Index

_

__call__() (xenonpy.datatools.dataset.Dataset method) (xenonpy.inverse.base.BaseLogLikelihood method) (xenonpy.inverse.base.BaseLogLikelihoodSet method) (xenonpy.inverse.base.BaseProposal method) (xenonpy.inverse.base.BaseResample method) (xenonpy.inverse.base.BaseSMC method) (xenonpy.mdl.base.BaseQuery method) (xenonpy.mdl.mdl.MDL method) (xenonpy.model.training.base.BaseLRScheduler method) (xenonpy.model.training.base.BaseOptimizer method) (xenonpy.model.training.checker.Checker method) (xenonpy.model.training.clip_grad.ClipNorm method) (xenonpy.model.training.clip_grad.ClipValue method) (xenonpy.model.training.extension.persist.Persist method) (xenonpy.model.training.trainer.Trainer method) (xenonpy.utils.parameter_gen.ParameterGenerator method) (xenonpy.utils.useful_cls.Singleton method)

A

absolute_path() (in module xenonpy.utils.useful_func) ada_delta() (xenonpy.model.nn.wrap.Optim static method) ada_grad() (xenonpy.model.nn.wrap.Optim static method) ada_max() (xenonpy.model.nn.wrap.Optim static method) Adadelta (class in xenonpy.model.training.optimizer) Adagrad (class in xenonpy.model.training.optimizer) Adam (class in xenonpy.model.training.optimizer) adam() (xenonpy.model.nn.wrap.Optim static method) Adamax (class in xenonpy.model.training.optimizer) add_char() (xenonpy.inverse.iqspr.modifier.NGram class method) (xenonpy.inverse.iqspr.NGram class method) after_proc() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.extension.persist.Persist method)

all_featurizers (xenonpy.descriptor.base.BaseDescriptor property) all_loglikelihoods (xenonpy.inverse.base.BaseLogLikelihoodSet property) api_key (xenonpy.mdl.base.BaseQuery property) (xenonpy.mdl.mdl.MDL property) argmax (xenonpy.model.training.extension.tensor_convert.TensorConverter property) ArrayDataset (class in xenonpy.model.training.dataset.array) ASGD (class in xenonpy.model.training.optimizer) asgd() (xenonpy.model.nn.wrap.Optim static method) atom_init (xenonpy.datatools.preset.Preset property) AtomPairFP (class in xenonpy.descriptor.fingerprint) authors (xenonpy.descriptor.base.BaseFeaturizer property) auto_reshape (xenonpy.model.training.extension.tensor_convert.TensorConverter property)

B

BaseCompositionFeaturizer (class in xenonpy.descriptor.base) BaseDescriptor (class in xenonpy.descriptor.base) BaseExtension (class in xenonpy.model.training.base) BaseFeaturizer (class in xenonpy.descriptor.base) BaseLogLikelihood (class in xenonpy.inverse.base) BaseLogLikelihoodSet (class in xenonpy.inverse.base) BaseLRScheduler (class in xenonpy.model.training.base) BaseOptimizer (class in xenonpy.model.training.base) BaseProposal (class in xenonpy.inverse.base) BaseQuery (class in xenonpy.mdl.base) BaseResample (class in xenonpy.inverse.base)

BaseRunner (class in xenonpy.model.training.base) BaseSMC (class in xenonpy.inverse.base) batch_norm() (xenonpy.model.nn.wrap.L1 static method) BCELoss (class in xenonpy.model.training.loss) BCEWithLogitsLoss (class in xenonpy.model.training.loss) before_proc() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.extension.persist.Persist method) (xenonpy.model.training.extension.validator.Validator method) blank (xenonpy.model.training.loss.CTCLoss attribute) box_cox() (xenonpy.datatools.transform.Scaler method) build() (xenonpy.datatools.preset.Preset method)

C

camel_to_snake() (in module xenonpy.utils.useful_func) check_device() (xenonpy.model.training.base.BaseRunner static method) check_query_vars() (xenonpy.mdl.base.BaseQuery method) Checker (class in xenonpy.model.training.checker) checkpoint_tuple (xenonpy.model.training.trainer.Trainer attribute) checkpoints (xenonpy.model.training.trainer.Trainer property) citations (xenonpy.descriptor.base.BaseFeaturizer property) classic (xenonpy.descriptor.compositions.Compositions attribute) (xenonpy.descriptor.fingerprint.DescriptorFeature attribute) classification (xenonpy.mdl.mdl.GetModelDetail attribute) (xenonpy.mdl.mdl.GetModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetailsWith attribute) (xenonpy.mdl.model.GetModelDetail attribute) (xenonpy.mdl.model.GetModelDetails attribute) (xenonpy.mdl.model.QueryModelDetails attribute) (xenonpy.mdl.model.QueryModelDetailsWith attribute) classification_metrics() (in module xenonpy.model.utils.metrics) classify (xenonpy.model.training.extension.validator.Validator attribute) clip_grad (xenonpy.model.training.trainer.Trainer property) ClipNorm (class in xenonpy.model.training.clip_grad) ClipValue (class in xenonpy.model.training.clip_grad) collate_fn() (xenonpy.model.training.dataset.cgcnn.CrystalGraphDataset static method) common (xenonpy.mdl.mdl.GetModelDetail attribute) (xenonpy.mdl.mdl.GetModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetailsWith attribute) (xenonpy.mdl.model.GetModelDetail attribute) (xenonpy.mdl.model.GetModelDetails attribute) (xenonpy.mdl.model.QueryModelDetails attribute) (xenonpy.mdl.model.QueryModelDetailsWith attribute)

Compositions (class in xenonpy.descriptor.compositions) config() (in module xenonpy.utils.useful_func) conv() (xenonpy.model.nn.wrap.L1 static method) ConvLayer (class in xenonpy.model.cgcnn) CosineAnnealingLR (class in xenonpy.model.training.lr_scheduler) CosineEmbeddingLoss (class in xenonpy.model.training.loss) Counting (class in xenonpy.descriptor.compositions) create_descriptor() (xenonpy.mdl.mdl.MDL method) create_method() (xenonpy.mdl.mdl.MDL method) create_modelset() (xenonpy.mdl.mdl.MDL method) create_property() (xenonpy.mdl.mdl.MDL method) CreateDescriptor (class in xenonpy.mdl.descriptor) (class in xenonpy.mdl.mdl) CreateMethod (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.method) CreateModelset (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.modelset) CreateProperty (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.property) CrossEntropyLoss (class in xenonpy.model.training.loss) CrystalGraphConvNet (class in xenonpy.model.cgcnn) CrystalGraphDataset (class in xenonpy.model.training.dataset.cgcnn) CrystalGraphFeaturizer (class in xenonpy.descriptor.cgcnn) csv (xenonpy.datatools.dataset.Dataset property) CTCLoss (class in xenonpy.model.training.loss) cuda (xenonpy.model.training.base.BaseRunner property) cv() (xenonpy.datatools.splitter.Splitter method) CyclicLR (class in xenonpy.model.training.lr_scheduler)

D

Dataset (class in xenonpy.datatools.dataset) del_char() (xenonpy.inverse.iqspr.modifier.NGram class method) (xenonpy.inverse.iqspr.NGram class method) del_range (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property) describe (xenonpy.model.training.checker.Checker property) (xenonpy.model.training.extension.persist.Persist property)

DescriptorFeature (class in xenonpy.descriptor.fingerprint) DescriptorHeatmap (class in xenonpy.visualization.heatmap) device (xenonpy.model.training.base.BaseRunner property) (xenonpy.model.training.trainer.Trainer property) draw() (xenonpy.visualization.heatmap.DescriptorHeatmap method)

E

early_stop() (xenonpy.model.training.trainer.Trainer method) ECFP (class in xenonpy.descriptor.fingerprint) edge_features() (xenonpy.descriptor.cgcnn.CrystalGraphFeaturizer method) elapsed (xenonpy.descriptor.base.BaseDescriptor property) (xenonpy.inverse.base.BaseLogLikelihoodSet property) (xenonpy.utils.useful_cls.Timer property) elements (xenonpy.datatools.preset.Preset property) elements_completed (xenonpy.datatools.preset.Preset property) empty_cache (xenonpy.model.training.extension.tensor_convert.TensorConverter property) endpoint (xenonpy.mdl.base.BaseQuery property) (xenonpy.mdl.mdl.MDL property) epochs (xenonpy.model.training.trainer.Trainer property)

eps (xenonpy.model.training.loss.PoissonNLLLoss attribute) (xenonpy.model.training.loss.TripletMarginLoss attribute) esmi2smi() (xenonpy.inverse.iqspr.modifier.NGram class method) (xenonpy.inverse.iqspr.NGram class method) estimator (xenonpy.inverse.iqspr.IQSPR property) (xenonpy.inverse.iqspr.iqspr.IQSPR property) (xenonpy.inverse.iqspr.IQSPR4DF property) (xenonpy.inverse.iqspr.iqspr4df.IQSPR4DF property) excel (xenonpy.datatools.dataset.Dataset property) exponential_lr() (xenonpy.model.nn.wrap.LrScheduler static method) ExponentialLR (class in xenonpy.model.training.lr_scheduler) extend() (xenonpy.model.training.base.BaseRunner method)

F

FCFP (class in xenonpy.descriptor.fingerprint) feature_labels (xenonpy.contrib.extend_descriptors.descriptor.frozen_featurizer_descriptor.FrozenFeaturizerDescriptor property) (xenonpy.contrib.extend_descriptors.descriptor.mordred_descriptor.Mordred2DDescriptor property) (xenonpy.contrib.extend_descriptors.descriptor.organic_comp_descriptor.OrganicCompDescriptor property) (xenonpy.descriptor.base.BaseDescriptor property) (xenonpy.descriptor.base.BaseFeaturizer property) (xenonpy.descriptor.cgcnn.CrystalGraphFeaturizer property) (xenonpy.descriptor.compositions.Counting property) (xenonpy.descriptor.compositions.GeometricMean property) (xenonpy.descriptor.compositions.HarmonicMean property) (xenonpy.descriptor.compositions.MaxPooling property) (xenonpy.descriptor.compositions.MinPooling property) (xenonpy.descriptor.compositions.WeightedAverage property) (xenonpy.descriptor.compositions.WeightedSum property) (xenonpy.descriptor.compositions.WeightedVariance property) (xenonpy.descriptor.fingerprint.AtomPairFP property) (xenonpy.descriptor.fingerprint.DescriptorFeature property) (xenonpy.descriptor.fingerprint.ECFP property) (xenonpy.descriptor.fingerprint.FCFP property) (xenonpy.descriptor.fingerprint.LayeredFP property) (xenonpy.descriptor.fingerprint.MACCS property) (xenonpy.descriptor.fingerprint.MHFP property) (xenonpy.descriptor.fingerprint.PatternFP property) (xenonpy.descriptor.fingerprint.RDKitFP property) (xenonpy.descriptor.fingerprint.TopologicalTorsionFP property) (xenonpy.descriptor.frozen_featurizer.FrozenFeaturizer property) (xenonpy.descriptor.structure.OrbitalFieldMatrix property) (xenonpy.descriptor.structure.RadialDistributionFunction property) featurize() (xenonpy.contrib.extend_descriptors.descriptor.frozen_featurizer_descriptor.FrozenFeaturizerDescriptor method) (xenonpy.contrib.extend_descriptors.descriptor.mordred_descriptor.Mordred2DDescriptor method) (xenonpy.contrib.extend_descriptors.descriptor.organic_comp_descriptor.OrganicCompDescriptor method) (xenonpy.descriptor.base.BaseCompositionFeaturizer method) (xenonpy.descriptor.base.BaseFeaturizer method) (xenonpy.descriptor.cgcnn.CrystalGraphFeaturizer method) (xenonpy.descriptor.fingerprint.AtomPairFP method) (xenonpy.descriptor.fingerprint.DescriptorFeature method) (xenonpy.descriptor.fingerprint.ECFP method) (xenonpy.descriptor.fingerprint.FCFP method) (xenonpy.descriptor.fingerprint.LayeredFP method) (xenonpy.descriptor.fingerprint.MACCS method) (xenonpy.descriptor.fingerprint.MHFP method) (xenonpy.descriptor.fingerprint.PatternFP method) (xenonpy.descriptor.fingerprint.RDKitFP method) (xenonpy.descriptor.fingerprint.TopologicalTorsionFP method) (xenonpy.descriptor.frozen_featurizer.FrozenFeaturizer method) (xenonpy.descriptor.structure.OrbitalFieldMatrix method) (xenonpy.descriptor.structure.RadialDistributionFunction method)

featurizers (xenonpy.descriptor.base.BaseDescriptor property) files (xenonpy.model.training.checker.Checker property) final_state (xenonpy.model.training.checker.Checker property) Fingerprints (class in xenonpy.descriptor.fingerprint) fit() (xenonpy.datatools.transform.PowerTransformer method) (xenonpy.datatools.transform.Scaler method) (xenonpy.descriptor.base.BaseDescriptor method) (xenonpy.descriptor.base.BaseFeaturizer method) (xenonpy.inverse.base.BaseLogLikelihood method) (xenonpy.inverse.base.BaseProposal method) (xenonpy.inverse.base.BaseResample method) (xenonpy.inverse.iqspr.estimator.GaussianLogLikelihood method) (xenonpy.inverse.iqspr.GaussianLogLikelihood method) (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) (xenonpy.model.training.trainer.Trainer method) (xenonpy.visualization.heatmap.DescriptorHeatmap method) fit_transform() (xenonpy.datatools.transform.Scaler method) (xenonpy.descriptor.base.BaseFeaturizer method) forward() (xenonpy.model.cgcnn.ConvLayer method) (xenonpy.model.cgcnn.CrystalGraphConvNet method) (xenonpy.model.nn.layer.Layer1d method) (xenonpy.model.sequential.LinearLayer method) (xenonpy.model.sequential.SequentialLinear method) (xenonpy.model.training.loss.BCELoss method) (xenonpy.model.training.loss.BCEWithLogitsLoss method) (xenonpy.model.training.loss.CosineEmbeddingLoss method) (xenonpy.model.training.loss.CrossEntropyLoss method) (xenonpy.model.training.loss.CTCLoss method) (xenonpy.model.training.loss.HingeEmbeddingLoss method) (xenonpy.model.training.loss.KLDivLoss method) (xenonpy.model.training.loss.L1Loss method) (xenonpy.model.training.loss.MarginRankingLoss method) (xenonpy.model.training.loss.MSELoss method) (xenonpy.model.training.loss.MultiLabelMarginLoss method) (xenonpy.model.training.loss.MultiLabelSoftMarginLoss method) (xenonpy.model.training.loss.MultiMarginLoss method) (xenonpy.model.training.loss.NLLLoss method) (xenonpy.model.training.loss.PoissonNLLLoss method) (xenonpy.model.training.loss.SmoothL1Loss method) (xenonpy.model.training.loss.SoftMarginLoss method) (xenonpy.model.training.loss.TripletMarginLoss method) (xenonpy.model.training.loss.TripletMarginWithDistanceLoss method) from_checker() (xenonpy.model.training.trainer.Trainer class method) from_http() (xenonpy.datatools.dataset.Dataset class method) FrozenFeaturizer (class in xenonpy.descriptor.frozen_featurizer) FrozenFeaturizerDescriptor (class in xenonpy.contrib.extend_descriptors.descriptor.frozen_featurizer_descriptor) full (xenonpy.model.training.loss.PoissonNLLLoss attribute)

G

GaussianLogLikelihood (class in xenonpy.inverse.iqspr) (class in xenonpy.inverse.iqspr.estimator) GeometricMean (class in xenonpy.descriptor.compositions) get_checkpoint() (xenonpy.model.training.extension.persist.Persist method) (xenonpy.model.training.trainer.Trainer method) get_data_loc() (in module xenonpy.utils.useful_func) get_dataset_url() (in module xenonpy.utils.useful_func) get_descriptor_detail() (xenonpy.mdl.mdl.MDL method) get_element_representation() (xenonpy.descriptor.structure.OrbitalFieldMatrix static method) get_method_detail() (xenonpy.mdl.mdl.MDL method) get_model_detail() (xenonpy.mdl.mdl.MDL method) get_model_details() (xenonpy.mdl.mdl.MDL method) get_model_urls() (xenonpy.mdl.mdl.MDL method) get_modelset_detail() (xenonpy.mdl.mdl.MDL method) get_prob() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) get_property_detail() (xenonpy.mdl.mdl.MDL method) get_sha256() (in module xenonpy.utils.useful_func) get_supplementary() (xenonpy.mdl.mdl.MDL method) get_training_env() (xenonpy.mdl.mdl.MDL method) get_training_info() (xenonpy.mdl.mdl.MDL method) GetDescriptorDetail (class in xenonpy.mdl.descriptor) (class in xenonpy.mdl.mdl) GetMethodDetail (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.method) GetModelDetail (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetModelDetails (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetModelsetDetail (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.modelset) GetModelUrl (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetModelUrls (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetProbError, [1] GetPropertyDetail (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.property) GetSupplementary (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetTrainingEnv (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetTrainingInfo (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) GetVersion (class in xenonpy.mdl.mdl) gql() (xenonpy.mdl.base.BaseQuery method) (xenonpy.mdl.descriptor.CreateDescriptor method) (xenonpy.mdl.descriptor.GetDescriptorDetail method) (xenonpy.mdl.descriptor.ListDescriptors method) (xenonpy.mdl.descriptor.QueryDescriptors method) (xenonpy.mdl.descriptor.QueryDescriptorsWith method) (xenonpy.mdl.descriptor.UpdateDescriptor method) (xenonpy.mdl.mdl.CreateDescriptor method) (xenonpy.mdl.mdl.CreateMethod method) (xenonpy.mdl.mdl.CreateModelset method) (xenonpy.mdl.mdl.CreateProperty method) (xenonpy.mdl.mdl.GetDescriptorDetail method) (xenonpy.mdl.mdl.GetMethodDetail method) (xenonpy.mdl.mdl.GetModelDetail method) (xenonpy.mdl.mdl.GetModelDetails method) (xenonpy.mdl.mdl.GetModelsetDetail method) (xenonpy.mdl.mdl.GetModelUrl method) (xenonpy.mdl.mdl.GetModelUrls method) (xenonpy.mdl.mdl.GetPropertyDetail method) (xenonpy.mdl.mdl.GetSupplementary method) (xenonpy.mdl.mdl.GetTrainingEnv method) (xenonpy.mdl.mdl.GetTrainingInfo method) (xenonpy.mdl.mdl.GetVersion method) (xenonpy.mdl.mdl.ListDescriptors method) (xenonpy.mdl.mdl.ListMethods method) (xenonpy.mdl.mdl.ListModelsets method) (xenonpy.mdl.mdl.ListModelsWithDescriptor method) (xenonpy.mdl.mdl.ListModelsWithMethod method) (xenonpy.mdl.mdl.ListModelsWithModelset method) (xenonpy.mdl.mdl.ListModelsWithProperty method) (xenonpy.mdl.mdl.ListProperties method) (xenonpy.mdl.mdl.QueryDescriptors method) (xenonpy.mdl.mdl.QueryDescriptorsWith method) (xenonpy.mdl.mdl.QueryMethods method) (xenonpy.mdl.mdl.QueryMethodsWith method) (xenonpy.mdl.mdl.QueryModelDetails method) (xenonpy.mdl.mdl.QueryModelDetailsWith method) (xenonpy.mdl.mdl.QueryModelsets method) (xenonpy.mdl.mdl.QueryModelsetsWith method) (xenonpy.mdl.mdl.QueryProperties method) (xenonpy.mdl.mdl.QueryPropertiesWith method) (xenonpy.mdl.mdl.UpdateDescriptor method) (xenonpy.mdl.mdl.UpdateMethod method) (xenonpy.mdl.mdl.UpdateModelset method) (xenonpy.mdl.mdl.UpdateProperty method) (xenonpy.mdl.mdl.UploadModel method) (xenonpy.mdl.method.CreateMethod method) (xenonpy.mdl.method.GetMethodDetail method) (xenonpy.mdl.method.ListMethods method) (xenonpy.mdl.method.QueryMethods method) (xenonpy.mdl.method.QueryMethodsWith method) (xenonpy.mdl.method.UpdateMethod method) (xenonpy.mdl.model.GetModelDetail method) (xenonpy.mdl.model.GetModelDetails method) (xenonpy.mdl.model.GetModelUrl method) (xenonpy.mdl.model.GetModelUrls method) (xenonpy.mdl.model.GetSupplementary method) (xenonpy.mdl.model.GetTrainingEnv method) (xenonpy.mdl.model.GetTrainingInfo method) (xenonpy.mdl.model.ListModelsWithDescriptor method) (xenonpy.mdl.model.ListModelsWithMethod method) (xenonpy.mdl.model.ListModelsWithModelset method) (xenonpy.mdl.model.ListModelsWithProperty method) (xenonpy.mdl.model.QueryModelDetails method) (xenonpy.mdl.model.QueryModelDetailsWith method) (xenonpy.mdl.model.UploadModel method) (xenonpy.mdl.modelset.CreateModelset method) (xenonpy.mdl.modelset.GetModelsetDetail method) (xenonpy.mdl.modelset.ListModelsets method) (xenonpy.mdl.modelset.QueryModelsets method) (xenonpy.mdl.modelset.QueryModelsetsWith method) (xenonpy.mdl.modelset.UpdateModelset method) (xenonpy.mdl.property.CreateProperty method) (xenonpy.mdl.property.GetPropertyDetail method) (xenonpy.mdl.property.ListProperties method) (xenonpy.mdl.property.QueryProperties method) (xenonpy.mdl.property.QueryPropertiesWith method) (xenonpy.mdl.property.UpdateProperty method)

H

HarmonicMean (class in xenonpy.descriptor.compositions)

HingeEmbeddingLoss (class in xenonpy.model.training.loss)

I

ignore_index (xenonpy.model.training.loss.CrossEntropyLoss attribute) (xenonpy.model.training.loss.NLLLoss attribute) (xenonpy.model.training.loss.NLLLoss2d attribute) Init (class in xenonpy.model.nn.wrap) init_state (xenonpy.model.training.checker.Checker property) input_proc() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.base.BaseRunner method) (xenonpy.model.training.extension.tensor_convert.TensorConverter method)

instance_norm() (xenonpy.model.nn.wrap.L1 static method) inverse_transform() (xenonpy.datatools.transform.PowerTransformer method) (xenonpy.datatools.transform.Scaler method) IQSPR (class in xenonpy.inverse.iqspr) (class in xenonpy.inverse.iqspr.iqspr) IQSPR4DF (class in xenonpy.inverse.iqspr) (class in xenonpy.inverse.iqspr.iqspr4df)

K

k_fold (xenonpy.datatools.splitter.Splitter property)

KLDivLoss (class in xenonpy.model.training.loss)

L

L1 (class in xenonpy.model.nn.wrap) L1Loss (class in xenonpy.model.training.loss) label_smoothing (xenonpy.model.training.loss.CrossEntropyLoss attribute) lambda_lr() (xenonpy.model.nn.wrap.LrScheduler static method) LambdaLR (class in xenonpy.model.training.lr_scheduler) Layer1d (class in xenonpy.model.nn.layer) LayeredFP (class in xenonpy.descriptor.fingerprint) LBFGS (class in xenonpy.model.training.optimizer) lbfgs() (xenonpy.model.nn.wrap.Optim static method) linear() (xenonpy.model.nn.wrap.L1 static method) LinearLayer (class in xenonpy.model.sequential) list_descriptors() (xenonpy.mdl.mdl.MDL method) list_methods() (xenonpy.mdl.mdl.MDL method) list_models_with_descriptor() (xenonpy.mdl.mdl.MDL method) list_models_with_method() (xenonpy.mdl.mdl.MDL method) list_models_with_modelset() (xenonpy.mdl.mdl.MDL method) list_models_with_property() (xenonpy.mdl.mdl.MDL method) list_modelsets() (xenonpy.mdl.mdl.MDL method) list_properties() (xenonpy.mdl.mdl.MDL method) ListDescriptors (class in xenonpy.mdl.descriptor) (class in xenonpy.mdl.mdl) ListMethods (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.method) ListModelsets (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.modelset)

ListModelsWithDescriptor (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) ListModelsWithMethod (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) ListModelsWithModelset (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) ListModelsWithProperty (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) ListProperties (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.property) load() (xenonpy.model.training.checker.Checker class method) (xenonpy.model.training.trainer.Trainer class method) log() (xenonpy.datatools.transform.Scaler method) log_input (xenonpy.model.training.loss.PoissonNLLLoss attribute) log_likelihood() (xenonpy.inverse.base.BaseLogLikelihood method) (xenonpy.inverse.base.BaseLogLikelihoodSet method) (xenonpy.inverse.base.BaseSMC method) (xenonpy.inverse.iqspr.estimator.GaussianLogLikelihood method) (xenonpy.inverse.iqspr.GaussianLogLikelihood method) LogLikelihoodError loss_func (xenonpy.model.training.trainer.Trainer property) loss_type (xenonpy.model.training.trainer.Trainer property) lr_scheduler (xenonpy.model.training.trainer.Trainer property) LrScheduler (class in xenonpy.model.nn.wrap)

M

MACCS (class in xenonpy.descriptor.fingerprint) margin (xenonpy.model.training.loss.CosineEmbeddingLoss attribute) (xenonpy.model.training.loss.HingeEmbeddingLoss attribute) (xenonpy.model.training.loss.MarginRankingLoss attribute) (xenonpy.model.training.loss.MultiMarginLoss attribute) (xenonpy.model.training.loss.TripletMarginLoss attribute) (xenonpy.model.training.loss.TripletMarginWithDistanceLoss attribute) MarginRankingLoss (class in xenonpy.model.training.loss) match() (xenonpy.utils.useful_cls.Switch method) max_len (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property) MaxPooling (class in xenonpy.descriptor.compositions) MDL (class in xenonpy.mdl.mdl) merge_table() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) MHFP (class in xenonpy.descriptor.fingerprint) min_len (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property) min_max() (xenonpy.datatools.transform.Scaler method) MinPooling (class in xenonpy.descriptor.compositions) mix_function() (xenonpy.descriptor.base.BaseCompositionFeaturizer method) (xenonpy.descriptor.compositions.Counting method) (xenonpy.descriptor.compositions.GeometricMean method) (xenonpy.descriptor.compositions.HarmonicMean method) (xenonpy.descriptor.compositions.MaxPooling method) (xenonpy.descriptor.compositions.MinPooling method) (xenonpy.descriptor.compositions.WeightedAverage method) (xenonpy.descriptor.compositions.WeightedSum method) (xenonpy.descriptor.compositions.WeightedVariance method) model (xenonpy.model.training.checker.Checker property) (xenonpy.model.training.trainer.Trainer property) model_class (xenonpy.model.training.checker.Checker property) model_name (xenonpy.model.training.checker.Checker property) model_params (xenonpy.model.training.checker.Checker property) model_structure (xenonpy.model.training.checker.Checker property) (xenonpy.model.training.extension.persist.Persist property) modifier (xenonpy.inverse.iqspr.IQSPR property) (xenonpy.inverse.iqspr.iqspr.IQSPR property) (xenonpy.inverse.iqspr.IQSPR4DF property) (xenonpy.inverse.iqspr.iqspr4df.IQSPR4DF property) modify() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) module setup xenonpy xenonpy.contrib xenonpy.contrib.extend_descriptors xenonpy.contrib.extend_descriptors.descriptor xenonpy.contrib.extend_descriptors.descriptor.frozen_featurizer_descriptor xenonpy.contrib.extend_descriptors.descriptor.mordred_descriptor xenonpy.contrib.extend_descriptors.descriptor.organic_comp_descriptor xenonpy.datatools xenonpy.datatools.dataset xenonpy.datatools.preset xenonpy.datatools.splitter xenonpy.datatools.transform xenonpy.descriptor xenonpy.descriptor.base xenonpy.descriptor.cgcnn xenonpy.descriptor.compositions xenonpy.descriptor.fingerprint xenonpy.descriptor.frozen_featurizer xenonpy.descriptor.structure xenonpy.inverse xenonpy.inverse.base xenonpy.inverse.iqspr xenonpy.inverse.iqspr.estimator xenonpy.inverse.iqspr.iqspr xenonpy.inverse.iqspr.iqspr4df xenonpy.inverse.iqspr.modifier xenonpy.mdl xenonpy.mdl.base xenonpy.mdl.descriptor xenonpy.mdl.mdl xenonpy.mdl.method xenonpy.mdl.model xenonpy.mdl.modelset xenonpy.mdl.property xenonpy.model xenonpy.model.cgcnn xenonpy.model.extern xenonpy.model.nn xenonpy.model.nn.layer xenonpy.model.nn.wrap xenonpy.model.sequential xenonpy.model.training xenonpy.model.training.base xenonpy.model.training.checker xenonpy.model.training.clip_grad xenonpy.model.training.dataset xenonpy.model.training.dataset.array xenonpy.model.training.dataset.cgcnn xenonpy.model.training.extension xenonpy.model.training.extension.persist xenonpy.model.training.extension.tensor_convert xenonpy.model.training.extension.validator xenonpy.model.training.loss xenonpy.model.training.lr_scheduler xenonpy.model.training.optimizer xenonpy.model.training.trainer xenonpy.model.utils xenonpy.model.utils.metrics xenonpy.utils xenonpy.utils.math xenonpy.utils.math.product xenonpy.utils.parameter_gen xenonpy.utils.useful_cls xenonpy.utils.useful_func xenonpy.visualization xenonpy.visualization.heatmap

MolConvertError, [1] Mordred2DDescriptor (class in xenonpy.contrib.extend_descriptors.descriptor.mordred_descriptor) MSELoss (class in xenonpy.model.training.loss) multi_step_lr() (xenonpy.model.nn.wrap.LrScheduler static method) MultiLabelMarginLoss (class in xenonpy.model.training.loss) MultiLabelSoftMarginLoss (class in xenonpy.model.training.loss) MultiMarginLoss (class in xenonpy.model.training.loss) MultiStepLR (class in xenonpy.model.training.lr_scheduler)

N

n_jobs (xenonpy.descriptor.base.BaseFeaturizer property) NGram (class in xenonpy.inverse.iqspr) (class in xenonpy.inverse.iqspr.modifier) ngram_table (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property)

NGramTrainingError, [1] NLLLoss (class in xenonpy.model.training.loss) NLLLoss2d (class in xenonpy.model.training.loss) no_model_saving (xenonpy.model.training.extension.persist.Persist property) node_features() (xenonpy.descriptor.cgcnn.CrystalGraphFeaturizer method) non_blocking (xenonpy.model.training.trainer.Trainer property)

O

old_smi (xenonpy.inverse.base.ProposalError attribute) on_checkpoint() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.extension.persist.Persist method) on_errors (xenonpy.descriptor.base.BaseDescriptor property) (xenonpy.descriptor.base.BaseFeaturizer property) on_errors() (xenonpy.inverse.base.BaseProposal method) (xenonpy.inverse.base.BaseSMC method) (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method)

on_reset() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.extension.validator.Validator method) Optim (class in xenonpy.model.nn.wrap) optimizer (xenonpy.model.training.trainer.Trainer property) OrbitalFieldMatrix (class in xenonpy.descriptor.structure) OrganicCompDescriptor (class in xenonpy.contrib.extend_descriptors.descriptor.organic_comp_descriptor) output_proc() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.base.BaseRunner method) (xenonpy.model.training.extension.tensor_convert.TensorConverter method)

P

p (xenonpy.model.training.loss.MultiMarginLoss attribute) (xenonpy.model.training.loss.TripletMarginLoss attribute) PackageInfo (class in setup) pandas (xenonpy.datatools.dataset.Dataset property) parallel_verbose (xenonpy.descriptor.base.BaseFeaturizer property) ParameterGenerator (class in xenonpy.utils.parameter_gen) path (xenonpy.model.training.checker.Checker property) (xenonpy.model.training.extension.persist.Persist property) PatternFP (class in xenonpy.descriptor.fingerprint) Persist (class in xenonpy.model.training.extension.persist) pickle (xenonpy.datatools.dataset.Dataset property) PoissonNLLLoss (class in xenonpy.model.training.loss) pooling() (xenonpy.model.cgcnn.CrystalGraphConvNet static method)

power_transformer() (xenonpy.datatools.transform.Scaler method) PowerTransformer (class in xenonpy.datatools.transform) predict() (xenonpy.inverse.iqspr.estimator.GaussianLogLikelihood method) (xenonpy.inverse.iqspr.GaussianLogLikelihood method) (xenonpy.model.training.trainer.Trainer method) Preset (class in xenonpy.datatools.preset) probability (xenonpy.model.training.extension.tensor_convert.TensorConverter property) Product (class in xenonpy.utils.math.product) proposal() (xenonpy.inverse.base.BaseProposal method) (xenonpy.inverse.base.BaseSMC method) (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) ProposalError pull() (xenonpy.mdl.mdl.MDL method)

Q

query_descriptors() (xenonpy.mdl.mdl.MDL method) query_methods() (xenonpy.mdl.mdl.MDL method) query_modelsets() (xenonpy.mdl.mdl.MDL method) query_properties() (xenonpy.mdl.mdl.MDL method) queryable (xenonpy.mdl.base.BaseQuery attribute) (xenonpy.mdl.descriptor.CreateDescriptor attribute) (xenonpy.mdl.descriptor.GetDescriptorDetail attribute) (xenonpy.mdl.descriptor.ListDescriptors attribute) (xenonpy.mdl.descriptor.QueryDescriptors attribute) (xenonpy.mdl.descriptor.QueryDescriptorsWith attribute) (xenonpy.mdl.descriptor.UpdateDescriptor attribute) (xenonpy.mdl.mdl.CreateDescriptor attribute) (xenonpy.mdl.mdl.CreateMethod attribute) (xenonpy.mdl.mdl.CreateModelset attribute) (xenonpy.mdl.mdl.CreateProperty attribute) (xenonpy.mdl.mdl.GetDescriptorDetail attribute) (xenonpy.mdl.mdl.GetMethodDetail attribute) (xenonpy.mdl.mdl.GetModelDetail attribute) (xenonpy.mdl.mdl.GetModelDetails attribute) (xenonpy.mdl.mdl.GetModelsetDetail attribute) (xenonpy.mdl.mdl.GetModelUrl attribute) (xenonpy.mdl.mdl.GetModelUrls attribute) (xenonpy.mdl.mdl.GetPropertyDetail attribute) (xenonpy.mdl.mdl.GetSupplementary attribute) (xenonpy.mdl.mdl.GetTrainingEnv attribute) (xenonpy.mdl.mdl.GetTrainingInfo attribute) (xenonpy.mdl.mdl.GetVersion attribute) (xenonpy.mdl.mdl.ListDescriptors attribute) (xenonpy.mdl.mdl.ListMethods attribute) (xenonpy.mdl.mdl.ListModelsets attribute) (xenonpy.mdl.mdl.ListModelsWithDescriptor attribute) (xenonpy.mdl.mdl.ListModelsWithMethod attribute) (xenonpy.mdl.mdl.ListModelsWithModelset attribute) (xenonpy.mdl.mdl.ListModelsWithProperty attribute) (xenonpy.mdl.mdl.ListProperties attribute) (xenonpy.mdl.mdl.QueryDescriptors attribute) (xenonpy.mdl.mdl.QueryDescriptorsWith attribute) (xenonpy.mdl.mdl.QueryMethods attribute) (xenonpy.mdl.mdl.QueryMethodsWith attribute) (xenonpy.mdl.mdl.QueryModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetailsWith attribute) (xenonpy.mdl.mdl.QueryModelsets attribute) (xenonpy.mdl.mdl.QueryModelsetsWith attribute) (xenonpy.mdl.mdl.QueryProperties attribute) (xenonpy.mdl.mdl.QueryPropertiesWith attribute) (xenonpy.mdl.mdl.UpdateDescriptor attribute) (xenonpy.mdl.mdl.UpdateMethod attribute) (xenonpy.mdl.mdl.UpdateModelset attribute) (xenonpy.mdl.mdl.UpdateProperty attribute) (xenonpy.mdl.mdl.UploadModel attribute) (xenonpy.mdl.method.CreateMethod attribute) (xenonpy.mdl.method.GetMethodDetail attribute) (xenonpy.mdl.method.ListMethods attribute) (xenonpy.mdl.method.QueryMethods attribute) (xenonpy.mdl.method.QueryMethodsWith attribute) (xenonpy.mdl.method.UpdateMethod attribute) (xenonpy.mdl.model.GetModelDetail attribute) (xenonpy.mdl.model.GetModelDetails attribute) (xenonpy.mdl.model.GetModelUrl attribute) (xenonpy.mdl.model.GetModelUrls attribute) (xenonpy.mdl.model.GetSupplementary attribute) (xenonpy.mdl.model.GetTrainingEnv attribute) (xenonpy.mdl.model.GetTrainingInfo attribute) (xenonpy.mdl.model.ListModelsWithDescriptor attribute) (xenonpy.mdl.model.ListModelsWithMethod attribute) (xenonpy.mdl.model.ListModelsWithModelset attribute) (xenonpy.mdl.model.ListModelsWithProperty attribute) (xenonpy.mdl.model.QueryModelDetails attribute) (xenonpy.mdl.model.QueryModelDetailsWith attribute) (xenonpy.mdl.model.UploadModel attribute) (xenonpy.mdl.modelset.CreateModelset attribute) (xenonpy.mdl.modelset.GetModelsetDetail attribute) (xenonpy.mdl.modelset.ListModelsets attribute) (xenonpy.mdl.modelset.QueryModelsets attribute) (xenonpy.mdl.modelset.QueryModelsetsWith attribute) (xenonpy.mdl.modelset.UpdateModelset attribute) (xenonpy.mdl.property.CreateProperty attribute) (xenonpy.mdl.property.GetPropertyDetail attribute) (xenonpy.mdl.property.ListProperties attribute) (xenonpy.mdl.property.QueryProperties attribute) (xenonpy.mdl.property.QueryPropertiesWith attribute) (xenonpy.mdl.property.UpdateProperty attribute)

QueryDescriptors (class in xenonpy.mdl.descriptor) (class in xenonpy.mdl.mdl) QueryDescriptorsWith (class in xenonpy.mdl.descriptor) (class in xenonpy.mdl.mdl) QueryMethods (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.method) QueryMethodsWith (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.method) QueryModelDetails (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) QueryModelDetailsWith (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model) QueryModelsets (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.modelset) QueryModelsetsWith (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.modelset) QueryProperties (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.property) QueryPropertiesWith (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.property)

R

r_prop() (xenonpy.model.nn.wrap.Optim static method) RadialDistributionFunction (class in xenonpy.descriptor.structure) random_state (xenonpy.datatools.splitter.Splitter property) RDKitFP (class in xenonpy.descriptor.fingerprint) reduce_lr_on_plateau() (xenonpy.model.nn.wrap.LrScheduler static method) ReduceLROnPlateau (class in xenonpy.model.training.lr_scheduler) reduction (xenonpy.model.training.loss.BCELoss attribute) (xenonpy.model.training.loss.BCEWithLogitsLoss attribute) (xenonpy.model.training.loss.KLDivLoss attribute) (xenonpy.model.training.loss.L1Loss attribute) (xenonpy.model.training.loss.MSELoss attribute) (xenonpy.model.training.loss.MultiLabelMarginLoss attribute) (xenonpy.model.training.loss.MultiLabelSoftMarginLoss attribute) (xenonpy.model.training.loss.NLLLoss2d attribute) (xenonpy.model.training.loss.SmoothL1Loss attribute) (xenonpy.model.training.loss.SoftMarginLoss attribute) regress (xenonpy.model.training.extension.validator.Validator attribute) regression (xenonpy.mdl.mdl.GetModelDetail attribute) (xenonpy.mdl.mdl.GetModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetails attribute) (xenonpy.mdl.mdl.QueryModelDetailsWith attribute) (xenonpy.mdl.model.GetModelDetail attribute) (xenonpy.mdl.model.GetModelDetails attribute) (xenonpy.mdl.model.QueryModelDetails attribute) (xenonpy.mdl.model.QueryModelDetailsWith attribute) regression_metrics() (in module xenonpy.model.utils.metrics)

remove_estimator() (xenonpy.inverse.iqspr.estimator.GaussianLogLikelihood method) (xenonpy.inverse.iqspr.GaussianLogLikelihood method) remove_extension() (xenonpy.model.training.base.BaseRunner method) remove_table() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) reorder_esmi() (xenonpy.inverse.iqspr.modifier.NGram class method) (xenonpy.inverse.iqspr.NGram class method) reorder_prob (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property) requirements() (setup.PackageInfo static method) resample() (xenonpy.inverse.base.BaseResample method) (xenonpy.inverse.base.BaseSMC method) (xenonpy.inverse.iqspr.IQSPR method) (xenonpy.inverse.iqspr.iqspr.IQSPR method) (xenonpy.inverse.iqspr.IQSPR4DF method) (xenonpy.inverse.iqspr.iqspr4df.IQSPR4DF method) ResampleError reset() (xenonpy.datatools.transform.Scaler method) (xenonpy.model.training.trainer.Trainer method) results (xenonpy.mdl.base.BaseQuery property) results_tuple (xenonpy.model.training.trainer.Trainer attribute) return_type (xenonpy.descriptor.base.BaseFeaturizer property) rms_prop() (xenonpy.model.nn.wrap.Optim static method) RMSprop (class in xenonpy.model.training.optimizer) roll() (xenonpy.datatools.splitter.Splitter method) Rprop (class in xenonpy.model.training.optimizer)

S

sample_next_char() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) sample_order (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property) Scaler (class in xenonpy.datatools.transform) SequentialLinear (class in xenonpy.model.sequential) set_checkpoint() (xenonpy.model.training.checker.Checker method) (xenonpy.model.training.trainer.Trainer method) set_env() (in module xenonpy.utils.useful_func) setup module SGD (class in xenonpy.model.training.optimizer) sgd() (xenonpy.model.nn.wrap.Optim static method) shuffle (xenonpy.datatools.splitter.Splitter property) Singleton (class in xenonpy.utils.useful_cls) size (xenonpy.datatools.splitter.Splitter property) SMCError smi2esmi() (xenonpy.inverse.iqspr.modifier.NGram class method) (xenonpy.inverse.iqspr.NGram class method) smi2list() (xenonpy.inverse.iqspr.modifier.NGram class method) (xenonpy.inverse.iqspr.NGram class method)

SmoothL1Loss (class in xenonpy.model.training.loss) SoftMarginLoss (class in xenonpy.model.training.loss) sparse_adam() (xenonpy.model.nn.wrap.Optim static method) SparseAdam (class in xenonpy.model.training.optimizer) split() (xenonpy.datatools.splitter.Splitter method) split_table() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method) Splitter (class in xenonpy.datatools.splitter) standard() (xenonpy.datatools.transform.Scaler method) start() (xenonpy.utils.useful_cls.Timer method) step_forward() (xenonpy.model.training.base.BaseExtension method) (xenonpy.model.training.extension.persist.Persist method) (xenonpy.model.training.extension.tensor_convert.TensorConverter method) (xenonpy.model.training.extension.validator.Validator method) step_lr() (xenonpy.model.nn.wrap.LrScheduler static method) StepLR (class in xenonpy.model.training.lr_scheduler) stop() (xenonpy.utils.useful_cls.Timer method) Structures (class in xenonpy.descriptor.structure) swap (xenonpy.model.training.loss.TripletMarginLoss attribute) (xenonpy.model.training.loss.TripletMarginWithDistanceLoss attribute) Switch (class in xenonpy.utils.useful_cls) sync() (xenonpy.datatools.preset.Preset method)

T

T_Extension_Dict (xenonpy.model.training.base.BaseRunner attribute) TensorConverter (class in xenonpy.model.training.extension.tensor_convert) tensors (xenonpy.model.training.dataset.array.ArrayDataset attribute) test_size (xenonpy.datatools.splitter.Splitter property) TimedMetaClass (class in xenonpy.utils.useful_cls) Timer (class in xenonpy.utils.useful_cls) timer (xenonpy.descriptor.base.BaseDescriptor property) (xenonpy.descriptor.compositions.Compositions property) (xenonpy.descriptor.fingerprint.Fingerprints property) (xenonpy.descriptor.structure.Structures property) (xenonpy.inverse.base.BaseLogLikelihood property) (xenonpy.inverse.base.BaseLogLikelihoodSet property) (xenonpy.inverse.base.BaseProposal property) (xenonpy.inverse.base.BaseResample property) (xenonpy.inverse.base.BaseSMC property) (xenonpy.inverse.iqspr.estimator.GaussianLogLikelihood property) (xenonpy.inverse.iqspr.GaussianLogLikelihood property) (xenonpy.inverse.iqspr.IQSPR property) (xenonpy.inverse.iqspr.iqspr.IQSPR property) (xenonpy.inverse.iqspr.IQSPR4DF property) (xenonpy.inverse.iqspr.iqspr4df.IQSPR4DF property) (xenonpy.inverse.iqspr.modifier.NGram property) (xenonpy.inverse.iqspr.NGram property) (xenonpy.mdl.base.BaseQuery property) (xenonpy.mdl.descriptor.CreateDescriptor property) (xenonpy.mdl.descriptor.GetDescriptorDetail property) (xenonpy.mdl.descriptor.ListDescriptors property) (xenonpy.mdl.descriptor.QueryDescriptors property) (xenonpy.mdl.descriptor.QueryDescriptorsWith property) (xenonpy.mdl.descriptor.UpdateDescriptor property) (xenonpy.mdl.mdl.CreateDescriptor property) (xenonpy.mdl.mdl.CreateMethod property) (xenonpy.mdl.mdl.CreateModelset property) (xenonpy.mdl.mdl.CreateProperty property) (xenonpy.mdl.mdl.GetDescriptorDetail property) (xenonpy.mdl.mdl.GetMethodDetail property) (xenonpy.mdl.mdl.GetModelDetail property) (xenonpy.mdl.mdl.GetModelDetails property) (xenonpy.mdl.mdl.GetModelsetDetail property) (xenonpy.mdl.mdl.GetModelUrl property) (xenonpy.mdl.mdl.GetModelUrls property) (xenonpy.mdl.mdl.GetPropertyDetail property) (xenonpy.mdl.mdl.GetSupplementary property) (xenonpy.mdl.mdl.GetTrainingEnv property) (xenonpy.mdl.mdl.GetTrainingInfo property) (xenonpy.mdl.mdl.GetVersion property) (xenonpy.mdl.mdl.ListDescriptors property) (xenonpy.mdl.mdl.ListMethods property) (xenonpy.mdl.mdl.ListModelsets property) (xenonpy.mdl.mdl.ListModelsWithDescriptor property) (xenonpy.mdl.mdl.ListModelsWithMethod property) (xenonpy.mdl.mdl.ListModelsWithModelset property) (xenonpy.mdl.mdl.ListModelsWithProperty property) (xenonpy.mdl.mdl.ListProperties property) (xenonpy.mdl.mdl.MDL property) (xenonpy.mdl.mdl.QueryDescriptors property) (xenonpy.mdl.mdl.QueryDescriptorsWith property) (xenonpy.mdl.mdl.QueryMethods property) (xenonpy.mdl.mdl.QueryMethodsWith property) (xenonpy.mdl.mdl.QueryModelDetails property) (xenonpy.mdl.mdl.QueryModelDetailsWith property) (xenonpy.mdl.mdl.QueryModelsets property) (xenonpy.mdl.mdl.QueryModelsetsWith property) (xenonpy.mdl.mdl.QueryProperties property) (xenonpy.mdl.mdl.QueryPropertiesWith property) (xenonpy.mdl.mdl.UpdateDescriptor property) (xenonpy.mdl.mdl.UpdateMethod property) (xenonpy.mdl.mdl.UpdateModelset property) (xenonpy.mdl.mdl.UpdateProperty property) (xenonpy.mdl.mdl.UploadModel property) (xenonpy.mdl.method.CreateMethod property) (xenonpy.mdl.method.GetMethodDetail property) (xenonpy.mdl.method.ListMethods property) (xenonpy.mdl.method.QueryMethods property) (xenonpy.mdl.method.QueryMethodsWith property) (xenonpy.mdl.method.UpdateMethod property) (xenonpy.mdl.model.GetModelDetail property) (xenonpy.mdl.model.GetModelDetails property) (xenonpy.mdl.model.GetModelUrl property) (xenonpy.mdl.model.GetModelUrls property) (xenonpy.mdl.model.GetSupplementary property) (xenonpy.mdl.model.GetTrainingEnv property) (xenonpy.mdl.model.GetTrainingInfo property) (xenonpy.mdl.model.ListModelsWithDescriptor property) (xenonpy.mdl.model.ListModelsWithMethod property) (xenonpy.mdl.model.ListModelsWithModelset property) (xenonpy.mdl.model.ListModelsWithProperty property) (xenonpy.mdl.model.QueryModelDetails property) (xenonpy.mdl.model.QueryModelDetailsWith property) (xenonpy.mdl.model.UploadModel property) (xenonpy.mdl.modelset.CreateModelset property) (xenonpy.mdl.modelset.GetModelsetDetail property) (xenonpy.mdl.modelset.ListModelsets property) (xenonpy.mdl.modelset.QueryModelsets property) (xenonpy.mdl.modelset.QueryModelsetsWith property) (xenonpy.mdl.modelset.UpdateModelset property) (xenonpy.mdl.property.CreateProperty property) (xenonpy.mdl.property.GetPropertyDetail property) (xenonpy.mdl.property.ListProperties property) (xenonpy.mdl.property.QueryProperties property) (xenonpy.mdl.property.QueryPropertiesWith property) (xenonpy.mdl.property.UpdateProperty property) (xenonpy.model.training.base.BaseRunner property) (xenonpy.model.training.trainer.Trainer property)

to() (xenonpy.datatools.dataset.Dataset class method) to_namedtuple() (xenonpy.model.training.trainer.Trainer method) TopologicalTorsionFP (class in xenonpy.descriptor.fingerprint) total_epochs (xenonpy.model.training.trainer.Trainer property) total_iterations (xenonpy.model.training.trainer.Trainer property) trained_model (xenonpy.model.training.checker.Checker property) Trainer (class in xenonpy.model.training.trainer) training (xenonpy.model.cgcnn.ConvLayer attribute) (xenonpy.model.cgcnn.CrystalGraphConvNet attribute) (xenonpy.model.nn.layer.Layer1d attribute) (xenonpy.model.sequential.LinearLayer attribute) (xenonpy.model.sequential.SequentialLinear attribute) (xenonpy.model.training.loss.NLLLoss2d attribute) training_info (xenonpy.model.training.checker.Checker property) (xenonpy.model.training.trainer.Trainer property) transform() (xenonpy.datatools.transform.PowerTransformer method) (xenonpy.datatools.transform.Scaler method) (xenonpy.descriptor.base.BaseDescriptor method) (xenonpy.descriptor.base.BaseFeaturizer method) TripletMarginLoss (class in xenonpy.model.training.loss) TripletMarginWithDistanceLoss (class in xenonpy.model.training.loss)

U

uniform() (xenonpy.model.nn.wrap.Init static method) unique() (xenonpy.inverse.base.BaseSMC method) (xenonpy.inverse.iqspr.IQSPR4DF method) (xenonpy.inverse.iqspr.iqspr4df.IQSPR4DF method) update_descriptor() (xenonpy.mdl.mdl.MDL method) update_method() (xenonpy.mdl.mdl.MDL method) update_modelset() (xenonpy.mdl.mdl.MDL method) update_property() (xenonpy.mdl.mdl.MDL method) update_targets() (xenonpy.inverse.iqspr.estimator.GaussianLogLikelihood method) (xenonpy.inverse.iqspr.GaussianLogLikelihood method)

UpdateDescriptor (class in xenonpy.mdl.descriptor) (class in xenonpy.mdl.mdl) UpdateMethod (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.method) UpdateModelset (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.modelset) UpdateProperty (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.property) upload_model() (xenonpy.mdl.mdl.MDL method) UploadModel (class in xenonpy.mdl.mdl) (class in xenonpy.mdl.model)

V

validate_dataset (xenonpy.model.training.trainer.Trainer property) Validator (class in xenonpy.model.training.extension.validator) validator() (xenonpy.inverse.iqspr.modifier.NGram method) (xenonpy.inverse.iqspr.NGram method)

variables (xenonpy.mdl.base.BaseQuery property) version (xenonpy.mdl.mdl.MDL property)

W

warming_up (xenonpy.model.training.extension.validator.Validator property) weight (xenonpy.model.training.loss.NLLLoss2d attribute)

WeightedAverage (class in xenonpy.descriptor.compositions) WeightedSum (class in xenonpy.descriptor.compositions) WeightedVariance (class in xenonpy.descriptor.compositions)

X

x_val (xenonpy.model.training.trainer.Trainer property) xenonpy module xenonpy.contrib module xenonpy.contrib.extend_descriptors module xenonpy.contrib.extend_descriptors.descriptor module xenonpy.contrib.extend_descriptors.descriptor.frozen_featurizer_descriptor module xenonpy.contrib.extend_descriptors.descriptor.mordred_descriptor module xenonpy.contrib.extend_descriptors.descriptor.organic_comp_descriptor module xenonpy.datatools module xenonpy.datatools.dataset module xenonpy.datatools.preset module xenonpy.datatools.splitter module xenonpy.datatools.transform module xenonpy.descriptor module xenonpy.descriptor.base module xenonpy.descriptor.cgcnn module xenonpy.descriptor.compositions module xenonpy.descriptor.fingerprint module xenonpy.descriptor.frozen_featurizer module xenonpy.descriptor.structure module xenonpy.inverse module xenonpy.inverse.base module xenonpy.inverse.iqspr module xenonpy.inverse.iqspr.estimator module xenonpy.inverse.iqspr.iqspr module xenonpy.inverse.iqspr.iqspr4df module xenonpy.inverse.iqspr.modifier module xenonpy.mdl module xenonpy.mdl.base module xenonpy.mdl.descriptor module xenonpy.mdl.mdl module xenonpy.mdl.method module xenonpy.mdl.model module xenonpy.mdl.modelset module

xenonpy.mdl.property module xenonpy.model module xenonpy.model.cgcnn module xenonpy.model.extern module xenonpy.model.nn module xenonpy.model.nn.layer module xenonpy.model.nn.wrap module xenonpy.model.sequential module xenonpy.model.training module xenonpy.model.training.base module xenonpy.model.training.checker module xenonpy.model.training.clip_grad module xenonpy.model.training.dataset module xenonpy.model.training.dataset.array module xenonpy.model.training.dataset.cgcnn module xenonpy.model.training.extension module xenonpy.model.training.extension.persist module xenonpy.model.training.extension.tensor_convert module xenonpy.model.training.extension.validator module xenonpy.model.training.loss module xenonpy.model.training.lr_scheduler module xenonpy.model.training.optimizer module xenonpy.model.training.trainer module xenonpy.model.utils module xenonpy.model.utils.metrics module xenonpy.utils module xenonpy.utils.math module xenonpy.utils.math.product module xenonpy.utils.parameter_gen module xenonpy.utils.useful_cls module xenonpy.utils.useful_func module xenonpy.visualization module xenonpy.visualization.heatmap module

Y

y_val (xenonpy.model.training.trainer.Trainer property)

yeo_johnson() (xenonpy.datatools.transform.Scaler method)

Z

zero_infinity (xenonpy.model.training.loss.CTCLoss attribute)