xenonpy package

Subpackages

• xenonpy.contrib package
  • Subpackages
    • xenonpy.contrib.extend_descriptors package
      • Subpackages
      • Module contents
    • xenonpy.contrib.ismd package
      • Submodules
      • xenonpy.contrib.ismd.reactant_pool module
      • xenonpy.contrib.ismd.reactor module
      • Module contents
  • Module contents
• xenonpy.datatools package
  • Submodules
  • xenonpy.datatools.dataset module
    • Dataset
      • Dataset.__call__()
      • Dataset.from_http()
      • Dataset.to()
      • Dataset.csv
      • Dataset.excel
      • Dataset.pandas
      • Dataset.pickle
  • xenonpy.datatools.preset module
    • Preset
      • Preset.build()
      • Preset.sync()
      • Preset.atom_init
      • Preset.elements
      • Preset.elements_completed
  • xenonpy.datatools.splitter module
    • Splitter
      • Splitter.cv()
      • Splitter.roll()
      • Splitter.split()
      • Splitter.k_fold
      • Splitter.random_state
      • Splitter.shuffle
      • Splitter.size
      • Splitter.test_size
  • xenonpy.datatools.transform module
    • PowerTransformer
      • PowerTransformer.fit()
      • PowerTransformer.inverse_transform()
      • PowerTransformer.transform()
    • Scaler
      • Scaler.box_cox()
      • Scaler.fit()
      • Scaler.fit_transform()
      • Scaler.inverse_transform()
      • Scaler.log()
      • Scaler.min_max()
      • Scaler.power_transformer()
      • Scaler.reset()
      • Scaler.standard()
      • Scaler.transform()
      • Scaler.yeo_johnson()
  • Module contents
• xenonpy.descriptor package
  • Submodules
  • xenonpy.descriptor.base module
    • BaseCompositionFeaturizer
      • BaseCompositionFeaturizer.featurize()
      • BaseCompositionFeaturizer.mix_function()
    • BaseDescriptor
      • BaseDescriptor.fit()
      • BaseDescriptor.transform()
      • BaseDescriptor.all_featurizers
      • BaseDescriptor.elapsed
      • BaseDescriptor.feature_labels
      • BaseDescriptor.featurizers
      • BaseDescriptor.on_errors
      • BaseDescriptor.timer
    • BaseFeaturizer
      • BaseFeaturizer.featurize()
      • BaseFeaturizer.fit()
      • BaseFeaturizer.fit_transform()
      • BaseFeaturizer.transform()
      • BaseFeaturizer.authors
      • BaseFeaturizer.citations
      • BaseFeaturizer.feature_labels
      • BaseFeaturizer.n_jobs
      • BaseFeaturizer.on_errors
      • BaseFeaturizer.parallel_verbose
      • BaseFeaturizer.return_type
  • xenonpy.descriptor.cgcnn module
    • CrystalGraphFeaturizer
      • CrystalGraphFeaturizer.edge_features()
      • CrystalGraphFeaturizer.featurize()
      • CrystalGraphFeaturizer.node_features()
      • CrystalGraphFeaturizer.feature_labels
  • xenonpy.descriptor.compositions module
    • Compositions
      • Compositions.classic
      • Compositions.timer
    • Counting
      • Counting.mix_function()
      • Counting.feature_labels
    • GeometricMean
      • GeometricMean.mix_function()
      • GeometricMean.feature_labels
    • HarmonicMean
      • HarmonicMean.mix_function()
      • HarmonicMean.feature_labels
    • MaxPooling
      • MaxPooling.mix_function()
      • MaxPooling.feature_labels
    • MinPooling
      • MinPooling.mix_function()
      • MinPooling.feature_labels
    • WeightedAverage
      • WeightedAverage.mix_function()
      • WeightedAverage.feature_labels
    • WeightedSum
      • WeightedSum.mix_function()
      • WeightedSum.feature_labels
    • WeightedVariance
      • WeightedVariance.mix_function()
      • WeightedVariance.feature_labels
  • xenonpy.descriptor.fingerprint module
    • AtomPairFP
      • AtomPairFP.featurize()
      • AtomPairFP.feature_labels
    • DescriptorFeature
      • DescriptorFeature.featurize()
      • DescriptorFeature.classic
      • DescriptorFeature.feature_labels
    • ECFP
      • ECFP.featurize()
      • ECFP.feature_labels
    • FCFP
      • FCFP.featurize()
      • FCFP.feature_labels
    • Fingerprints
      • Fingerprints.timer
    • LayeredFP
      • LayeredFP.featurize()
      • LayeredFP.feature_labels
    • MACCS
      • MACCS.featurize()
      • MACCS.feature_labels
    • MHFP
      • MHFP.featurize()
      • MHFP.feature_labels
    • PatternFP
      • PatternFP.featurize()
      • PatternFP.feature_labels
    • RDKitFP
      • RDKitFP.featurize()
      • RDKitFP.feature_labels
    • TopologicalTorsionFP
      • TopologicalTorsionFP.featurize()
      • TopologicalTorsionFP.feature_labels
  • xenonpy.descriptor.frozen_featurizer module
    • FrozenFeaturizer
      • FrozenFeaturizer.featurize()
      • FrozenFeaturizer.feature_labels
  • xenonpy.descriptor.structure module
    • OrbitalFieldMatrix
      • OrbitalFieldMatrix.featurize()
      • OrbitalFieldMatrix.get_element_representation()
      • OrbitalFieldMatrix.feature_labels
    • RadialDistributionFunction
      • RadialDistributionFunction.featurize()
      • RadialDistributionFunction.feature_labels
    • Structures
      • Structures.timer
  • Module contents
• xenonpy.inverse package
  • Subpackages
    • xenonpy.inverse.iqspr package
      • Submodules
      • xenonpy.inverse.iqspr.estimator module
      • xenonpy.inverse.iqspr.iqspr module
      • xenonpy.inverse.iqspr.iqspr4df module
      • xenonpy.inverse.iqspr.modifier module
      • Module contents
  • Submodules
  • xenonpy.inverse.base module
    • LogLikelihoodError
    • ProposalError
      • ProposalError.old_smi
    • ResampleError
    • SMCError
    • BaseLogLikelihood
      • BaseLogLikelihood.__call__()
      • BaseLogLikelihood.fit()
      • BaseLogLikelihood.log_likelihood()
      • BaseLogLikelihood.timer
    • BaseLogLikelihoodSet
      • BaseLogLikelihoodSet.__call__()
      • BaseLogLikelihoodSet.log_likelihood()
      • BaseLogLikelihoodSet.all_loglikelihoods
      • BaseLogLikelihoodSet.elapsed
      • BaseLogLikelihoodSet.timer
    • BaseProposal
      • BaseProposal.__call__()
      • BaseProposal.fit()
      • BaseProposal.on_errors()
      • BaseProposal.proposal()
      • BaseProposal.timer
    • BaseResample
      • BaseResample.__call__()
      • BaseResample.fit()
      • BaseResample.resample()
      • BaseResample.timer
    • BaseSMC
      • BaseSMC.__call__()
      • BaseSMC.log_likelihood()
      • BaseSMC.on_errors()
      • BaseSMC.proposal()
      • BaseSMC.resample()
      • BaseSMC.unique()
      • BaseSMC.timer
  • Module contents
• xenonpy.mdl package
  • Submodules
  • xenonpy.mdl.base module
    • BaseQuery
      • BaseQuery.__call__()
      • BaseQuery.check_query_vars()
      • BaseQuery.gql()
      • BaseQuery.api_key
      • BaseQuery.endpoint
      • BaseQuery.queryable
      • BaseQuery.results
      • BaseQuery.timer
      • BaseQuery.variables
  • xenonpy.mdl.descriptor module
    • CreateDescriptor
      • CreateDescriptor.gql()
      • CreateDescriptor.queryable
      • CreateDescriptor.timer
    • GetDescriptorDetail
      • GetDescriptorDetail.gql()
      • GetDescriptorDetail.queryable
      • GetDescriptorDetail.timer
    • ListDescriptors
      • ListDescriptors.gql()
      • ListDescriptors.queryable
      • ListDescriptors.timer
    • QueryDescriptors
      • QueryDescriptors.gql()
      • QueryDescriptors.queryable
      • QueryDescriptors.timer
    • QueryDescriptorsWith
      • QueryDescriptorsWith.gql()
      • QueryDescriptorsWith.queryable
      • QueryDescriptorsWith.timer
    • UpdateDescriptor
      • UpdateDescriptor.gql()
      • UpdateDescriptor.queryable
      • UpdateDescriptor.timer
  • xenonpy.mdl.mdl module
    • CreateDescriptor
      • CreateDescriptor.gql()
      • CreateDescriptor.queryable
      • CreateDescriptor.timer
    • CreateMethod
      • CreateMethod.gql()
      • CreateMethod.queryable
      • CreateMethod.timer
    • CreateModelset
      • CreateModelset.gql()
      • CreateModelset.queryable
      • CreateModelset.timer
    • CreateProperty
      • CreateProperty.gql()
      • CreateProperty.queryable
      • CreateProperty.timer
    • GetDescriptorDetail
      • GetDescriptorDetail.gql()
      • GetDescriptorDetail.queryable
      • GetDescriptorDetail.timer
    • GetMethodDetail
      • GetMethodDetail.gql()
      • GetMethodDetail.queryable
      • GetMethodDetail.timer
    • GetModelDetail
      • GetModelDetail.gql()
      • GetModelDetail.classification
      • GetModelDetail.common
      • GetModelDetail.queryable
      • GetModelDetail.regression
      • GetModelDetail.timer
    • GetModelDetails
      • GetModelDetails.gql()
      • GetModelDetails.classification
      • GetModelDetails.common
      • GetModelDetails.queryable
      • GetModelDetails.regression
      • GetModelDetails.timer
    • GetModelUrl
      • GetModelUrl.gql()
      • GetModelUrl.queryable
      • GetModelUrl.timer
    • GetModelUrls
      • GetModelUrls.gql()
      • GetModelUrls.queryable
      • GetModelUrls.timer
    • GetModelsetDetail
      • GetModelsetDetail.gql()
      • GetModelsetDetail.queryable
      • GetModelsetDetail.timer
    • GetPropertyDetail
      • GetPropertyDetail.gql()
      • GetPropertyDetail.queryable
      • GetPropertyDetail.timer
    • GetSupplementary
      • GetSupplementary.gql()
      • GetSupplementary.queryable
      • GetSupplementary.timer
    • GetTrainingEnv
      • GetTrainingEnv.gql()
      • GetTrainingEnv.queryable
      • GetTrainingEnv.timer
    • GetTrainingInfo
      • GetTrainingInfo.gql()
      • GetTrainingInfo.queryable
      • GetTrainingInfo.timer
    • GetVersion
      • GetVersion.gql()
      • GetVersion.queryable
      • GetVersion.timer
    • ListDescriptors
      • ListDescriptors.gql()
      • ListDescriptors.queryable
      • ListDescriptors.timer
    • ListMethods
      • ListMethods.gql()
      • ListMethods.queryable
      • ListMethods.timer
    • ListModelsWithDescriptor
      • ListModelsWithDescriptor.gql()
      • ListModelsWithDescriptor.queryable
      • ListModelsWithDescriptor.timer
    • ListModelsWithMethod
      • ListModelsWithMethod.gql()
      • ListModelsWithMethod.queryable
      • ListModelsWithMethod.timer
    • ListModelsWithModelset
      • ListModelsWithModelset.gql()
      • ListModelsWithModelset.queryable
      • ListModelsWithModelset.timer
    • ListModelsWithProperty
      • ListModelsWithProperty.gql()
      • ListModelsWithProperty.queryable
      • ListModelsWithProperty.timer
    • ListModelsets
      • ListModelsets.gql()
      • ListModelsets.queryable
      • ListModelsets.timer
    • ListProperties
      • ListProperties.gql()
      • ListProperties.queryable
      • ListProperties.timer
    • MDL
      • MDL.__call__()
      • MDL.create_descriptor()
      • MDL.create_method()
      • MDL.create_modelset()
      • MDL.create_property()
      • MDL.get_descriptor_detail()
      • MDL.get_method_detail()
      • MDL.get_model_detail()
      • MDL.get_model_details()
      • MDL.get_model_urls()
      • MDL.get_modelset_detail()
      • MDL.get_property_detail()
      • MDL.get_supplementary()
      • MDL.get_training_env()
      • MDL.get_training_info()
      • MDL.list_descriptors()
      • MDL.list_methods()
      • MDL.list_models_with_descriptor()
      • MDL.list_models_with_method()
      • MDL.list_models_with_modelset()
      • MDL.list_models_with_property()
      • MDL.list_modelsets()
      • MDL.list_properties()
      • MDL.pull()
      • MDL.query_descriptors()
      • MDL.query_methods()
      • MDL.query_modelsets()
      • MDL.query_properties()
      • MDL.update_descriptor()
      • MDL.update_method()
      • MDL.update_modelset()
      • MDL.update_property()
      • MDL.upload_model()
      • MDL.api_key
      • MDL.endpoint
      • MDL.timer
      • MDL.version
    • QueryDescriptors
      • QueryDescriptors.gql()
      • QueryDescriptors.queryable
      • QueryDescriptors.timer
    • QueryDescriptorsWith
      • QueryDescriptorsWith.gql()
      • QueryDescriptorsWith.queryable
      • QueryDescriptorsWith.timer
    • QueryMethods
      • QueryMethods.gql()
      • QueryMethods.queryable
      • QueryMethods.timer
    • QueryMethodsWith
      • QueryMethodsWith.gql()
      • QueryMethodsWith.queryable
      • QueryMethodsWith.timer
    • QueryModelDetails
      • QueryModelDetails.gql()
      • QueryModelDetails.classification
      • QueryModelDetails.common
      • QueryModelDetails.queryable
      • QueryModelDetails.regression
      • QueryModelDetails.timer
    • QueryModelDetailsWith
      • QueryModelDetailsWith.gql()
      • QueryModelDetailsWith.classification
      • QueryModelDetailsWith.common
      • QueryModelDetailsWith.queryable
      • QueryModelDetailsWith.regression
      • QueryModelDetailsWith.timer
    • QueryModelsets
      • QueryModelsets.gql()
      • QueryModelsets.queryable
      • QueryModelsets.timer
    • QueryModelsetsWith
      • QueryModelsetsWith.gql()
      • QueryModelsetsWith.queryable
      • QueryModelsetsWith.timer
    • QueryProperties
      • QueryProperties.gql()
      • QueryProperties.queryable
      • QueryProperties.timer
    • QueryPropertiesWith
      • QueryPropertiesWith.gql()
      • QueryPropertiesWith.queryable
      • QueryPropertiesWith.timer
    • UpdateDescriptor
      • UpdateDescriptor.gql()
      • UpdateDescriptor.queryable
      • UpdateDescriptor.timer
    • UpdateMethod
      • UpdateMethod.gql()
      • UpdateMethod.queryable
      • UpdateMethod.timer
    • UpdateModelset
      • UpdateModelset.gql()
      • UpdateModelset.queryable
      • UpdateModelset.timer
    • UpdateProperty
      • UpdateProperty.gql()
      • UpdateProperty.queryable
      • UpdateProperty.timer
    • UploadModel
      • UploadModel.gql()
      • UploadModel.queryable
      • UploadModel.timer
  • xenonpy.mdl.method module
    • CreateMethod
      • CreateMethod.gql()
      • CreateMethod.queryable
      • CreateMethod.timer
    • GetMethodDetail
      • GetMethodDetail.gql()
      • GetMethodDetail.queryable
      • GetMethodDetail.timer
    • ListMethods
      • ListMethods.gql()
      • ListMethods.queryable
      • ListMethods.timer
    • QueryMethods
      • QueryMethods.gql()
      • QueryMethods.queryable
      • QueryMethods.timer
    • QueryMethodsWith
      • QueryMethodsWith.gql()
      • QueryMethodsWith.queryable
      • QueryMethodsWith.timer
    • UpdateMethod
      • UpdateMethod.gql()
      • UpdateMethod.queryable
      • UpdateMethod.timer
  • xenonpy.mdl.model module
    • GetModelDetail
      • GetModelDetail.gql()
      • GetModelDetail.classification
      • GetModelDetail.common
      • GetModelDetail.queryable
      • GetModelDetail.regression
      • GetModelDetail.timer
    • GetModelDetails
      • GetModelDetails.gql()
      • GetModelDetails.classification
      • GetModelDetails.common
      • GetModelDetails.queryable
      • GetModelDetails.regression
      • GetModelDetails.timer
    • GetModelUrl
      • GetModelUrl.gql()
      • GetModelUrl.queryable
      • GetModelUrl.timer
    • GetModelUrls
      • GetModelUrls.gql()
      • GetModelUrls.queryable
      • GetModelUrls.timer
    • GetSupplementary
      • GetSupplementary.gql()
      • GetSupplementary.queryable
      • GetSupplementary.timer
    • GetTrainingEnv
      • GetTrainingEnv.gql()
      • GetTrainingEnv.queryable
      • GetTrainingEnv.timer
    • GetTrainingInfo
      • GetTrainingInfo.gql()
      • GetTrainingInfo.queryable
      • GetTrainingInfo.timer
    • ListModelsWithDescriptor
      • ListModelsWithDescriptor.gql()
      • ListModelsWithDescriptor.queryable
      • ListModelsWithDescriptor.timer
    • ListModelsWithMethod
      • ListModelsWithMethod.gql()
      • ListModelsWithMethod.queryable
      • ListModelsWithMethod.timer
    • ListModelsWithModelset
      • ListModelsWithModelset.gql()
      • ListModelsWithModelset.queryable
      • ListModelsWithModelset.timer
    • ListModelsWithProperty
      • ListModelsWithProperty.gql()
      • ListModelsWithProperty.queryable
      • ListModelsWithProperty.timer
    • QueryModelDetails
      • QueryModelDetails.gql()
      • QueryModelDetails.classification
      • QueryModelDetails.common
      • QueryModelDetails.queryable
      • QueryModelDetails.regression
      • QueryModelDetails.timer
    • QueryModelDetailsWith
      • QueryModelDetailsWith.gql()
      • QueryModelDetailsWith.classification
      • QueryModelDetailsWith.common
      • QueryModelDetailsWith.queryable
      • QueryModelDetailsWith.regression
      • QueryModelDetailsWith.timer
    • UploadModel
      • UploadModel.gql()
      • UploadModel.queryable
      • UploadModel.timer
  • xenonpy.mdl.modelset module
    • CreateModelset
      • CreateModelset.gql()
      • CreateModelset.queryable
      • CreateModelset.timer
    • GetModelsetDetail
      • GetModelsetDetail.gql()
      • GetModelsetDetail.queryable
      • GetModelsetDetail.timer
    • ListModelsets
      • ListModelsets.gql()
      • ListModelsets.queryable
      • ListModelsets.timer
    • QueryModelsets
      • QueryModelsets.gql()
      • QueryModelsets.queryable
      • QueryModelsets.timer
    • QueryModelsetsWith
      • QueryModelsetsWith.gql()
      • QueryModelsetsWith.queryable
      • QueryModelsetsWith.timer
    • UpdateModelset
      • UpdateModelset.gql()
      • UpdateModelset.queryable
      • UpdateModelset.timer
  • xenonpy.mdl.property module
    • CreateProperty
      • CreateProperty.gql()
      • CreateProperty.queryable
      • CreateProperty.timer
    • GetPropertyDetail
      • GetPropertyDetail.gql()
      • GetPropertyDetail.queryable
      • GetPropertyDetail.timer
    • ListProperties
      • ListProperties.gql()
      • ListProperties.queryable
      • ListProperties.timer
    • QueryProperties
      • QueryProperties.gql()
      • QueryProperties.queryable
      • QueryProperties.timer
    • QueryPropertiesWith
      • QueryPropertiesWith.gql()
      • QueryPropertiesWith.queryable
      • QueryPropertiesWith.timer
    • UpdateProperty
      • UpdateProperty.gql()
      • UpdateProperty.queryable
      • UpdateProperty.timer
  • Module contents
• xenonpy.model package
  • Subpackages
    • xenonpy.model.nn package
      • Submodules
      • xenonpy.model.nn.layer module
      • xenonpy.model.nn.wrap module
      • Module contents
    • xenonpy.model.training package
      • Subpackages
      • Submodules
      • xenonpy.model.training.base module
      • xenonpy.model.training.checker module
      • xenonpy.model.training.clip_grad module
      • xenonpy.model.training.loss module
      • xenonpy.model.training.lr_scheduler module
      • xenonpy.model.training.optimizer module
      • xenonpy.model.training.trainer module
      • Module contents
    • xenonpy.model.utils package
      • Submodules
      • xenonpy.model.utils.metrics module
      • Module contents
  • Submodules
  • xenonpy.model.cgcnn module
    • ConvLayer
      • ConvLayer.forward()
      • ConvLayer.training
    • CrystalGraphConvNet
      • CrystalGraphConvNet.forward()
      • CrystalGraphConvNet.pooling()
      • CrystalGraphConvNet.training
  • xenonpy.model.extern module
  • xenonpy.model.sequential module
    • LinearLayer
      • LinearLayer.forward()
      • LinearLayer.training
    • SequentialLinear
      • SequentialLinear.forward()
      • SequentialLinear.training
  • Module contents
• xenonpy.utils package
  • Subpackages
    • xenonpy.utils.math package
      • Submodules
      • xenonpy.utils.math.product module
      • Module contents
  • Submodules
  • xenonpy.utils.parameter_gen module
    • ParameterGenerator
      • ParameterGenerator.__call__()
  • xenonpy.utils.useful_cls module
    • Singleton
      • Singleton.__call__()
    • Switch
      • Switch.match()
    • TimedMetaClass
    • Timer
      • Timer.start()
      • Timer.stop()
      • Timer.elapsed
  • xenonpy.utils.useful_func module
    • absolute_path()
    • camel_to_snake()
    • config()
    • get_data_loc()
    • get_dataset_url()
    • get_sha256()
    • set_env()
  • Module contents
• xenonpy.visualization package
  • Submodules
  • xenonpy.visualization.heatmap module
    • DescriptorHeatmap
      • DescriptorHeatmap.draw()
      • DescriptorHeatmap.fit()
  • Module contents

Module contents