool.targetmate.io) Smilespred (class in chemicalchecker.tool.smilespred.smilespred) SNAPNetwork (class in chemicalchecker.util.network.network) split_edgelist() (Node2Vec method) split_h5() (Traintest static method) split_h5_blocks() (AE_SiameseTraintest static method) (Traintest static method) Splitter (class in chemicalchecker.tool.targetmate.utils.splitters) StackDNNBuilder (class in chemicalchecker.tool.adanet.dnn_stack_generator) StackDNNGenerator (class in chemicalchecker.tool.adanet.dnn_stack_generator) StackedModel (class in chemicalchecker.tool.targetmate.base) StandardStratifiedShuffleSplit (class in chemicalchecker.tool.targetmate.utils.splitters) StatsPlots (class in chemicalchecker.util.pipeline.tasks_web.task_web_statsplots) status() (HPC method) (local method) (sge method) (slurm method) (slurmGPU method) StratifiedShuffleScaffoldSplit (class in chemicalchecker.tool.targetmate.utils.splitters) submitMultiJob() (HPC method) (local method) (sge method) (slurm method) (slurmGPU method) submodules (AlphaDropoutCP property) (NanMaskingLayer property), [1] subsample() (char method) (clus method) (DataSignature method) (Default method) (in module chemicalchecker.core.sign3) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) subsampling_probs() (in module chemicalchecker.core.sign3) supports_masking (AlphaDropoutCP property) (NanMaskingLayer property), [1] sw_name (Traintest attribute) sw_name_right (AE_SiameseTraintest attribute) symlink_to() (ChemicalChecker method)

T

TargetMateClassifierSetup (class in chemicalchecker.tool.targetmate.tmsetup) TargetMateRegressorSetup (class in chemicalchecker.tool.targetmate.tmsetup) TargetMateSetup (class in chemicalchecker.tool.targetmate.tmsetup) TargetMateStackedClassifier (class in chemicalchecker.tool.targetmate.ml) Tasker (class in chemicalchecker.tool.targetmate.utils.tasks) TcpClassifier (class in chemicalchecker.tool.targetmate.nonconformist.cp) test_all_downloaded() (Datasource static method) test_all_valid_url() (Datasource static method) test_connection() (in module chemicalchecker.database.database) thOpt (class in chemicalchecker.tool.targetmate.evaluation.validation) timecall() (in module chemicalchecker.util.decorator.profilehooks) tm_from_disk() (in module chemicalchecker.tool.targetmate.ml) to_csv() (BaseSignature method) (char method) (clus method) (Default method) (Molrepo static method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method)

to_edgelist() (Node2Vec method) to_feature_string() (Preprocess method) to_features() (Preprocess method) toJSON() (PerformanceBinary method) ToppedClassifier (class in chemicalchecker.tool.targetmate.utils.topped) ToppedSampler (class in chemicalchecker.tool.targetmate.utils.splitters) toy_matrix() (Example method) toy_pairs() (Example method) TraceFuncCoverage (class in chemicalchecker.util.decorator.profilehooks) train_and_evaluate() (AdaNetWrapper method) train_confidence() (sign3 method) train_prior_model() (sign3 method) train_prior_signature_model() (sign3 method) train_SNN() (sign3 method) trainable_variables (AlphaDropoutCP property) (NanMaskingLayer property), [1] trainable_weights (AlphaDropoutCP property) (NanMaskingLayer property), [1] Traintest (class in chemicalchecker.util.splitter.traintest) transform() (Aggregate method) (Gaussianize method) (Sanitizer method) TripletIterator (class in chemicalchecker.util.splitter.neighbortriplet) TripletSampler (class in chemicalchecker.util.sampler.triplets) truth_inv() (Performances static method) TSNE (class in chemicalchecker.core.projector.tsne)

U

UMAP (class in chemicalchecker.core.projector.umap_) UniprotKB (class in chemicalchecker.database.uniprotkb) UniprotKbError

Universe (class in chemicalchecker.tool.targetmate.universes.univs) UniverseLoader (class in chemicalchecker.tool.targetmate.universes.univs) UnsupervisedMetricLearn (class in chemicalchecker.util.transform.metric_learn)

V

valid_url (Datasource property) validate() (BaseSignature method) (char method) (clus method) (Default method) (neig method) (PCA method) (proj method) (sign0 method) (sign1 method) (sign2 method) (sign3 method) (sign4 method) (TSNE method) (UMAP method) (Validation method) validate_url() (Downloader static method) Validation (class in chemicalchecker.core.validation) (class in chemicalchecker.tool.targetmate.evaluation.validation)

validation_score() (in module chemicalchecker.tool.targetmate.evaluation.score) VanillaClassifierConfigs (class in chemicalchecker.tool.targetmate.models.vanillaconfigs) variable_dtype (AlphaDropoutCP property) (NanMaskingLayer property), [1] variables (AlphaDropoutCP property) (NanMaskingLayer property), [1] vstack_signatures() (char static method) (clus static method) (DataSignature static method) (Default static method) (neig static method) (PCA static method) (proj static method) (sign0 static method) (sign1 static method) (sign2 static method) (sign3 static method) (sign4 static method) (TSNE static method) (UMAP static method)

W

w_d() (in module chemicalchecker.util.transform.gaussianize) w_t() (in module chemicalchecker.util.transform.gaussianize) waiter() (BaseSignaturizer method) (Fingerprinter method) (HPCUtils method) (Model method) (ModelSetup method) (Prediction method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) (Validation method)

was_sparse() (sign1 method) weights (AlphaDropoutCP property) (NanMaskingLayer property), [1] wipe() (BaseSignaturizer method) (Fingerprinter method) (Model method) (ModelSetup method) (SignaturedModel method) (Signaturizer method) (SignaturizerSetup method) (StackedModel method) (TargetMateClassifierSetup method) (TargetMateRegressorSetup method) (TargetMateSetup method) (TargetMateStackedClassifier method) with_name_scope() (AlphaDropoutCP class method) (NanMaskingLayer class method), [1] Word2VecWrapper (class in chemicalchecker.tool.node2vec.word2vec)

Z

z_transform() (in module chemicalchecker.util.decomposition.correlation)