Index

_

__call__() (kgcnn.crystal.base.CrystalPreprocessor method) (kgcnn.graph.base.GraphPostProcessorBase method) (kgcnn.graph.base.GraphPreProcessorBase method) (kgcnn.molecule.dynamics.ase_calc.AtomsToGraphConverter method) (kgcnn.molecule.dynamics.base.MolDynamicsModelPredictor method) (kgcnn.molecule.encoder.OneHotEncoder method) (kgcnn.training.schedule.LinearWarmupExponentialDecay method) __getitem__() (kgcnn.io.file.RaggedTensorHDFile method) (kgcnn.io.file.RaggedTensorNumpyFile method) __init__() (kgcnn.crystal.preprocessor.KNNAsymmetricUnitCell method) (kgcnn.crystal.preprocessor.KNNNonPeriodicUnitCell method) (kgcnn.crystal.preprocessor.KNNSuperCell method) (kgcnn.crystal.preprocessor.KNNUnitCell method) (kgcnn.crystal.preprocessor.RadiusAsymmetricUnitCell method) (kgcnn.crystal.preprocessor.RadiusNonPeriodicUnitCell method) (kgcnn.crystal.preprocessor.RadiusSuperCell method) (kgcnn.crystal.preprocessor.RadiusUnitCell method) (kgcnn.crystal.preprocessor.VoronoiAsymmetricUnitCell method) (kgcnn.crystal.preprocessor.VoronoiNonPeriodicUnitCell method) (kgcnn.crystal.preprocessor.VoronoiSuperCell method) (kgcnn.crystal.preprocessor.VoronoiUnitCell method) (kgcnn.data.base.MemoryGraphDataset method) (kgcnn.data.base.MemoryGraphList method) (kgcnn.data.crystal.CrystalDataset method) (kgcnn.data.datasets.ClinToxDataset.ClinToxDataset method) (kgcnn.data.datasets.CoraDataset.CoraDataset method) (kgcnn.data.datasets.CoraLuDataset.CoraLuDataset method) (kgcnn.data.datasets.ESOLDataset.ESOLDataset method) (kgcnn.data.datasets.FreeSolvDataset.FreeSolvDataset method) (kgcnn.data.datasets.GraphTUDataset2020.GraphTUDataset2020 method) (kgcnn.data.datasets.ISO17Dataset.ISO17Dataset method) (kgcnn.data.datasets.LipopDataset.LipopDataset method) (kgcnn.data.datasets.MatBenchDataset2020.MatBenchDataset2020 method) (kgcnn.data.datasets.MatProjectDielectricDataset.MatProjectDielectricDataset method) (kgcnn.data.datasets.MatProjectEFormDataset.MatProjectEFormDataset method) (kgcnn.data.datasets.MatProjectGapDataset.MatProjectGapDataset method) (kgcnn.data.datasets.MatProjectIsMetalDataset.MatProjectIsMetalDataset method) (kgcnn.data.datasets.MatProjectJdft2dDataset.MatProjectJdft2dDataset method) (kgcnn.data.datasets.MatProjectLogGVRHDataset.MatProjectLogGVRHDataset method) (kgcnn.data.datasets.MatProjectLogKVRHDataset.MatProjectLogKVRHDataset method) (kgcnn.data.datasets.MatProjectPerovskitesDataset.MatProjectPerovskitesDataset method) (kgcnn.data.datasets.MatProjectPhononsDataset.MatProjectPhononsDataset method) (kgcnn.data.datasets.MD17Dataset.MD17Dataset method) (kgcnn.data.datasets.MD17RevisedDataset.MD17RevisedDataset method) (kgcnn.data.datasets.MoleculeNetDataset2018.MoleculeNetDataset2018 method) (kgcnn.data.datasets.MUTAGDataset.MUTAGDataset method) (kgcnn.data.datasets.MutagenicityDataset.MutagenicityDataset method) (kgcnn.data.datasets.PROTEINSDataset.PROTEINSDataset method) (kgcnn.data.datasets.QM7bDataset.QM7bDataset method) (kgcnn.data.datasets.QM7Dataset.QM7Dataset method) (kgcnn.data.datasets.QM8Dataset.QM8Dataset method) (kgcnn.data.datasets.QM9Dataset.QM9Dataset method) (kgcnn.data.datasets.QM9MolNetDataset.QM9MolNetDataset method) (kgcnn.data.datasets.SIDERDataset.SIDERDataset method) (kgcnn.data.datasets.Tox21MolNetDataset.Tox21MolNetDataset method) (kgcnn.data.download.DownloadDataset method) (kgcnn.data.force.ForceDataset method) (kgcnn.data.moleculenet.MoleculeNetDataset method) (kgcnn.data.qm.QMDataset method) (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.tudataset.GraphTUDataset method) (kgcnn.graph.base.GraphDict method) (kgcnn.graph.base.GraphPostProcessorBase method) (kgcnn.graph.base.GraphPreProcessorBase method) (kgcnn.io.file.RaggedTensorHDFile method) (kgcnn.io.file.RaggedTensorNumpyFile method) (kgcnn.layers.activ.LeakyRelu method) (kgcnn.layers.activ.LeakySoftplus method) (kgcnn.layers.activ.Swish method) (kgcnn.layers.aggr.Aggregate method) (kgcnn.layers.aggr.AggregateLocalEdges method) (kgcnn.layers.aggr.AggregateLocalEdgesAttention method) (kgcnn.layers.aggr.AggregateLocalEdgesLSTM method) (kgcnn.layers.aggr.AggregateWeightedLocalEdges method) (kgcnn.layers.aggr.RelationalAggregateLocalEdges method) (kgcnn.layers.attention.AttentionHeadGAT method) (kgcnn.layers.attention.AttentionHeadGATV2 method) (kgcnn.layers.attention.AttentiveHeadFP method) (kgcnn.layers.casting.CastBatchedAttributesToDisjoint method) (kgcnn.layers.casting.CastBatchedGraphStateToDisjoint method) (kgcnn.layers.casting.CastBatchedIndicesToDisjoint method) (kgcnn.layers.casting.CastDisjointToBatchedAttributes method) (kgcnn.layers.casting.CastDisjointToBatchedGraphState method) (kgcnn.layers.casting.CastRaggedAttributesToDisjoint method) (kgcnn.layers.casting.CastRaggedIndicesToDisjoint method) (kgcnn.layers.conv.GCN method) (kgcnn.layers.conv.GIN method) (kgcnn.layers.conv.GINE method) (kgcnn.layers.conv.SchNetCFconv method) (kgcnn.layers.conv.SchNetInteraction method) (kgcnn.layers.gather.GatherEdgesPairs method) (kgcnn.layers.gather.GatherNodes method) (kgcnn.layers.gather.GatherNodesIngoing method) (kgcnn.layers.gather.GatherNodesOutgoing method) (kgcnn.layers.gather.GatherState method) (kgcnn.layers.geom.BesselBasisLayer method) (kgcnn.layers.geom.CosCutOff method) (kgcnn.layers.geom.CosCutOffEnvelope method) (kgcnn.layers.geom.DisplacementVectorsASU method) (kgcnn.layers.geom.DisplacementVectorsUnitCell method) (kgcnn.layers.geom.EdgeAngle method) (kgcnn.layers.geom.EdgeDirectionNormalized method) (kgcnn.layers.geom.EuclideanNorm method) (kgcnn.layers.geom.FracToRealCoordinates method) (kgcnn.layers.geom.GaussBasisLayer method) (kgcnn.layers.geom.NodeDistanceEuclidean method) (kgcnn.layers.geom.NodePosition method) (kgcnn.layers.geom.PositionEncodingBasisLayer method) (kgcnn.layers.geom.RealToFracCoordinates method) (kgcnn.layers.geom.ScalarProduct method) (kgcnn.layers.geom.ShiftPeriodicLattice method) (kgcnn.layers.geom.SphericalBasisLayer method) (kgcnn.layers.geom.VectorAngle method) (kgcnn.layers.message.MatMulMessages method) (kgcnn.layers.message.MessagePassingBase method) (kgcnn.layers.mlp.MLP method) (kgcnn.layers.mlp.RelationalMLP method) (kgcnn.layers.modules.ZerosLike method) (kgcnn.layers.norm.GraphInstanceNormalization method) (kgcnn.layers.norm.GraphNormalization method) (kgcnn.layers.polynom.AssociatedLegendrePolynomialPlm method) (kgcnn.layers.polynom.LegendrePolynomialPn method) (kgcnn.layers.polynom.SphericalBesselJnExplicit method) (kgcnn.layers.polynom.SphericalHarmonicsYl method) (kgcnn.layers.pooling.PoolingEmbeddingAttention method) (kgcnn.layers.pooling.PoolingNodes method) (kgcnn.layers.pooling.PoolingNodesAttentive method) (kgcnn.layers.pooling.PoolingWeightedNodes method) (kgcnn.layers.relational.RelationalDense method) (kgcnn.layers.scale.ExtensiveMolecularLabelScaler method) (kgcnn.layers.scale.QMGraphLabelScaler method) (kgcnn.layers.scale.StandardLabelScaler method) (kgcnn.layers.set2set.PoolingSet2SetEncoder method) (kgcnn.layers.update.GRUUpdate method) (kgcnn.layers.update.ResidualLayer method) (kgcnn.literature.GNNExplain.GNNExplainer method) (kgcnn.literature.GNNExplain.GNNExplainerOptimizer method) (kgcnn.literature.MEGAN.MEGAN method) (kgcnn.models.force.EnergyForceModel method) (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.convert.MolConverter method) (kgcnn.molecule.dynamics.ase_calc.AtomsToGraphConverter method) (kgcnn.molecule.dynamics.base.MolDynamicsModelPredictor method) (kgcnn.molecule.encoder.OneHotEncoder method) (kgcnn.molecule.external.ballloon.BalloonInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) (kgcnn.optimizers.optimizers.Adan method) (kgcnn.training.callbacks.LearningRateLoggingCallback method) (kgcnn.training.hyper.HyperParameter method) (kgcnn.training.schedule.KerasPolynomialDecaySchedule method) (kgcnn.training.schedule.LinearWarmupExponentialDecay method) (kgcnn.training.scheduler.CosineAnnealingLRScheduler method) (kgcnn.training.scheduler.LinearLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmupExponentialLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmupExponentialLRScheduler method) (kgcnn.training.scheduler.LinearWarmupLinearLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmUpScheduler method) (kgcnn.training.scheduler.PolynomialDecayScheduler method)

__len__() (kgcnn.io.file.RaggedTensorHDFile method) (kgcnn.io.file.RaggedTensorNumpyFile method) _assign_properties() (kgcnn.graph.base.GraphProcessorBase static method) _check_encoder() (kgcnn.molecule.base.MolGraphInterface static method) _check_for_inner_shape() (in module kgcnn.io.file) _check_properties_list() (kgcnn.molecule.base.MolGraphInterface static method) _compute_cutoff_envelope() (kgcnn.layers.geom.CosCutOffEnvelope static method) _compute_euclidean_norm() (kgcnn.layers.geom.EuclideanNorm static method) _compute_fans() (in module kgcnn.initializers.initializers) _compute_fourier_encoding() (kgcnn.layers.geom.PositionEncodingBasisLayer static method) _compute_gauss_basis() (kgcnn.layers.geom.GaussBasisLayer static method) _estimate_nn_radius_from_density() (in module kgcnn.crystal.graph_builder) _ExtensiveMolecularScalerBase (class in kgcnn.data.transform.scaler.molecule) _fit() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) _fit_transform() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) _get_attr_from_graph() (in module kgcnn.crystal.graph_builder) _get_cube() (in module kgcnn.crystal.graph_builder) _get_geometric_properties_of_unit_cell() (in module kgcnn.crystal.graph_builder) _get_max_diameter() (in module kgcnn.crystal.graph_builder) _get_mesh() (in module kgcnn.crystal.graph_builder) _get_norm() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) _get_scale_per_batch() (kgcnn.layers.set2set.PoolingSet2SetEncoder static method) _get_scale_per_sample() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) _get_super_cell_grid_frac_coords() (in module kgcnn.crystal.graph_builder) _inverse_transform() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) _map_callbacks() (kgcnn.data.crystal.CrystalDataset method) _multi_kernel_initializer() (kgcnn.layers.relational.RelationalDense method) _obtain_properties() (kgcnn.graph.base.GraphProcessorBase static method) _plot_predict() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) _predict() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) _scalar_product() (kgcnn.layers.geom.ScalarProduct static method) _standardize() (kgcnn.initializers.initializers.HeOrthogonal static method) _StandardScalerSklearnMixin (class in kgcnn.data.transform.scaler.standard) _test_timing() (kgcnn.molecule.dynamics.base.MolDynamicsModelPredictor method) _to_unit_cell() (in module kgcnn.crystal.graph_builder) _transform() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) _translate_properties() (kgcnn.molecule.dynamics.base.MolDynamicsModelPredictor static method) _verify_data_directory() (kgcnn.data.base.MemoryGraphDataset method)

A

Adan (class in kgcnn.optimizers.optimizers) add_edge_information() (in module kgcnn.crystal.graph_builder) add_edges_reverse_indices() (in module kgcnn.graph.methods) add_hs() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) add_knn_bonds() (in module kgcnn.crystal.graph_builder) add_radius_bonds() (in module kgcnn.crystal.graph_builder) add_self_loops_to_edge_indices() (in module kgcnn.graph.methods) add_voronoi_bonds() (in module kgcnn.crystal.graph_builder) AddEdgeSelfLoops (class in kgcnn.graph.preprocessor) Aggregate (class in kgcnn.layers.aggr) aggregate_message() (kgcnn.layers.message.MessagePassingBase method) AggregateLocalEdges (class in kgcnn.layers.aggr) AggregateLocalEdgesAttention (class in kgcnn.layers.aggr) AggregateLocalEdgesLSTM (class in kgcnn.layers.aggr) AggregateWeightedLocalEdges (class in kgcnn.layers.aggr) any_symbolic_tensors() (in module kgcnn.backend) append() (kgcnn.data.base.MemoryGraphList method) (kgcnn.io.file.RaggedTensorHDFile method)

append_multiple() (kgcnn.io.file.RaggedTensorHDFile method) apply_preprocessor() (kgcnn.graph.base.GraphDict method) assert_has_valid_key() (kgcnn.graph.base.GraphDict method) assert_valid_model_input() (kgcnn.data.base.MemoryGraphDataset method) assertAllClose() (kgcnn.utils.tests.TestCase static method) assertAllEqual() (kgcnn.utils.tests.TestCase method) assertLen() (kgcnn.utils.tests.TestCase method) assertNotAllClose() (kgcnn.utils.tests.TestCase method) assign_property() (kgcnn.data.base.MemoryGraphList method) (kgcnn.graph.base.GraphDict method) AssociatedLegendrePolynomialPlm (class in kgcnn.layers.polynom) AsymmetricUnitCell (class in kgcnn.crystal.preprocessor) atom_fun_dict (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel attribute) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit attribute) AtomicChargesRepresentation (class in kgcnn.graph.preprocessor) AtomsToGraphConverter (class in kgcnn.molecule.dynamics.ase_calc) AttentionHeadGAT (class in kgcnn.layers.attention) AttentionHeadGATV2 (class in kgcnn.layers.attention) AttentiveHeadFP (class in kgcnn.layers.attention) AUCNoNaN (class in kgcnn.metrics.metrics)

B

BalancedBinaryAccuracyNoNaN (class in kgcnn.metrics.metrics) BalloonInterface (class in kgcnn.molecule.external.ballloon) batch_dot() (kgcnn.layers.relational.RelationalDense static method) BesselBasisLayer (class in kgcnn.layers.geom) BinaryAccuracyNoNaN (class in kgcnn.metrics.metrics) BinaryCrossentropyNoNaN (class in kgcnn.losses.losses) bond_fun_dict (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel attribute) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit attribute) broadcast_shapes() (in module kgcnn.ops.axis) build() (kgcnn.layers.aggr.Aggregate method) (kgcnn.layers.aggr.AggregateLocalEdges method) (kgcnn.layers.aggr.AggregateLocalEdgesAttention method) (kgcnn.layers.aggr.AggregateLocalEdgesLSTM method) (kgcnn.layers.aggr.AggregateWeightedLocalEdges method) (kgcnn.layers.aggr.RelationalAggregateLocalEdges method) (kgcnn.layers.attention.AttentionHeadGAT method) (kgcnn.layers.attention.AttentionHeadGATV2 method) (kgcnn.layers.attention.AttentiveHeadFP method) (kgcnn.layers.casting.CastBatchedAttributesToDisjoint method) (kgcnn.layers.casting.CastBatchedGraphStateToDisjoint method) (kgcnn.layers.casting.CastBatchedIndicesToDisjoint method) (kgcnn.layers.casting.CastDisjointToBatchedAttributes method) (kgcnn.layers.casting.CastDisjointToBatchedGraphState method) (kgcnn.layers.casting.CastDisjointToRaggedAttributes method) (kgcnn.layers.casting.CastRaggedAttributesToDisjoint method) (kgcnn.layers.casting.CastRaggedIndicesToDisjoint method) (kgcnn.layers.conv.GCN method) (kgcnn.layers.conv.GIN method) (kgcnn.layers.conv.GINE method) (kgcnn.layers.conv.SchNetCFconv method) (kgcnn.layers.conv.SchNetInteraction method) (kgcnn.layers.gather.GatherEdgesPairs method) (kgcnn.layers.gather.GatherNodes method) (kgcnn.layers.gather.GatherNodesIngoing method) (kgcnn.layers.gather.GatherNodesOutgoing method) (kgcnn.layers.gather.GatherState method) (kgcnn.layers.geom.DisplacementVectorsASU method) (kgcnn.layers.geom.DisplacementVectorsUnitCell method) (kgcnn.layers.geom.EdgeAngle method) (kgcnn.layers.geom.EdgeDirectionNormalized method) (kgcnn.layers.geom.EuclideanNorm method) (kgcnn.layers.geom.FracToRealCoordinates method) (kgcnn.layers.geom.NodeDistanceEuclidean method) (kgcnn.layers.geom.NodePosition method) (kgcnn.layers.geom.RealToFracCoordinates method) (kgcnn.layers.geom.ScalarProduct method) (kgcnn.layers.geom.ShiftPeriodicLattice method) (kgcnn.layers.geom.VectorAngle method) (kgcnn.layers.message.MatMulMessages method) (kgcnn.layers.message.MessagePassingBase method) (kgcnn.layers.mlp.MLP method) (kgcnn.layers.mlp.RelationalMLP method) (kgcnn.layers.modules.Embedding method) (kgcnn.layers.modules.ExpandDims method) (kgcnn.layers.modules.SqueezeDims method) (kgcnn.layers.modules.ZerosLike method) (kgcnn.layers.norm.GraphBatchNormalization method) (kgcnn.layers.norm.GraphLayerNormalization method) (kgcnn.layers.norm.GraphNormalization method) (kgcnn.layers.polynom.AssociatedLegendrePolynomialPlm method) (kgcnn.layers.polynom.LegendrePolynomialPn method) (kgcnn.layers.polynom.SphericalBesselJnExplicit method) (kgcnn.layers.polynom.SphericalHarmonicsYl method) (kgcnn.layers.pooling.PoolingEmbeddingAttention method) (kgcnn.layers.pooling.PoolingNodes method) (kgcnn.layers.pooling.PoolingNodesAttentive method) (kgcnn.layers.pooling.PoolingWeightedNodes method) (kgcnn.layers.relational.RelationalDense method) (kgcnn.layers.scale.ExtensiveMolecularLabelScaler method) (kgcnn.layers.scale.QMGraphLabelScaler method) (kgcnn.layers.scale.StandardLabelScaler method) (kgcnn.layers.set2set.PoolingSet2SetEncoder method) (kgcnn.layers.update.GRUUpdate method) (kgcnn.layers.update.ResidualLayer method) (kgcnn.literature.MEGAN.ExplanationSparsityRegularization method) (kgcnn.literature.MEGAN.MEGAN method) (kgcnn.models.force.EnergyForceModel method) (kgcnn.optimizers.optimizers.Adan method)

C

calculate() (kgcnn.molecule.dynamics.ase_calc.KgcnnSingleCalculator method) call() (kgcnn.crystal.base.CrystalPreprocessor method) (kgcnn.crystal.preprocessor.AsymmetricUnitCell method) (kgcnn.crystal.preprocessor.KNNAsymmetricUnitCell method) (kgcnn.crystal.preprocessor.KNNNonPeriodicUnitCell method) (kgcnn.crystal.preprocessor.KNNSuperCell method) (kgcnn.crystal.preprocessor.KNNUnitCell method) (kgcnn.crystal.preprocessor.RadiusAsymmetricUnitCell method) (kgcnn.crystal.preprocessor.RadiusNonPeriodicUnitCell method) (kgcnn.crystal.preprocessor.RadiusSuperCell method) (kgcnn.crystal.preprocessor.RadiusUnitCell method) (kgcnn.crystal.preprocessor.UnitCell method) (kgcnn.crystal.preprocessor.VoronoiAsymmetricUnitCell method) (kgcnn.crystal.preprocessor.VoronoiNonPeriodicUnitCell method) (kgcnn.crystal.preprocessor.VoronoiSuperCell method) (kgcnn.crystal.preprocessor.VoronoiUnitCell method) (kgcnn.graph.base.GraphPostProcessorBase method) (kgcnn.graph.base.GraphPreProcessorBase method) (kgcnn.graph.postprocessor.ExtensiveEnergyForceScalerPostprocessor method) (kgcnn.graph.preprocessor.AddEdgeSelfLoops method) (kgcnn.graph.preprocessor.AtomicChargesRepresentation method) (kgcnn.graph.preprocessor.CountNodesAndEdges method) (kgcnn.graph.preprocessor.ExpandDistanceGaussianBasis method) (kgcnn.graph.preprocessor.MakeDenseAdjacencyMatrix method) (kgcnn.graph.preprocessor.MakeMask method) (kgcnn.graph.preprocessor.MakeUndirectedEdges method) (kgcnn.graph.preprocessor.NormalizeEdgeWeightsSymmetric method) (kgcnn.graph.preprocessor.PadProperty method) (kgcnn.graph.preprocessor.PrincipalMomentsOfInertia method) (kgcnn.graph.preprocessor.SetAngle method) (kgcnn.graph.preprocessor.SetEdgeIndicesReverse method) (kgcnn.graph.preprocessor.SetEdgeWeightsUniform method) (kgcnn.graph.preprocessor.SetRange method) (kgcnn.graph.preprocessor.SetRangeFromEdges method) (kgcnn.graph.preprocessor.SetRangePeriodic method) (kgcnn.graph.preprocessor.ShiftToUnitCell method) (kgcnn.graph.preprocessor.SortEdgeIndices method) (kgcnn.layers.activ.LeakyRelu method) (kgcnn.layers.activ.LeakySoftplus method) (kgcnn.layers.activ.Swish method) (kgcnn.layers.aggr.Aggregate method) (kgcnn.layers.aggr.AggregateLocalEdges method) (kgcnn.layers.aggr.AggregateLocalEdgesAttention method) (kgcnn.layers.aggr.AggregateLocalEdgesLSTM method) (kgcnn.layers.aggr.AggregateWeightedLocalEdges method) (kgcnn.layers.aggr.RelationalAggregateLocalEdges method) (kgcnn.layers.attention.AttentionHeadGAT method) (kgcnn.layers.attention.AttentionHeadGATV2 method) (kgcnn.layers.attention.AttentiveHeadFP method) (kgcnn.layers.casting.CastBatchedAttributesToDisjoint method) (kgcnn.layers.casting.CastBatchedGraphStateToDisjoint method) (kgcnn.layers.casting.CastBatchedIndicesToDisjoint method) (kgcnn.layers.casting.CastDisjointToBatchedAttributes method) (kgcnn.layers.casting.CastDisjointToBatchedGraphState method) (kgcnn.layers.casting.CastDisjointToRaggedAttributes method) (kgcnn.layers.casting.CastRaggedAttributesToDisjoint method) (kgcnn.layers.casting.CastRaggedIndicesToDisjoint method) (kgcnn.layers.conv.GCN method) (kgcnn.layers.conv.GIN method) (kgcnn.layers.conv.GINE method) (kgcnn.layers.conv.SchNetCFconv method) (kgcnn.layers.conv.SchNetInteraction method) (kgcnn.layers.gather.GatherEdgesPairs method) (kgcnn.layers.gather.GatherNodes method) (kgcnn.layers.gather.GatherNodesIngoing method) (kgcnn.layers.gather.GatherNodesOutgoing method) (kgcnn.layers.gather.GatherState method) (kgcnn.layers.geom.BesselBasisLayer method) (kgcnn.layers.geom.CosCutOff method) (kgcnn.layers.geom.CosCutOffEnvelope method) (kgcnn.layers.geom.DisplacementVectorsASU method) (kgcnn.layers.geom.DisplacementVectorsUnitCell method) (kgcnn.layers.geom.EdgeAngle method) (kgcnn.layers.geom.EdgeDirectionNormalized method) (kgcnn.layers.geom.EuclideanNorm method) (kgcnn.layers.geom.FracToRealCoordinates method) (kgcnn.layers.geom.GaussBasisLayer method) (kgcnn.layers.geom.NodeDistanceEuclidean method) (kgcnn.layers.geom.NodePosition method) (kgcnn.layers.geom.PositionEncodingBasisLayer method) (kgcnn.layers.geom.RealToFracCoordinates method) (kgcnn.layers.geom.ScalarProduct method) (kgcnn.layers.geom.ShiftPeriodicLattice method) (kgcnn.layers.geom.SphericalBasisLayer method) (kgcnn.layers.geom.VectorAngle method) (kgcnn.layers.message.MatMulMessages method) (kgcnn.layers.message.MessagePassingBase method) (kgcnn.layers.mlp.MLP method) (kgcnn.layers.mlp.RelationalMLP method) (kgcnn.layers.modules.Embedding method) (kgcnn.layers.modules.ExpandDims method) (kgcnn.layers.modules.SqueezeDims method) (kgcnn.layers.modules.ZerosLike method) (kgcnn.layers.norm.GraphBatchNormalization method) (kgcnn.layers.norm.GraphLayerNormalization method) (kgcnn.layers.norm.GraphNormalization method) (kgcnn.layers.polynom.AssociatedLegendrePolynomialPlm method) (kgcnn.layers.polynom.LegendrePolynomialPn method) (kgcnn.layers.polynom.SphericalBesselJnExplicit method) (kgcnn.layers.polynom.SphericalHarmonicsYl method) (kgcnn.layers.pooling.PoolingEmbeddingAttention method) (kgcnn.layers.pooling.PoolingNodes method) (kgcnn.layers.pooling.PoolingNodesAttentive method) (kgcnn.layers.pooling.PoolingWeightedNodes method) (kgcnn.layers.relational.RelationalDense method) (kgcnn.layers.scale.ExtensiveMolecularLabelScaler method) (kgcnn.layers.scale.QMGraphLabelScaler method) (kgcnn.layers.scale.StandardLabelScaler method) (kgcnn.layers.set2set.PoolingSet2SetEncoder method) (kgcnn.layers.update.GRUUpdate method) (kgcnn.layers.update.ResidualLayer method) (kgcnn.literature.GNNExplain.GNNExplainerOptimizer method) (kgcnn.literature.MEGAN.ExplanationSparsityRegularization method) (kgcnn.literature.MEGAN.MEGAN method) (kgcnn.losses.losses.BinaryCrossentropyNoNaN method) (kgcnn.losses.losses.ForceMeanAbsoluteError method) (kgcnn.losses.losses.MeanAbsoluteError method) (kgcnn.models.force.EnergyForceModel method) (kgcnn.molecule.preprocessor.SetMolAttributes method) (kgcnn.molecule.preprocessor.SetMolBondIndices method)

CastBatchedAttributesToDisjoint (class in kgcnn.layers.casting) CastBatchedGraphStateToDisjoint (class in kgcnn.layers.casting) CastBatchedIndicesToDisjoint (class in kgcnn.layers.casting) CastDisjointToBatchedAttributes (class in kgcnn.layers.casting) CastDisjointToBatchedGraphState (class in kgcnn.layers.casting) CastDisjointToRaggedAttributes (class in kgcnn.layers.casting) CastRaggedAttributesToDisjoint (class in kgcnn.layers.casting) CastRaggedIndicesToDisjoint (class in kgcnn.layers.casting) change_attributes_in_all_layers() (in module kgcnn.models.utils) check_device() (in module kgcnn.utils.devices) clean() (kgcnn.data.base.MemoryGraphList method) (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) ClinToxDataset (class in kgcnn.data.datasets.ClinToxDataset) collect_files_in_file_directory() (kgcnn.data.base.MemoryGraphDataset method) compare_static_shapes() (in module kgcnn.utils.tests) compile() (kgcnn.training.hyper.HyperParameter method) compute_output_shape() (kgcnn.layers.aggr.Aggregate method) (kgcnn.layers.aggr.AggregateLocalEdges method) (kgcnn.layers.aggr.AggregateLocalEdgesAttention method) (kgcnn.layers.aggr.AggregateWeightedLocalEdges method) (kgcnn.layers.casting.CastBatchedAttributesToDisjoint method) (kgcnn.layers.casting.CastBatchedGraphStateToDisjoint method) (kgcnn.layers.casting.CastBatchedIndicesToDisjoint method) (kgcnn.layers.casting.CastDisjointToBatchedGraphState method) (kgcnn.layers.casting.CastRaggedAttributesToDisjoint method) (kgcnn.layers.casting.CastRaggedIndicesToDisjoint method) (kgcnn.layers.gather.GatherNodes method) (kgcnn.layers.gather.GatherNodesIngoing method) (kgcnn.layers.gather.GatherNodesOutgoing method) (kgcnn.layers.gather.GatherState method) (kgcnn.layers.geom.EuclideanNorm method) (kgcnn.layers.geom.NodePosition method) (kgcnn.layers.norm.GraphBatchNormalization method) (kgcnn.layers.norm.GraphLayerNormalization method) (kgcnn.layers.pooling.PoolingNodes method) (kgcnn.layers.relational.RelationalDense method) (kgcnn.layers.scale.ExtensiveMolecularLabelScaler method) (kgcnn.layers.scale.QMGraphLabelScaler method) (kgcnn.layers.scale.StandardLabelScaler method) (kgcnn.layers.set2set.PoolingSet2SetEncoder method) compute_output_spec() (kgcnn.layers.casting.CastBatchedAttributesToDisjoint method) (kgcnn.layers.casting.CastBatchedGraphStateToDisjoint method) (kgcnn.layers.casting.CastBatchedIndicesToDisjoint method) (kgcnn.layers.casting.CastRaggedAttributesToDisjoint method) (kgcnn.layers.casting.CastRaggedIndicesToDisjoint method) compute_partial_charges() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) compute_reverse_edges_index_map() (in module kgcnn.graph.methods) convert_scaled_adjacency_to_list() (in module kgcnn.graph.methods) coordinates_from_distance_matrix() (in module kgcnn.graph.methods) coordinates_to_distancematrix() (in module kgcnn.graph.methods) copy() (kgcnn.data.base.MemoryGraphList method) (kgcnn.graph.base.GraphDict method) CoraDataset (class in kgcnn.data.datasets.CoraDataset) CoraLuDataset (class in kgcnn.data.datasets.CoraLuDataset) CosCutOff (class in kgcnn.layers.geom) CosCutOffEnvelope (class in kgcnn.layers.geom) CosineAnnealingLRScheduler (class in kgcnn.training.scheduler) coulomb_matrix_to_inverse_distance_proton() (in module kgcnn.graph.methods) CountNodesAndEdges (class in kgcnn.graph.preprocessor) cross() (in module kgcnn.ops.core) CrystalDataset (class in kgcnn.data.crystal) CrystalPreprocessor (class in kgcnn.crystal.base)

D

dataset_class() (kgcnn.training.hyper.HyperParameter property) dataset_module() (kgcnn.training.hyper.HyperParameter property) dataset_name() (kgcnn.training.hyper.HyperParameter property) datasets_download_info (kgcnn.data.datasets.MatBenchDataset2020.MatBenchDataset2020 attribute) (kgcnn.data.datasets.MD17Dataset.MD17Dataset attribute) (kgcnn.data.datasets.MoleculeNetDataset2018.MoleculeNetDataset2018 attribute) datasets_prepare_data_info (kgcnn.data.datasets.MatBenchDataset2020.MatBenchDataset2020 attribute) (kgcnn.data.datasets.MoleculeNetDataset2018.MoleculeNetDataset2018 attribute) datasets_read_in_memory_info (kgcnn.data.datasets.MatBenchDataset2020.MatBenchDataset2020 attribute) (kgcnn.data.datasets.MoleculeNetDataset2018.MoleculeNetDataset2018 attribute) decompose_ragged_tensor() (in module kgcnn.ops.core) define_adjacency_from_distance() (in module kgcnn.graph.methods) deserialize() (in module kgcnn.data.serial) (in module kgcnn.data.transform.scaler.serial) (in module kgcnn.models.serial) (in module kgcnn.utils.serial) deserialize_encoder() (in module kgcnn.molecule.serial)

DisplacementVectorsASU (class in kgcnn.layers.geom) DisplacementVectorsUnitCell (class in kgcnn.layers.geom) distance_for_range_indices() (in module kgcnn.graph.methods) distance_for_range_indices_periodic() (in module kgcnn.graph.methods) distance_to_gauss_basis() (in module kgcnn.graph.methods) doing_regression() (kgcnn.literature.MEGAN.MEGAN property) download_database() (kgcnn.data.download.DownloadDataset static method) download_dataset_to_disk() (kgcnn.data.download.DownloadDataset method) download_info (kgcnn.data.datasets.CoraDataset.CoraDataset attribute) (kgcnn.data.datasets.CoraLuDataset.CoraLuDataset attribute) (kgcnn.data.datasets.ISO17Dataset.ISO17Dataset attribute) (kgcnn.data.datasets.MD17RevisedDataset.MD17RevisedDataset attribute) (kgcnn.data.datasets.QM7bDataset.QM7bDataset attribute) (kgcnn.data.datasets.QM7Dataset.QM7Dataset attribute) (kgcnn.data.datasets.QM8Dataset.QM8Dataset attribute) (kgcnn.data.datasets.QM9Dataset.QM9Dataset attribute) (kgcnn.data.datasets.QM9MolNetDataset.QM9MolNetDataset attribute) DownloadDataset (class in kgcnn.data.download)

E

edge_attributes (kgcnn.crystal.base.CrystalPreprocessor attribute) (kgcnn.crystal.preprocessor.AsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.KNNAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.KNNNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.KNNSuperCell attribute) (kgcnn.crystal.preprocessor.KNNUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusSuperCell attribute) (kgcnn.crystal.preprocessor.RadiusUnitCell attribute) (kgcnn.crystal.preprocessor.UnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiSuperCell attribute) (kgcnn.crystal.preprocessor.VoronoiUnitCell attribute) edge_attributes() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) edge_indices() (kgcnn.molecule.base.MolGraphInterface property) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel property) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit property) edge_number() (kgcnn.molecule.base.MolGraphInterface property) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel property) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit property)

EdgeAngle (class in kgcnn.layers.geom) EdgeDirectionNormalized (class in kgcnn.layers.geom) Embedding (class in kgcnn.layers.modules) empty() (kgcnn.data.base.MemoryGraphList method) EnergyForceExtensiveLabelScaler (class in kgcnn.data.transform.scaler.force) EnergyForceModel (class in kgcnn.models.force) envelope() (kgcnn.layers.geom.BesselBasisLayer method) (kgcnn.layers.geom.SphericalBasisLayer method) error() (kgcnn.data.base.MemoryGraphDataset method) ESOLDataset (class in kgcnn.data.datasets.ESOLDataset) EuclideanNorm (class in kgcnn.layers.geom) exists() (kgcnn.io.file.RaggedTensorHDFile method) (kgcnn.io.file.RaggedTensorNumpyFile method) expand_bessel_basis() (kgcnn.layers.geom.BesselBasisLayer method) ExpandDims (class in kgcnn.layers.modules) ExpandDistanceGaussianBasis (class in kgcnn.graph.preprocessor) explain() (kgcnn.literature.GNNExplain.GNNExplainer method) explain_importances() (kgcnn.literature.MEGAN.MEGAN method) ExplanationSparsityRegularization (class in kgcnn.literature.MEGAN) ExtensiveEnergyForceScalerPostprocessor (class in kgcnn.graph.postprocessor) ExtensiveMolecularLabelScaler (class in kgcnn.data.transform.scaler.molecule) (class in kgcnn.layers.scale) ExtensiveMolecularScaler (class in kgcnn.data.transform.scaler.molecule) extract_gz_file() (kgcnn.data.download.DownloadDataset static method)

F

f_et() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) file_directory_path() (kgcnn.data.base.MemoryGraphDataset property) file_path() (kgcnn.data.base.MemoryGraphDataset property) file_path_force_xyz() (kgcnn.data.force.ForceDataset property) file_path_mol() (kgcnn.data.moleculenet.MoleculeNetDataset property) (kgcnn.data.qm.QMDataset property) file_path_smiles() (kgcnn.data.moleculenet.MoleculeNetDataset property) file_path_xyz() (kgcnn.data.qm.QMDataset property) find_graph_properties() (kgcnn.graph.base.GraphDict method) fit() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularScaler method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardScaler method) (kgcnn.training.hyper.HyperParameter method) fit_dataset() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) fit_transform() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularScaler method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardScaler method) fit_transform_dataset() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method)

fits_in_memory (kgcnn.data.base.MemoryGraphDataset attribute) fn_force_mae() (kgcnn.metrics.metrics.ScaledForceMeanAbsoluteError method) ForceDataset (class in kgcnn.data.force) ForceMeanAbsoluteError (class in kgcnn.losses.losses) FracToRealCoordinates (class in kgcnn.layers.geom) FreeSolvDataset (class in kgcnn.data.datasets.FreeSolvDataset) from_config() (kgcnn.molecule.encoder.OneHotEncoder class method) (kgcnn.molecule.external.ballloon.BalloonInterface class method) (kgcnn.training.callbacks.LearningRateLoggingCallback class method) (kgcnn.training.scheduler.CosineAnnealingLRScheduler class method) (kgcnn.training.scheduler.LinearLearningRateScheduler class method) (kgcnn.training.scheduler.LinearWarmupExponentialLearningRateScheduler class method) (kgcnn.training.scheduler.LinearWarmupExponentialLRScheduler class method) (kgcnn.training.scheduler.LinearWarmupLinearLearningRateScheduler class method) (kgcnn.training.scheduler.LinearWarmUpScheduler class method) (kgcnn.training.scheduler.PolynomialDecayScheduler class method) from_list() (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) from_mol_block() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) from_networkx() (kgcnn.graph.base.GraphDict method) from_smiles() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) from_xyz() (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method)

G

GatherEdgesPairs (class in kgcnn.layers.gather) GatherNodes (class in kgcnn.layers.gather) GatherNodesIngoing (class in kgcnn.layers.gather) GatherNodesOutgoing (class in kgcnn.layers.gather) GatherState (class in kgcnn.layers.gather) GaussBasisLayer (class in kgcnn.layers.geom) GCN (class in kgcnn.layers.conv) get() (in module kgcnn.layers.scale) (kgcnn.data.base.MemoryGraphList method) get_angle() (in module kgcnn.graph.methods) get_angle_between_edges() (in module kgcnn.graph.methods) get_angle_indices() (in module kgcnn.graph.methods) get_atomic_mass() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable method) get_atomic_radius() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable method) get_config() (kgcnn.crystal.base.CrystalPreprocessor method) (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularScaler method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) (kgcnn.data.transform.scaler.standard.StandardLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardScaler method) (kgcnn.graph.base.GraphPostProcessorBase method) (kgcnn.graph.base.GraphPreProcessorBase method) (kgcnn.initializers.initializers.GlorotOrthogonal method) (kgcnn.initializers.initializers.HeOrthogonal method) (kgcnn.layers.activ.LeakyRelu method) (kgcnn.layers.activ.LeakySoftplus method) (kgcnn.layers.activ.Swish method) (kgcnn.layers.aggr.Aggregate method) (kgcnn.layers.aggr.AggregateLocalEdges method) (kgcnn.layers.aggr.AggregateLocalEdgesAttention method) (kgcnn.layers.aggr.AggregateLocalEdgesLSTM method) (kgcnn.layers.aggr.AggregateWeightedLocalEdges method) (kgcnn.layers.aggr.RelationalAggregateLocalEdges method) (kgcnn.layers.attention.AttentionHeadGAT method) (kgcnn.layers.attention.AttentionHeadGATV2 method) (kgcnn.layers.attention.AttentiveHeadFP method) (kgcnn.layers.attention.MultiHeadGATV2Layer method) (kgcnn.layers.casting.CastDisjointToBatchedAttributes method) (kgcnn.layers.conv.GCN method) (kgcnn.layers.conv.GIN method) (kgcnn.layers.conv.GINE method) (kgcnn.layers.conv.SchNetCFconv method) (kgcnn.layers.conv.SchNetInteraction method) (kgcnn.layers.gather.GatherEdgesPairs method) (kgcnn.layers.gather.GatherNodes method) (kgcnn.layers.gather.GatherNodesIngoing method) (kgcnn.layers.gather.GatherNodesOutgoing method) (kgcnn.layers.geom.BesselBasisLayer method) (kgcnn.layers.geom.CosCutOff method) (kgcnn.layers.geom.CosCutOffEnvelope method) (kgcnn.layers.geom.EdgeAngle method) (kgcnn.layers.geom.EdgeDirectionNormalized method) (kgcnn.layers.geom.EuclideanNorm method) (kgcnn.layers.geom.GaussBasisLayer method) (kgcnn.layers.geom.NodeDistanceEuclidean method) (kgcnn.layers.geom.NodePosition method) (kgcnn.layers.geom.PositionEncodingBasisLayer method) (kgcnn.layers.geom.RealToFracCoordinates method) (kgcnn.layers.geom.ScalarProduct method) (kgcnn.layers.geom.SphericalBasisLayer method) (kgcnn.layers.geom.VectorAngle method) (kgcnn.layers.message.MatMulMessages method) (kgcnn.layers.message.MessagePassingBase method) (kgcnn.layers.mlp.MLP method) (kgcnn.layers.mlp.RelationalMLP method) (kgcnn.layers.modules.Embedding method) (kgcnn.layers.modules.ExpandDims method) (kgcnn.layers.modules.SqueezeDims method) (kgcnn.layers.norm.GraphBatchNormalization method) (kgcnn.layers.norm.GraphLayerNormalization method) (kgcnn.layers.norm.GraphNormalization method) (kgcnn.layers.polynom.AssociatedLegendrePolynomialPlm method) (kgcnn.layers.polynom.LegendrePolynomialPn method) (kgcnn.layers.polynom.SphericalBesselJnExplicit method) (kgcnn.layers.polynom.SphericalHarmonicsYl method) (kgcnn.layers.pooling.PoolingEmbeddingAttention method) (kgcnn.layers.pooling.PoolingNodes method) (kgcnn.layers.pooling.PoolingNodesAttentive method) (kgcnn.layers.pooling.PoolingWeightedNodes method) (kgcnn.layers.relational.RelationalDense method) (kgcnn.layers.scale.ExtensiveMolecularLabelScaler method) (kgcnn.layers.scale.QMGraphLabelScaler method) (kgcnn.layers.scale.StandardLabelScaler method) (kgcnn.layers.set2set.PoolingSet2SetEncoder method) (kgcnn.layers.update.GRUUpdate method) (kgcnn.layers.update.ResidualLayer method) (kgcnn.literature.MEGAN.MEGAN method) (kgcnn.losses.losses.ForceMeanAbsoluteError method) (kgcnn.losses.losses.MeanAbsoluteError method) (kgcnn.metrics.metrics.BalancedBinaryAccuracyNoNaN method) (kgcnn.metrics.metrics.BinaryAccuracyNoNaN method) (kgcnn.metrics.metrics.ScaledForceMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledRootMeanSquaredError method) (kgcnn.models.force.EnergyForceModel method) (kgcnn.molecule.dynamics.ase_calc.AtomsToGraphConverter method) (kgcnn.molecule.encoder.OneHotEncoder method) (kgcnn.molecule.external.ballloon.BalloonInterface method) (kgcnn.optimizers.optimizers.Adan method) (kgcnn.training.callbacks.LearningRateLoggingCallback method) (kgcnn.training.schedule.KerasPolynomialDecaySchedule method) (kgcnn.training.schedule.LinearWarmupExponentialDecay method) (kgcnn.training.scheduler.CosineAnnealingLRScheduler method) (kgcnn.training.scheduler.LinearLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmupExponentialLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmupExponentialLRScheduler method) (kgcnn.training.scheduler.LinearWarmupLinearLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmUpScheduler method) (kgcnn.training.scheduler.PolynomialDecayScheduler method)

get_connectivity_from_inverse_distance_matrix() (in module kgcnn.molecule.methods) get_electronegativity() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable method) get_explanation() (kgcnn.literature.GNNExplain.GNNExplainer method) (kgcnn.literature.GNNExplain.GNNInterface method) get_geom_from_xyz_file() (kgcnn.data.qm.QMDataset method) get_ionization_energy() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable method) get_mask() (kgcnn.literature.GNNExplain.GNNExplainerOptimizer method) get_mean_shift() (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) get_model_class() (in module kgcnn.models.utils) get_mol_blocks_from_sdf_file() (kgcnn.data.moleculenet.MoleculeNetDataset method) (kgcnn.data.qm.QMDataset method) get_number_of_edges() (kgcnn.literature.GNNExplain.GNNInterface method) get_number_of_node_features() (kgcnn.literature.GNNExplain.GNNInterface method) get_number_of_nodes() (kgcnn.literature.GNNExplain.GNNInterface method) get_oxidation_states() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable method) get_positive_axis() (in module kgcnn.ops.axis) get_postprocessor() (in module kgcnn.graph.serial) get_preprocessor() (in module kgcnn.graph.serial) get_principal_moments_of_inertia() (in module kgcnn.graph.methods) get_ridge_area() (in module kgcnn.crystal.graph_builder) get_scaling() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) get_structures_from_json_file() (kgcnn.data.crystal.CrystalDataset method) get_symbol() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable method) get_symmetrized_graph() (in module kgcnn.crystal.graph_builder) get_train_test_indices() (kgcnn.data.base.MemoryGraphDataset method) get_weights() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) GIN (class in kgcnn.layers.conv) GINE (class in kgcnn.layers.conv) GlorotOrthogonal (class in kgcnn.initializers.initializers) GNNExplainer (class in kgcnn.literature.GNNExplain) GNNExplainer.InspectionCallback (class in kgcnn.literature.GNNExplain) GNNExplainerOptimizer (class in kgcnn.literature.GNNExplain) GNNInterface (class in kgcnn.literature.GNNExplain) graph_attributes (kgcnn.crystal.base.CrystalPreprocessor attribute) (kgcnn.crystal.preprocessor.AsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.KNNAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.KNNNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.KNNSuperCell attribute) (kgcnn.crystal.preprocessor.KNNUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusSuperCell attribute) (kgcnn.crystal.preprocessor.RadiusUnitCell attribute) (kgcnn.crystal.preprocessor.UnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiSuperCell attribute) (kgcnn.crystal.preprocessor.VoronoiUnitCell attribute) graph_attributes() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) GraphBatchNormalization (class in kgcnn.layers.norm) GraphDict (class in kgcnn.graph.base) GraphInstanceNormalization (class in kgcnn.layers.norm) GraphLayerNormalization (class in kgcnn.layers.norm) GraphMLP (in module kgcnn.layers.mlp) GraphNormalization (class in kgcnn.layers.norm) GraphNumpyContainer (in module kgcnn.graph.base) GraphPostProcessorBase (class in kgcnn.graph.base) GraphPreProcessorBase (class in kgcnn.graph.base) GraphProcessorBase (class in kgcnn.graph.base) GraphTUDataset (class in kgcnn.data.tudataset) GraphTUDataset2020 (class in kgcnn.data.datasets.GraphTUDataset2020) GRUUpdate (class in kgcnn.layers.update)

H

has_special_characters() (kgcnn.graph.base.GraphProcessorBase static method) has_valid_key() (kgcnn.graph.base.GraphDict method) hash() (kgcnn.crystal.base.CrystalPreprocessor method)

HeOrthogonal (class in kgcnn.initializers.initializers) hyper_category() (kgcnn.training.hyper.HyperParameter property) HyperParameter (class in kgcnn.training.hyper)

I

implemented_properties (kgcnn.molecule.dynamics.ase_calc.KgcnnSingleCalculator attribute) info() (kgcnn.data.base.MemoryGraphDataset method) init_qstar_0() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) init_qstar_pool() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) init_qstar_ref() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) initial_learning_rate() (kgcnn.training.schedule.LinearWarmupExponentialDecay property) Input() (in module kgcnn.layers.modules) insert() (kgcnn.data.base.MemoryGraphList method) inverse_transform() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularScaler method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardScaler method)

inverse_transform_dataset() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) invert_distance() (in module kgcnn.graph.methods) ISO17Dataset (class in kgcnn.data.datasets.ISO17Dataset)

K

KerasPolynomialDecaySchedule (class in kgcnn.training.schedule) kgcnn module kgcnn.backend module kgcnn.crystal module kgcnn.crystal.base module kgcnn.crystal.graph_builder module kgcnn.crystal.periodic_table module kgcnn.crystal.periodic_table.periodic_table module kgcnn.crystal.preprocessor module kgcnn.data module kgcnn.data.base module kgcnn.data.crystal module kgcnn.data.datasets module kgcnn.data.datasets.ClinToxDataset module kgcnn.data.datasets.CoraDataset module kgcnn.data.datasets.CoraLuDataset module kgcnn.data.datasets.ESOLDataset module kgcnn.data.datasets.FreeSolvDataset module kgcnn.data.datasets.GraphTUDataset2020 module kgcnn.data.datasets.ISO17Dataset module kgcnn.data.datasets.LipopDataset module kgcnn.data.datasets.MatBenchDataset2020 module kgcnn.data.datasets.MatProjectDielectricDataset module kgcnn.data.datasets.MatProjectEFormDataset module kgcnn.data.datasets.MatProjectGapDataset module kgcnn.data.datasets.MatProjectIsMetalDataset module kgcnn.data.datasets.MatProjectJdft2dDataset module kgcnn.data.datasets.MatProjectLogGVRHDataset module kgcnn.data.datasets.MatProjectLogKVRHDataset module kgcnn.data.datasets.MatProjectPerovskitesDataset module kgcnn.data.datasets.MatProjectPhononsDataset module kgcnn.data.datasets.MD17Dataset module kgcnn.data.datasets.MD17RevisedDataset module kgcnn.data.datasets.MoleculeNetDataset2018 module kgcnn.data.datasets.MUTAGDataset module kgcnn.data.datasets.MutagenicityDataset module kgcnn.data.datasets.PROTEINSDataset module kgcnn.data.datasets.QM7bDataset module kgcnn.data.datasets.QM7Dataset module kgcnn.data.datasets.QM8Dataset module kgcnn.data.datasets.QM9Dataset module kgcnn.data.datasets.QM9MolNetDataset module kgcnn.data.datasets.SIDERDataset module kgcnn.data.datasets.Tox21MolNetDataset module kgcnn.data.download module kgcnn.data.force module kgcnn.data.moleculenet module kgcnn.data.qm module kgcnn.data.serial module kgcnn.data.transform module kgcnn.data.transform.base module kgcnn.data.transform.scaler module kgcnn.data.transform.scaler.force module kgcnn.data.transform.scaler.molecule module kgcnn.data.transform.scaler.serial module kgcnn.data.transform.scaler.standard module kgcnn.data.tudataset module kgcnn.data.utils module kgcnn.graph module kgcnn.graph.base module kgcnn.graph.methods module kgcnn.graph.postprocessor module kgcnn.graph.preprocessor module kgcnn.graph.serial module kgcnn.initializers module kgcnn.initializers.initializers module kgcnn.io module kgcnn.io.file module kgcnn.io.graphlist module kgcnn.io.loader module kgcnn.layers module kgcnn.layers.activ module kgcnn.layers.aggr module kgcnn.layers.attention module kgcnn.layers.casting module kgcnn.layers.conv module kgcnn.layers.gather module kgcnn.layers.geom module kgcnn.layers.message module kgcnn.layers.mlp module kgcnn.layers.modules module kgcnn.layers.norm module

kgcnn.layers.polynom module kgcnn.layers.pooling module kgcnn.layers.relational module kgcnn.layers.scale module kgcnn.layers.set2set module kgcnn.layers.update module kgcnn.literature module kgcnn.literature.AttentiveFP module kgcnn.literature.CGCNN module kgcnn.literature.CMPNN module kgcnn.literature.DGIN module kgcnn.literature.DimeNetPP module kgcnn.literature.DMPNN module kgcnn.literature.EGNN module kgcnn.literature.GAT module kgcnn.literature.GATv2 module kgcnn.literature.GCN module kgcnn.literature.GIN module kgcnn.literature.GNNExplain module kgcnn.literature.GNNFilm module kgcnn.literature.GraphSAGE module kgcnn.literature.HamNet module kgcnn.literature.HDNNP2nd module kgcnn.literature.INorp module kgcnn.literature.MAT module kgcnn.literature.MEGAN module kgcnn.literature.Megnet module kgcnn.literature.MoGAT module kgcnn.literature.MXMNet module kgcnn.literature.NMPN module kgcnn.literature.PAiNN module kgcnn.literature.RGCN module kgcnn.literature.rGIN module kgcnn.literature.Schnet module kgcnn.losses module kgcnn.losses.losses module kgcnn.metrics module kgcnn.metrics.metrics module kgcnn.metrics.utils module kgcnn.models module kgcnn.models.casting module kgcnn.models.force module kgcnn.models.multi module kgcnn.models.serial module kgcnn.models.utils module kgcnn.molecule module kgcnn.molecule.base module kgcnn.molecule.convert module kgcnn.molecule.dynamics module kgcnn.molecule.dynamics.ase_calc module kgcnn.molecule.dynamics.base module kgcnn.molecule.encoder module kgcnn.molecule.external module kgcnn.molecule.external.ballloon module kgcnn.molecule.graph_babel module kgcnn.molecule.graph_rdkit module kgcnn.molecule.io module kgcnn.molecule.methods module kgcnn.molecule.preprocessor module kgcnn.molecule.serial module kgcnn.ops module kgcnn.ops.activ module kgcnn.ops.axis module kgcnn.ops.core module kgcnn.ops.scatter module kgcnn.optimizers module kgcnn.optimizers.optimizers module kgcnn.training module kgcnn.training.callbacks module kgcnn.training.history module kgcnn.training.hyper module kgcnn.training.schedule module kgcnn.training.scheduler module kgcnn.utils module kgcnn.utils.devices module kgcnn.utils.plots module kgcnn.utils.serial module kgcnn.utils.tests module KgcnnSingleCalculator (class in kgcnn.molecule.dynamics.ase_calc) KNNAsymmetricUnitCell (class in kgcnn.crystal.preprocessor) KNNNonPeriodicUnitCell (class in kgcnn.crystal.preprocessor) KNNSuperCell (class in kgcnn.crystal.preprocessor) KNNUnitCell (class in kgcnn.crystal.preprocessor)

L

leaky_relu() (in module kgcnn.ops.activ) leaky_softplus() (in module kgcnn.ops.activ) LeakyRelu (class in kgcnn.layers.activ) LeakySoftplus (class in kgcnn.layers.activ) LearningRateLoggingCallback (class in kgcnn.training.callbacks) LegendrePolynomialPn (class in kgcnn.layers.polynom) length() (kgcnn.data.base.MemoryGraphList property) linear_warmup_schedule_epoch_lr() (kgcnn.training.scheduler.LinearWarmUpScheduler method) LinearLearningRateScheduler (class in kgcnn.training.scheduler) LinearWarmupExponentialDecay (class in kgcnn.training.schedule) LinearWarmupExponentialLearningRateScheduler (class in kgcnn.training.scheduler) LinearWarmupExponentialLRScheduler (class in kgcnn.training.scheduler) LinearWarmupLinearLearningRateScheduler (class in kgcnn.training.scheduler)

LinearWarmUpScheduler (class in kgcnn.training.scheduler) LipopDataset (class in kgcnn.data.datasets.LipopDataset) load() (kgcnn.data.base.MemoryGraphDataset method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) (kgcnn.molecule.dynamics.base.MolDynamicsModelPredictor method) load_history_list() (in module kgcnn.training.history) load_hyper_file() (in module kgcnn.data.utils) load_json_file() (in module kgcnn.data.utils) load_pickle_file() (in module kgcnn.data.utils) load_time_list() (in module kgcnn.training.history) load_yaml_file() (in module kgcnn.data.utils)

M

make_conformer() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) make_crystal_model() (in module kgcnn.literature.CGCNN) (in module kgcnn.literature.DimeNetPP) (in module kgcnn.literature.Megnet) (in module kgcnn.literature.NMPN) (in module kgcnn.literature.PAiNN) (in module kgcnn.literature.Schnet) make_model() (in module kgcnn.literature.AttentiveFP) (in module kgcnn.literature.CMPNN) (in module kgcnn.literature.DGIN) (in module kgcnn.literature.DimeNetPP) (in module kgcnn.literature.DMPNN) (in module kgcnn.literature.EGNN) (in module kgcnn.literature.GAT) (in module kgcnn.literature.GATv2) (in module kgcnn.literature.GCN) (in module kgcnn.literature.GIN) (in module kgcnn.literature.GNNFilm) (in module kgcnn.literature.GraphSAGE) (in module kgcnn.literature.HamNet) (in module kgcnn.literature.HDNNP2nd) (in module kgcnn.literature.INorp) (in module kgcnn.literature.MAT) (in module kgcnn.literature.MEGAN) (in module kgcnn.literature.Megnet) (in module kgcnn.literature.MoGAT) (in module kgcnn.literature.MXMNet) (in module kgcnn.literature.NMPN) (in module kgcnn.literature.PAiNN) (in module kgcnn.literature.RGCN) (in module kgcnn.literature.rGIN) (in module kgcnn.literature.Schnet) make_model_atom_wise() (in module kgcnn.literature.HDNNP2nd) make_model_behler() (in module kgcnn.literature.HDNNP2nd) make_model_edge() (in module kgcnn.literature.GIN) make_model_weighted() (in module kgcnn.literature.GCN) (in module kgcnn.literature.HDNNP2nd) MakeDenseAdjacencyMatrix (class in kgcnn.graph.preprocessor) MakeMask (class in kgcnn.graph.preprocessor) MakeUndirectedEdges (class in kgcnn.graph.preprocessor) map_list() (kgcnn.data.base.MemoryGraphList method) map_molecule_callbacks() (in module kgcnn.data.moleculenet) masked_predict() (kgcnn.literature.GNNExplain.GNNInterface method) MatBenchDataset2020 (class in kgcnn.data.datasets.MatBenchDataset2020) MatMulMessages (class in kgcnn.layers.message) MatProjectDielectricDataset (class in kgcnn.data.datasets.MatProjectDielectricDataset) MatProjectEFormDataset (class in kgcnn.data.datasets.MatProjectEFormDataset) MatProjectGapDataset (class in kgcnn.data.datasets.MatProjectGapDataset) MatProjectIsMetalDataset (class in kgcnn.data.datasets.MatProjectIsMetalDataset) MatProjectJdft2dDataset (class in kgcnn.data.datasets.MatProjectJdft2dDataset) MatProjectLogGVRHDataset (class in kgcnn.data.datasets.MatProjectLogGVRHDataset) MatProjectLogKVRHDataset (class in kgcnn.data.datasets.MatProjectLogKVRHDataset) MatProjectPerovskitesDataset (class in kgcnn.data.datasets.MatProjectPerovskitesDataset) MatProjectPhononsDataset (class in kgcnn.data.datasets.MatProjectPhononsDataset) max_atomic_number (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase attribute) (kgcnn.layers.scale.ExtensiveMolecularLabelScaler attribute) (kgcnn.layers.scale.QMGraphLabelScaler attribute) MD17Dataset (class in kgcnn.data.datasets.MD17Dataset) MD17RevisedDataset (class in kgcnn.data.datasets.MD17RevisedDataset) MeanAbsoluteError (class in kgcnn.losses.losses) MEGAN (class in kgcnn.literature.MEGAN) MemoryGeometricGraphDataset (in module kgcnn.data.base) MemoryGraphDataset (class in kgcnn.data.base) MemoryGraphList (class in kgcnn.data.base) merge_metrics() (in module kgcnn.metrics.utils) merge_models() (in module kgcnn.models.multi) message_function() (kgcnn.layers.message.MessagePassingBase method) MessagePassingBase (class in kgcnn.layers.message) MLP (class in kgcnn.layers.mlp) model_class() (kgcnn.training.hyper.HyperParameter property) model_module() (kgcnn.training.hyper.HyperParameter property) model_name() (kgcnn.training.hyper.HyperParameter property) module kgcnn kgcnn.backend kgcnn.crystal kgcnn.crystal.base kgcnn.crystal.graph_builder kgcnn.crystal.periodic_table kgcnn.crystal.periodic_table.periodic_table kgcnn.crystal.preprocessor kgcnn.data kgcnn.data.base kgcnn.data.crystal kgcnn.data.datasets kgcnn.data.datasets.ClinToxDataset kgcnn.data.datasets.CoraDataset kgcnn.data.datasets.CoraLuDataset kgcnn.data.datasets.ESOLDataset kgcnn.data.datasets.FreeSolvDataset kgcnn.data.datasets.GraphTUDataset2020 kgcnn.data.datasets.ISO17Dataset kgcnn.data.datasets.LipopDataset kgcnn.data.datasets.MatBenchDataset2020 kgcnn.data.datasets.MatProjectDielectricDataset kgcnn.data.datasets.MatProjectEFormDataset kgcnn.data.datasets.MatProjectGapDataset kgcnn.data.datasets.MatProjectIsMetalDataset kgcnn.data.datasets.MatProjectJdft2dDataset kgcnn.data.datasets.MatProjectLogGVRHDataset kgcnn.data.datasets.MatProjectLogKVRHDataset kgcnn.data.datasets.MatProjectPerovskitesDataset kgcnn.data.datasets.MatProjectPhononsDataset kgcnn.data.datasets.MD17Dataset kgcnn.data.datasets.MD17RevisedDataset kgcnn.data.datasets.MoleculeNetDataset2018 kgcnn.data.datasets.MUTAGDataset kgcnn.data.datasets.MutagenicityDataset kgcnn.data.datasets.PROTEINSDataset kgcnn.data.datasets.QM7bDataset kgcnn.data.datasets.QM7Dataset kgcnn.data.datasets.QM8Dataset kgcnn.data.datasets.QM9Dataset kgcnn.data.datasets.QM9MolNetDataset kgcnn.data.datasets.SIDERDataset kgcnn.data.datasets.Tox21MolNetDataset kgcnn.data.download kgcnn.data.force kgcnn.data.moleculenet kgcnn.data.qm kgcnn.data.serial kgcnn.data.transform kgcnn.data.transform.base kgcnn.data.transform.scaler kgcnn.data.transform.scaler.force kgcnn.data.transform.scaler.molecule kgcnn.data.transform.scaler.serial kgcnn.data.transform.scaler.standard kgcnn.data.tudataset kgcnn.data.utils kgcnn.graph kgcnn.graph.base kgcnn.graph.methods kgcnn.graph.postprocessor kgcnn.graph.preprocessor kgcnn.graph.serial kgcnn.initializers kgcnn.initializers.initializers kgcnn.io kgcnn.io.file kgcnn.io.graphlist kgcnn.io.loader kgcnn.layers kgcnn.layers.activ kgcnn.layers.aggr kgcnn.layers.attention kgcnn.layers.casting kgcnn.layers.conv kgcnn.layers.gather kgcnn.layers.geom kgcnn.layers.message kgcnn.layers.mlp kgcnn.layers.modules kgcnn.layers.norm kgcnn.layers.polynom kgcnn.layers.pooling kgcnn.layers.relational kgcnn.layers.scale kgcnn.layers.set2set kgcnn.layers.update kgcnn.literature kgcnn.literature.AttentiveFP kgcnn.literature.CGCNN kgcnn.literature.CMPNN kgcnn.literature.DGIN kgcnn.literature.DimeNetPP kgcnn.literature.DMPNN kgcnn.literature.EGNN kgcnn.literature.GAT kgcnn.literature.GATv2 kgcnn.literature.GCN kgcnn.literature.GIN kgcnn.literature.GNNExplain kgcnn.literature.GNNFilm kgcnn.literature.GraphSAGE kgcnn.literature.HamNet kgcnn.literature.HDNNP2nd kgcnn.literature.INorp kgcnn.literature.MAT kgcnn.literature.MEGAN kgcnn.literature.Megnet kgcnn.literature.MoGAT kgcnn.literature.MXMNet kgcnn.literature.NMPN kgcnn.literature.PAiNN kgcnn.literature.RGCN kgcnn.literature.rGIN kgcnn.literature.Schnet kgcnn.losses kgcnn.losses.losses kgcnn.metrics kgcnn.metrics.metrics kgcnn.metrics.utils kgcnn.models kgcnn.models.casting kgcnn.models.force kgcnn.models.multi kgcnn.models.serial kgcnn.models.utils kgcnn.molecule kgcnn.molecule.base kgcnn.molecule.convert kgcnn.molecule.dynamics kgcnn.molecule.dynamics.ase_calc kgcnn.molecule.dynamics.base kgcnn.molecule.encoder kgcnn.molecule.external kgcnn.molecule.external.ballloon kgcnn.molecule.graph_babel kgcnn.molecule.graph_rdkit kgcnn.molecule.io kgcnn.molecule.methods kgcnn.molecule.preprocessor kgcnn.molecule.serial kgcnn.ops kgcnn.ops.activ kgcnn.ops.axis kgcnn.ops.core kgcnn.ops.scatter kgcnn.optimizers kgcnn.optimizers.optimizers kgcnn.training kgcnn.training.callbacks kgcnn.training.history kgcnn.training.hyper kgcnn.training.schedule kgcnn.training.scheduler kgcnn.utils kgcnn.utils.devices kgcnn.utils.plots kgcnn.utils.serial kgcnn.utils.tests

mol_fun_dict (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel attribute) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit attribute) MolConverter (class in kgcnn.molecule.convert) MolDynamicsModelPredictor (class in kgcnn.molecule.dynamics.base) MolecularGraphOpenBabel (class in kgcnn.molecule.graph_babel) MolecularGraphRDKit (class in kgcnn.molecule.graph_rdkit) MoleculeNetDataset (class in kgcnn.data.moleculenet) MoleculeNetDataset2018 (class in kgcnn.data.datasets.MoleculeNetDataset2018) MolGraphInterface (class in kgcnn.molecule.base) MultiHeadGATV2Layer (class in kgcnn.layers.attention) MUTAGDataset (class in kgcnn.data.datasets.MUTAGDataset) MutagenicityDataset (class in kgcnn.data.datasets.MutagenicityDataset)

N

node_attributes (kgcnn.crystal.base.CrystalPreprocessor attribute) (kgcnn.crystal.preprocessor.AsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.KNNAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.KNNNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.KNNSuperCell attribute) (kgcnn.crystal.preprocessor.KNNUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.RadiusSuperCell attribute) (kgcnn.crystal.preprocessor.RadiusUnitCell attribute) (kgcnn.crystal.preprocessor.UnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiAsymmetricUnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiNonPeriodicUnitCell attribute) (kgcnn.crystal.preprocessor.VoronoiSuperCell attribute) (kgcnn.crystal.preprocessor.VoronoiUnitCell attribute)

node_attributes() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) node_coordinates() (kgcnn.molecule.base.MolGraphInterface property) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel property) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit property) node_number() (kgcnn.molecule.base.MolGraphInterface property) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel property) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit property) node_symbol() (kgcnn.molecule.base.MolGraphInterface property) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel property) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit property) NodeDistanceEuclidean (class in kgcnn.layers.geom) NodePosition (class in kgcnn.layers.geom) norm() (in module kgcnn.ops.core) NormalizeEdgeWeightsSymmetric (class in kgcnn.graph.preprocessor)

O

obtain_property() (kgcnn.data.base.MemoryGraphList method) (kgcnn.graph.base.GraphDict method) on_epoch_begin() (kgcnn.literature.GNNExplain.GNNExplainer.InspectionCallback method) on_epoch_end() (kgcnn.literature.GNNExplain.GNNExplainer.InspectionCallback method) (kgcnn.training.callbacks.LearningRateLoggingCallback method) on_train_batch_begin() (kgcnn.training.scheduler.LinearWarmUpScheduler method)

OneHotEncoder (class in kgcnn.molecule.encoder) openbabel_smile_to_mol() (in module kgcnn.molecule.convert) openbabel_xyz_to_mol() (in module kgcnn.molecule.convert) optimize_conformer() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method)

P

pad_at_axis() (in module kgcnn.io.loader) pad_np_array_list_batch_dim() (in module kgcnn.data.utils) PadProperty (class in kgcnn.graph.preprocessor) pairwise_diff() (in module kgcnn.crystal.graph_builder) parse_list_to_xyz_str() (in module kgcnn.molecule.io) parse_mol_str() (in module kgcnn.molecule.io) parse_oxidation_state_string() (kgcnn.crystal.periodic_table.periodic_table.PeriodicTable static method) partial_fit() (kgcnn.data.transform.scaler.standard.StandardLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardScaler method) PeriodicTable (class in kgcnn.crystal.periodic_table.periodic_table) plot_predict_true() (in module kgcnn.utils.plots) plot_train_test_loss() (in module kgcnn.utils.plots) PolynomialDecayScheduler (class in kgcnn.training.scheduler) PoolingEmbeddingAttention (class in kgcnn.layers.pooling) PoolingNodes (class in kgcnn.layers.pooling) PoolingNodesAttention (in module kgcnn.layers.pooling) PoolingNodesAttentive (class in kgcnn.layers.pooling) PoolingSet2SetEncoder (class in kgcnn.layers.set2set) PoolingWeightedNodes (class in kgcnn.layers.pooling)

PositionEncodingBasisLayer (class in kgcnn.layers.geom) possible_trajectory_names (kgcnn.data.datasets.MD17RevisedDataset.MD17RevisedDataset attribute) predict() (kgcnn.literature.GNNExplain.GNNInterface method) prepare_data() (kgcnn.data.crystal.CrystalDataset method) (kgcnn.data.datasets.MatBenchDataset2020.MatBenchDataset2020 method) (kgcnn.data.datasets.QM7bDataset.QM7bDataset method) (kgcnn.data.datasets.QM7Dataset.QM7Dataset method) (kgcnn.data.datasets.QM9Dataset.QM9Dataset method) (kgcnn.data.force.ForceDataset method) (kgcnn.data.moleculenet.MoleculeNetDataset method) (kgcnn.data.qm.QMDataset method) present_explanation() (kgcnn.literature.GNNExplain.GNNExplainer method) (kgcnn.literature.GNNExplain.GNNInterface method) PrincipalMomentsOfInertia (class in kgcnn.graph.preprocessor) PROTEINSDataset (class in kgcnn.data.datasets.PROTEINSDataset) prune_knn_bonds() (in module kgcnn.crystal.graph_builder) prune_radius_bonds() (in module kgcnn.crystal.graph_builder) prune_voronoi_bonds() (in module kgcnn.crystal.graph_builder) pymatgen_json_file_path() (kgcnn.data.crystal.CrystalDataset property)

Q

QM7bDataset (class in kgcnn.data.datasets.QM7bDataset) QM7Dataset (class in kgcnn.data.datasets.QM7Dataset) QM8Dataset (class in kgcnn.data.datasets.QM8Dataset) QM9Dataset (class in kgcnn.data.datasets.QM9Dataset)

QM9MolNetDataset (class in kgcnn.data.datasets.QM9MolNetDataset) QMDataset (class in kgcnn.data.qm) QMGraphLabelScaler (class in kgcnn.data.transform.scaler.molecule) (class in kgcnn.layers.scale)

R

RadiusAsymmetricUnitCell (class in kgcnn.crystal.preprocessor) RadiusNonPeriodicUnitCell (class in kgcnn.crystal.preprocessor) RadiusSuperCell (class in kgcnn.crystal.preprocessor) RadiusUnitCell (class in kgcnn.crystal.preprocessor) ragged_tensor_from_nested_numpy() (in module kgcnn.data.utils) RaggedTensorHDFile (class in kgcnn.io.file) RaggedTensorNumpyFile (class in kgcnn.io.file) range_neighbour_lattice() (in module kgcnn.graph.methods) rdkit_smile_to_mol() (in module kgcnn.molecule.convert) rdkit_xyz_to_mol() (in module kgcnn.molecule.convert) read() (kgcnn.io.file.RaggedTensorHDFile method) (kgcnn.io.file.RaggedTensorNumpyFile method) read_csv_simple() (kgcnn.data.tudataset.GraphTUDataset static method) read_in_memory() (kgcnn.data.crystal.CrystalDataset method) (kgcnn.data.datasets.ClinToxDataset.ClinToxDataset method) (kgcnn.data.datasets.CoraDataset.CoraDataset method) (kgcnn.data.datasets.CoraLuDataset.CoraLuDataset method) (kgcnn.data.datasets.ISO17Dataset.ISO17Dataset method) (kgcnn.data.datasets.MD17Dataset.MD17Dataset method) (kgcnn.data.datasets.MD17RevisedDataset.MD17RevisedDataset method) (kgcnn.data.datasets.MUTAGDataset.MUTAGDataset method) (kgcnn.data.datasets.MutagenicityDataset.MutagenicityDataset method) (kgcnn.data.datasets.PROTEINSDataset.PROTEINSDataset method) (kgcnn.data.datasets.QM7Dataset.QM7Dataset method) (kgcnn.data.datasets.QM9Dataset.QM9Dataset method) (kgcnn.data.datasets.SIDERDataset.SIDERDataset method) (kgcnn.data.datasets.Tox21MolNetDataset.Tox21MolNetDataset method) (kgcnn.data.force.ForceDataset method) (kgcnn.data.moleculenet.MoleculeNetDataset method) (kgcnn.data.qm.QMDataset method) (kgcnn.data.tudataset.GraphTUDataset method)

read_in_memory_xyz() (kgcnn.data.qm.QMDataset method) read_in_table_file() (kgcnn.data.base.MemoryGraphDataset method) read_mol_list_from_sdf_file() (in module kgcnn.molecule.io) read_smiles_file() (in module kgcnn.molecule.io) read_xyz_file() (in module kgcnn.molecule.io) RealToFracCoordinates (class in kgcnn.layers.geom) regression_augmentation() (kgcnn.literature.MEGAN.MEGAN method) RelationalAggregateLocalEdges (class in kgcnn.layers.aggr) RelationalDense (class in kgcnn.layers.relational) RelationalMLP (class in kgcnn.layers.mlp) relocate() (kgcnn.data.base.MemoryGraphDataset method) remove_duplicate_edges() (in module kgcnn.crystal.graph_builder) remove_hs() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) remove_uncharacterized() (kgcnn.data.datasets.QM9Dataset.QM9Dataset method) rename_property_on_graphs() (kgcnn.data.base.MemoryGraphList method) repeat_static_length() (in module kgcnn.ops.core) report() (kgcnn.molecule.encoder.OneHotEncoder method) rescale_edge_weights_degree_sym() (in module kgcnn.graph.methods) reset_state() (kgcnn.metrics.metrics.ScaledForceMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledRootMeanSquaredError method) ResidualLayer (class in kgcnn.layers.update) result() (kgcnn.metrics.metrics.BalancedBinaryAccuracyNoNaN method) results_file_path() (kgcnn.training.hyper.HyperParameter method) run() (kgcnn.molecule.external.ballloon.BalloonInterface method)

S

save() (kgcnn.data.base.MemoryGraphDataset method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) (kgcnn.molecule.dynamics.base.MolDynamicsModelPredictor method) (kgcnn.training.hyper.HyperParameter method) save_history_score() (in module kgcnn.training.history) save_json_file() (in module kgcnn.data.utils) save_pickle_file() (in module kgcnn.data.utils) save_structures_to_json_file() (kgcnn.data.crystal.CrystalDataset method) save_weights() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) save_yaml_file() (in module kgcnn.data.utils) ScalarProduct (class in kgcnn.layers.geom) scale_() (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler property) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin property) ScaledForceMeanAbsoluteError (class in kgcnn.metrics.metrics) ScaledMeanAbsoluteError (class in kgcnn.metrics.metrics) ScaledRootMeanSquaredError (class in kgcnn.metrics.metrics) scatter_reduce_max() (in module kgcnn.ops.scatter) scatter_reduce_mean() (in module kgcnn.ops.scatter) scatter_reduce_min() (in module kgcnn.ops.scatter) scatter_reduce_softmax() (in module kgcnn.ops.scatter) scatter_reduce_sum() (in module kgcnn.ops.scatter) schedule_epoch_lr() (kgcnn.training.scheduler.CosineAnnealingLRScheduler method) (kgcnn.training.scheduler.LinearLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmupExponentialLearningRateScheduler method) (kgcnn.training.scheduler.LinearWarmupExponentialLRScheduler method) (kgcnn.training.scheduler.LinearWarmupLinearLearningRateScheduler method) (kgcnn.training.scheduler.PolynomialDecayScheduler method) SchNetCFconv (class in kgcnn.layers.conv) SchNetInteraction (class in kgcnn.layers.conv) search_properties() (kgcnn.graph.base.GraphDict method) serialize() (in module kgcnn.utils.serial) set() (kgcnn.data.base.MemoryGraphList method) (kgcnn.graph.base.GraphDict method) set_attributes() (kgcnn.data.moleculenet.MoleculeNetDataset method) (kgcnn.data.qm.QMDataset method) set_config() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularScaler method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) set_cuda_device() (in module kgcnn.utils.devices)

set_methods() (kgcnn.data.base.MemoryGraphDataset method) set_multi_target_labels() (kgcnn.data.base.MemoryGraphDataset method) set_representation() (kgcnn.data.crystal.CrystalDataset method) set_scale() (kgcnn.layers.scale.ExtensiveMolecularLabelScaler method) (kgcnn.layers.scale.QMGraphLabelScaler method) (kgcnn.layers.scale.StandardLabelScaler method) (kgcnn.metrics.metrics.ScaledForceMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledRootMeanSquaredError method) set_train_test_indices_k_fold() (kgcnn.data.base.MemoryGraphDataset method) set_weights() (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) SetAngle (class in kgcnn.graph.preprocessor) SetEdgeIndicesReverse (class in kgcnn.graph.preprocessor) SetEdgeWeightsUniform (class in kgcnn.graph.preprocessor) SetMolAttributes (class in kgcnn.molecule.preprocessor) SetMolBondIndices (class in kgcnn.molecule.preprocessor) SetRange (class in kgcnn.graph.preprocessor) SetRangeFromEdges (class in kgcnn.graph.preprocessor) SetRangePeriodic (class in kgcnn.graph.preprocessor) setup_dataset_dir() (kgcnn.data.download.DownloadDataset static method) setup_dataset_main() (kgcnn.data.download.DownloadDataset static method) shift_coordinates_to_unit_cell() (in module kgcnn.graph.methods) shifted_sigmoid() (in module kgcnn.literature.MEGAN) shifted_softplus() (in module kgcnn.ops.activ) ShiftPeriodicLattice (class in kgcnn.layers.geom) ShiftToUnitCell (class in kgcnn.graph.preprocessor) SIDERDataset (class in kgcnn.data.datasets.SIDERDataset) smile_to_mol() (kgcnn.molecule.convert.MolConverter method) softplus2() (in module kgcnn.ops.activ) sort_edge_indices() (in module kgcnn.graph.methods) SortEdgeIndices (class in kgcnn.graph.preprocessor) spherical_bessel_jn() (in module kgcnn.layers.polynom) spherical_bessel_jn_normalization_prefactor() (in module kgcnn.layers.polynom) spherical_bessel_jn_zeros() (in module kgcnn.layers.polynom) SphericalBasisLayer (class in kgcnn.layers.geom) SphericalBesselJnExplicit (class in kgcnn.layers.polynom) SphericalHarmonicsYl (class in kgcnn.layers.polynom) SqueezeDims (class in kgcnn.layers.modules) StandardLabelScaler (class in kgcnn.data.transform.scaler.standard) (class in kgcnn.layers.scale) StandardScaler (class in kgcnn.data.transform.scaler.standard) structure_to_empty_graph() (in module kgcnn.crystal.graph_builder) Swish (class in kgcnn.layers.activ) swish() (in module kgcnn.ops.activ)

T

template_cast_dict_input() (in module kgcnn.models.casting) template_cast_list_input() (in module kgcnn.models.casting) template_cast_output() (in module kgcnn.models.casting) tensor() (kgcnn.data.base.MemoryGraphList method) TestCase (class in kgcnn.utils.tests) tf_associated_legendre_polynomial() (in module kgcnn.layers.polynom) tf_dataset_disjoint() (kgcnn.data.base.MemoryGraphList method) tf_dataset_disjoint_generator() (in module kgcnn.io.loader) tf_legendre_polynomial_pn() (in module kgcnn.layers.polynom) tf_spherical_bessel_jn() (in module kgcnn.layers.polynom) tf_spherical_bessel_jn_explicit() (in module kgcnn.layers.polynom) tf_spherical_harmonics_yl() (in module kgcnn.layers.polynom) to_asymmetric_unit_graph() (in module kgcnn.crystal.graph_builder) to_dict() (kgcnn.graph.base.GraphDict method) to_mol_block() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method)

to_networkx() (kgcnn.graph.base.GraphDict method) to_non_periodic_unit_cell() (in module kgcnn.crystal.graph_builder) to_smiles() (kgcnn.molecule.base.MolGraphInterface method) (kgcnn.molecule.graph_babel.MolecularGraphOpenBabel method) (kgcnn.molecule.graph_rdkit.MolecularGraphRDKit method) to_supercell_graph() (in module kgcnn.crystal.graph_builder) Tox21MolNetDataset (class in kgcnn.data.datasets.Tox21MolNetDataset) transform() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularLabelScaler method) (kgcnn.data.transform.scaler.molecule.ExtensiveMolecularScaler method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardLabelScaler method) (kgcnn.data.transform.scaler.standard.StandardScaler method) transform_dataset() (kgcnn.data.transform.scaler.force.EnergyForceExtensiveLabelScaler method) (kgcnn.data.transform.scaler.molecule._ExtensiveMolecularScalerBase method) (kgcnn.data.transform.scaler.molecule.QMGraphLabelScaler method) (kgcnn.data.transform.scaler.standard._StandardScalerSklearnMixin method) tudataset_ids (kgcnn.data.datasets.GraphTUDataset2020.GraphTUDataset2020 attribute)

U

UnitCell (class in kgcnn.crystal.preprocessor) unpack_tar_file() (kgcnn.data.download.DownloadDataset static method) unpack_zip_file() (kgcnn.data.download.DownloadDataset static method) update() (kgcnn.data.base.MemoryGraphList method) (kgcnn.graph.base.GraphDict method) update_model_kwargs() (in module kgcnn.models.utils) update_model_kwargs_logic() (in module kgcnn.models.utils)

update_nodes() (kgcnn.layers.message.MessagePassingBase method) update_q() (kgcnn.layers.set2set.PoolingSet2SetEncoder method) update_state() (kgcnn.metrics.metrics.AUCNoNaN method) (kgcnn.metrics.metrics.BalancedBinaryAccuracyNoNaN method) (kgcnn.metrics.metrics.ScaledMeanAbsoluteError method) (kgcnn.metrics.metrics.ScaledRootMeanSquaredError method) update_step() (kgcnn.optimizers.optimizers.Adan method)

V

validate() (kgcnn.data.base.MemoryGraphList method) (kgcnn.graph.base.GraphDict method) VectorAngle (class in kgcnn.layers.geom) verify() (kgcnn.training.hyper.HyperParameter method)

VoronoiAsymmetricUnitCell (class in kgcnn.crystal.preprocessor) VoronoiNonPeriodicUnitCell (class in kgcnn.crystal.preprocessor) VoronoiSuperCell (class in kgcnn.crystal.preprocessor) VoronoiUnitCell (class in kgcnn.crystal.preprocessor)

W

warning() (kgcnn.data.base.MemoryGraphDataset method) write() (kgcnn.io.file.RaggedTensorHDFile method) (kgcnn.io.file.RaggedTensorNumpyFile method)

write_list_to_xyz_file() (in module kgcnn.molecule.io) write_mol_block_list_to_sdf() (in module kgcnn.molecule.io) write_smiles_file() (in module kgcnn.molecule.io)

X

xyz_to_mol() (kgcnn.molecule.convert.MolConverter method)

Z

ZerosLike (class in kgcnn.layers.modules)