Index

_

__call__() (xanesnet.components.init.InitFn method) __cat_dim__() (xanesnet.datasets.torchgeometric.gemnet.GemNetData method) __enter__() (xanesnet.serialization.prediction_readers.PredictionReader method) __exit__() (xanesnet.serialization.prediction_readers.PredictionReader method) __getitem__() (xanesnet.datasets.base.base.Dataset method) (xanesnet.datasources.base.DataSource method) (xanesnet.datasources.multipmgjson.MultiPMGJSONSource method) (xanesnet.datasources.multixyzspec.MultiXYZSpecSource method) (xanesnet.datasources.pmgjson.PMGJSONSource method) (xanesnet.datasources.xyzspec.XYZSpecSource method) (xanesnet.serialization.prediction_readers.HDF5Reader method) (xanesnet.serialization.prediction_readers.JSONReader method) (xanesnet.serialization.prediction_readers.NumpyReader method) (xanesnet.serialization.prediction_readers.PredictionReader method) (xanesnet.serialization.prediction_readers.PreloadedPredictionReader method) (xanesnet.serialization.prediction_readers.StructureMatchedPredictionReader method) __inc__() (xanesnet.datasets.torchgeometric.gemnet.GemNetData method) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphData method) __init__() (xanesnet.analysis.aggregators.base.Aggregator method) (xanesnet.analysis.aggregators.base.AggregatorResult method) (xanesnet.analysis.aggregators.bias_variance.BiasVarianceAggregator method) (xanesnet.analysis.aggregators.ranking.RankingAggregator method) (xanesnet.analysis.aggregators.scalar.ScalarAggregator method) (xanesnet.analysis.aggregators.spectrum.SpectrumAggregator method) (xanesnet.analysis.aggregators.vector.VectorAggregator method) (xanesnet.analysis.collectors.base.Collector method) (xanesnet.analysis.collectors.descriptor.DescriptorCollector method) (xanesnet.analysis.collectors.loss.LossCollector method) (xanesnet.analysis.custom_modules.base.CustomModule method) (xanesnet.analysis.custom_modules.tensorboard.events.ScalarSeries method) (xanesnet.analysis.custom_modules.tensorboard.events.TrainingHistory method) (xanesnet.analysis.custom_modules.tensorboard.module.TensorBoardModule method) (xanesnet.analysis.plotters.base.Plotter method) (xanesnet.analysis.plotters.bias_variance.BiasVariancePlotter method) (xanesnet.analysis.plotters.common.stat_tables.CombinedTable method) (xanesnet.analysis.plotters.common.stat_tables.SingleTable method) (xanesnet.analysis.plotters.common.stat_tables.TableSource method) (xanesnet.analysis.plotters.common.style.PlotStyle method) (xanesnet.analysis.plotters.energy_resolved.EnergyResolvedLossPlotter method) (xanesnet.analysis.plotters.error_correlation.ErrorCorrelationPlotter method) (xanesnet.analysis.plotters.mean_spectrum.MeanSpectrumPlotter method) (xanesnet.analysis.plotters.parity.ParityPlotter method) (xanesnet.analysis.plotters.pca.PcaPlotter method) (xanesnet.analysis.plotters.scalar.ScalarPlotter method) (xanesnet.analysis.plotters.selector_overview.SelectorOverviewPlotter method) (xanesnet.analysis.plotters.spectra.AllSpectraPlotter method) (xanesnet.analysis.plotters.spectra_comparison.SpectraComparisonPlotter method) (xanesnet.analysis.plotters.stat_table.StatTablePlotter method) (xanesnet.analysis.plotters.stat_table_latex.StatTableLatexPlotter method) (xanesnet.analysis.reporters.base.Reporter method) (xanesnet.analysis.reporters.scalar.ScalarReporter method) (xanesnet.analysis.reporters.statistics.StatisticsReporter method) (xanesnet.analysis.result.AnalysisResults method) (xanesnet.analysis.result.MethodLabel method) (xanesnet.analysis.selectors.base.Selector method) (xanesnet.analysis.selectors.bernoulli.BernoulliSelector method) (xanesnet.analysis.selectors.by_element.ElementSelector method) (xanesnet.analysis.selectors.by_index.IndexSelector method) (xanesnet.analysis.selectors.by_range.IndexRangeSelector method) (xanesnet.analysis.selectors.chain.ChainSelector method) (xanesnet.analysis.selectors.identity.IdentitySelector method) (xanesnet.analysis.selectors.structure_cluster.StructureClusterSelector method) (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.checkpointing.checkpointer.Checkpointer method) (xanesnet.components.init.InitFn method) (xanesnet.components.lrscheduler.ConstantLRScheduler method) (xanesnet.components.lrscheduler.ExponentialLRScheduler method) (xanesnet.components.lrscheduler.LinearLRScheduler method) (xanesnet.components.lrscheduler.MultiStepLRScheduler method) (xanesnet.components.lrscheduler.NoOpLRScheduler method) (xanesnet.components.lrscheduler.StepLRScheduler method) (xanesnet.components.optim.AdagradOptimizer method) (xanesnet.components.optim.AdamOptimizer method) (xanesnet.components.optim.AdamWOptimizer method) (xanesnet.components.optim.RMSpropOptimizer method) (xanesnet.components.optim.SGDOptimizer method) (xanesnet.datasets.base.base.Dataset method) (xanesnet.datasets.base.torch_dataset.TorchDataset method) (xanesnet.datasets.base.torchgeometric_dataset.TorchGeometricDataset method) (xanesnet.datasets.torch.descriptor.DescriptorData method) (xanesnet.datasets.torch.descriptor.DescriptorDataset method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadDataset method) (xanesnet.datasets.torch.envembed.EnvEmbedData method) (xanesnet.datasets.torch.envembed.EnvEmbedDataset method) (xanesnet.datasets.torch.mp.descriptor.DescriptorDatasetMp method) (xanesnet.datasets.torch.mp.descriptor_multihead.DescriptorMultiheadDatasetMp method) (xanesnet.datasets.torch.mp.envembed.EnvEmbedDatasetMp method) (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch method) (xanesnet.datasets.torchgeometric.e3ee.E3EEDataset method) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch method) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullDataset method) (xanesnet.datasets.torchgeometric.gemnet.GemNetDataset method) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphDataset method) (xanesnet.datasets.torchgeometric.mp.e3ee.E3EEDatasetMp method) (xanesnet.datasets.torchgeometric.mp.e3ee_full.E3EEFullDatasetMp method) (xanesnet.datasets.torchgeometric.mp.gemnet.GemNetDatasetMp method) (xanesnet.datasets.torchgeometric.mp.geometrygraph.GeometryGraphDatasetMp method) (xanesnet.datasources.base.DataSource method) (xanesnet.datasources.multipmgjson.MultiPMGJSONSource method) (xanesnet.datasources.multixyzspec.MultiXYZSpecSource method) (xanesnet.datasources.pmgjson.PMGJSONSource method) (xanesnet.datasources.xyzspec.XYZSpecSource method) (xanesnet.descriptors.base.Descriptor method) (xanesnet.descriptors.direct.DIRECT method) (xanesnet.descriptors.mace.MACE method) (xanesnet.descriptors.pdos.PDOS method) (xanesnet.descriptors.rdc.RDC method) (xanesnet.descriptors.soap.SOAP method) (xanesnet.descriptors.wacsf.WACSF method) (xanesnet.encodings.affine.AffineEncoding method) (xanesnet.encodings.base.SpectraEncoding method) (xanesnet.encodings.combined.CombinedEncoding method) (xanesnet.encodings.concat.ConcatEncoding method) (xanesnet.encodings.fourier.FourierEncoding method) (xanesnet.encodings.gaussian.GaussianEncoding method) (xanesnet.encodings.minmax.MinMaxEncoding method) (xanesnet.encodings.none.NoneEncoding method) (xanesnet.encodings.scale.ScaleEncoding method) (xanesnet.encodings.subtract_average.SubtractAverageEncoding method) (xanesnet.encodings.zscore.ZScoreEncoding method) (xanesnet.graphs.base.GraphBuilder method) (xanesnet.graphs.radius.CovRadiusGraphBuilder method) (xanesnet.graphs.radius.RadiusGraphBuilder method) (xanesnet.graphs.voronoi.VoronoiGraphBuilder method) (xanesnet.losses.base.Loss method) (xanesnet.losses.bcewithlogits.BCEWithLogitsLoss method) (xanesnet.losses.combined.CombinedLoss method) (xanesnet.losses.emd.EMDLoss method) (xanesnet.losses.l1.L1Loss method) (xanesnet.losses.mse.MSELoss method) (xanesnet.losses.msssim.MultiScale_SSIM method) (xanesnet.losses.specplus.SpectralLossPlus method) (xanesnet.losses.wcc.WCCLoss method) (xanesnet.models.base.Model method) (xanesnet.models.dimenet.dimenet.BesselBasisLayer method) (xanesnet.models.dimenet.dimenet.DimeNet method) (xanesnet.models.dimenet.dimenet.EmbeddingBlock method) (xanesnet.models.dimenet.dimenet.Envelope method) (xanesnet.models.dimenet.dimenet.InteractionBlock method) (xanesnet.models.dimenet.dimenet.OutputBlock method) (xanesnet.models.dimenet.dimenet.ResidualLayer method) (xanesnet.models.dimenet.dimenet.SphericalBasisLayer method) (xanesnet.models.dimenet.dimenet_pp.DimeNetPlusPlus method) (xanesnet.models.dimenet.dimenet_pp.InteractionBlock method) (xanesnet.models.dimenet.dimenet_pp.OutputBlock method) (xanesnet.models.dimenet.dimenet_pp.ResidualLayer method) (xanesnet.models.e3ee.e3ee.E3EE method) (xanesnet.models.e3ee.layers.atom_encoder.EquivariantAtomEncoder method) (xanesnet.models.e3ee.layers.basic.CosineCutoff method) (xanesnet.models.e3ee.layers.basic.EnergyRBFEmbedding method) (xanesnet.models.e3ee.layers.basic.GaussianRBF method) (xanesnet.models.e3ee.layers.basic.IrrepNorm method) (xanesnet.models.e3ee.layers.basic.MLP method) (xanesnet.models.e3ee.layers.basic.RadialMLP method) (xanesnet.models.e3ee.layers.branch_attention.EnergyConditionedAtomAttention method) (xanesnet.models.e3ee.layers.branch_convolution.EnergyConditionedAtomConvolution method) (xanesnet.models.e3ee.layers.branch_convolution.EnergyConditionedEquivariantAtomConvolution method) (xanesnet.models.e3ee.layers.branch_eq_attention.EnergyConditionedEquivariantAtomAttention method) (xanesnet.models.e3ee.layers.branch_equivariant.EnergyConditionedEquivariantTargetSiteHead method) (xanesnet.models.e3ee.layers.branch_equivariant.EnergyIrrepModulation method) (xanesnet.models.e3ee.layers.branch_fusion.GatedBranchFusion method) (xanesnet.models.e3ee.layers.branch_path.PairElementEnergyScattering method) (xanesnet.models.e3ee.layers.branch_path.TargetSitePathAggregator method) (xanesnet.models.e3ee.layers.branch_target_site.EnergyConditionedTargetSiteBranch method) (xanesnet.models.e3ee.layers.interactions.EquivariantInteractionBlock method) (xanesnet.models.e3ee_full.e3ee_full.E3EEFull method) (xanesnet.models.e3ee_full.layers.atom_encoder.EquivariantAtomEncoder method) (xanesnet.models.e3ee_full.layers.basic.CosineCutoff method) (xanesnet.models.e3ee_full.layers.basic.EnergyRBFEmbedding method) (xanesnet.models.e3ee_full.layers.basic.GaussianRBF method) (xanesnet.models.e3ee_full.layers.basic.IrrepNorm method) (xanesnet.models.e3ee_full.layers.basic.MLP method) (xanesnet.models.e3ee_full.layers.basic.RadialMLP method) (xanesnet.models.e3ee_full.layers.branch_all_atom.AllAtomEnergyBranch method) (xanesnet.models.e3ee_full.layers.branch_attention.AllAtomAtomAttention method) (xanesnet.models.e3ee_full.layers.branch_convolution.AllAtomAtomConvolution method) (xanesnet.models.e3ee_full.layers.branch_convolution.AllAtomEquivariantAtomConvolution method) (xanesnet.models.e3ee_full.layers.branch_eq_attention.AllAtomEquivariantAtomAttention method) (xanesnet.models.e3ee_full.layers.branch_equivariant.AllAtomEquivariantHead method) (xanesnet.models.e3ee_full.layers.branch_equivariant.EnergyIrrepModulation method) (xanesnet.models.e3ee_full.layers.branch_fusion.GatedBranchFusion method) (xanesnet.models.e3ee_full.layers.branch_path.AllAtomPathAggregator method) (xanesnet.models.e3ee_full.layers.branch_path.PairElementEnergyScattering method) (xanesnet.models.e3ee_full.layers.interactions.EquivariantInteractionBlock method) (xanesnet.models.envembed.envembed.EnvEmbed method) (xanesnet.models.envembed.layers.coeff_head.CoeffHeadGroupedResidualPreLN method) (xanesnet.models.envembed.layers.coeff_head.ResidualPreLNBlock method) (xanesnet.models.envembed.layers.encoder.SoftRadialShellsEncoder method) (xanesnet.models.gemnet.layers.basis.BesselBasisLayer method) (xanesnet.models.gemnet.layers.basis.SphericalBasisLayer method) (xanesnet.models.gemnet.layers.basis.TensorBasisLayer method) (xanesnet.models.gemnet.layers.envelope.Envelope method) (xanesnet.models.gemnet.layers.scaling.ScaleFactor method) (xanesnet.models.gemnet.layers.scaling.ScalingFactor method) (xanesnet.serialization.auto_config.statistics.SpectralStatistics method) (xanesnet.serialization.auto_config.statistics.SpectralStatisticsCollector method) (xanesnet.serialization.checkpoints.Checkpoint method) (xanesnet.serialization.config.Config method) (xanesnet.serialization.jsonl_stream.JSONLStream method) (xanesnet.serialization.prediction_readers.HDF5Reader method) (xanesnet.serialization.prediction_readers.JSONReader method) (xanesnet.serialization.prediction_readers.NumpyReader method) (xanesnet.serialization.prediction_readers.PredictionReader method) (xanesnet.serialization.prediction_readers.PreloadedPredictionReader method) (xanesnet.serialization.prediction_readers.StructureMatchedPredictionReader method) (xanesnet.serialization.prediction_writers.HDF5Writer method) (xanesnet.serialization.prediction_writers.PredictionWriter method) (xanesnet.utils.logger.LevelFilter method) (xanesnet.utils.logger.TeeLogger method) (xanesnet.utils.math.gaussian.SpectralBasis method) (xanesnet.utils.math.gaussian.SpectralPost method) (xanesnet.utils.registry.Registry method)

__iter__() (xanesnet.analysis.selectors.base.Selector method) (xanesnet.analysis.selectors.bernoulli.BernoulliSelector method) (xanesnet.analysis.selectors.by_element.ElementSelector method) (xanesnet.analysis.selectors.by_index.IndexSelector method) (xanesnet.analysis.selectors.by_range.IndexRangeSelector method) (xanesnet.analysis.selectors.chain.ChainSelector method) (xanesnet.analysis.selectors.identity.IdentitySelector method) (xanesnet.analysis.selectors.structure_cluster.StructureClusterSelector method) (xanesnet.datasources.base.DataSource method) (xanesnet.datasources.multipmgjson.MultiPMGJSONSource method) (xanesnet.datasources.multixyzspec.MultiXYZSpecSource method) (xanesnet.datasources.pmgjson.PMGJSONSource method) (xanesnet.datasources.xyzspec.XYZSpecSource method) (xanesnet.serialization.jsonl_stream.JSONLStream method) (xanesnet.serialization.prediction_readers.PredictionReader method) __len__() (xanesnet.analysis.selectors.base.Selector method) (xanesnet.analysis.selectors.bernoulli.BernoulliSelector method) (xanesnet.analysis.selectors.by_element.ElementSelector method) (xanesnet.analysis.selectors.by_index.IndexSelector method) (xanesnet.analysis.selectors.by_range.IndexRangeSelector method) (xanesnet.analysis.selectors.chain.ChainSelector method) (xanesnet.analysis.selectors.identity.IdentitySelector method) (xanesnet.analysis.selectors.structure_cluster.StructureClusterSelector method) (xanesnet.datasets.base.base.Dataset method) (xanesnet.datasources.base.DataSource method) (xanesnet.datasources.multipmgjson.MultiPMGJSONSource method) (xanesnet.datasources.multixyzspec.MultiXYZSpecSource method) (xanesnet.datasources.pmgjson.PMGJSONSource method) (xanesnet.datasources.xyzspec.XYZSpecSource method) (xanesnet.serialization.jsonl_stream.JSONLStream method) (xanesnet.serialization.prediction_readers.HDF5Reader method) (xanesnet.serialization.prediction_readers.JSONReader method) (xanesnet.serialization.prediction_readers.NumpyReader method) (xanesnet.serialization.prediction_readers.PredictionReader method) (xanesnet.serialization.prediction_readers.PreloadedPredictionReader method) (xanesnet.serialization.prediction_readers.StructureMatchedPredictionReader method) __new__() (xanesnet.serialization.tensorboard.TensorBoardLogger static method) __next__() (xanesnet.serialization.prediction_readers.PredictionReader method) __repr__() (xanesnet.analysis.aggregators.base.Aggregator method) (xanesnet.analysis.collectors.base.Collector method) (xanesnet.analysis.custom_modules.base.CustomModule method) (xanesnet.analysis.plotters.base.Plotter method) (xanesnet.analysis.reporters.base.Reporter method) (xanesnet.analysis.selectors.base.Selector method) __str__() (xanesnet.analysis.aggregators.base.Aggregator method) (xanesnet.analysis.collectors.base.Collector method) (xanesnet.analysis.custom_modules.base.CustomModule method) (xanesnet.analysis.plotters.base.Plotter method) (xanesnet.analysis.reporters.base.Reporter method) (xanesnet.analysis.selectors.base.Selector method) (xanesnet.analysis.selectors.by_element.ElementSelector method) (xanesnet.analysis.selectors.chain.ChainSelector method) (xanesnet.analysis.selectors.structure_cluster.StructureClusterSelector method)

A

AdagradOptimizer (class in xanesnet.components.optim) AdamOptimizer (class in xanesnet.components.optim) AdamWOptimizer (class in xanesnet.components.optim) add() (xanesnet.serialization.prediction_writers.PredictionWriter method) add_colorbar() (in module xanesnet.analysis.plotters.common.layout) add_figure_legend() (in module xanesnet.analysis.plotters.common.style) add_grid_label() (in module xanesnet.analysis.plotters.common.layout) add_legend() (in module xanesnet.analysis.plotters.common.style) add_note() (in module xanesnet.analysis.plotters.common.style) add_structure_legend() (in module xanesnet.analysis.plotters.common.structures) AffineEncoding (class in xanesnet.encodings.affine) aggregate() (xanesnet.analysis.aggregators.base.Aggregator method) (xanesnet.analysis.aggregators.bias_variance.BiasVarianceAggregator method) (xanesnet.analysis.aggregators.ranking.RankingAggregator method) (xanesnet.analysis.aggregators.scalar.ScalarAggregator method) (xanesnet.analysis.aggregators.spectrum.SpectrumAggregator method) (xanesnet.analysis.aggregators.vector.VectorAggregator method) aggregation() (xanesnet.analysis.result.AnalysisResults method) Aggregator (class in xanesnet.analysis.aggregators.base) aggregator_dir_name() (in module xanesnet.analysis.plotters.common.stat_tables) aggregator_index (xanesnet.analysis.aggregators.base.AggregatorResult attribute) aggregator_results (xanesnet.analysis.result.AnalysisResults attribute) aggregator_type (xanesnet.analysis.aggregators.base.AggregatorResult attribute) AggregatorResult (class in xanesnet.analysis.aggregators.base) AllAtomAtomAttention (class in xanesnet.models.e3ee_full.layers.branch_attention)

AllAtomAtomConvolution (class in xanesnet.models.e3ee_full.layers.branch_convolution) AllAtomEnergyBranch (class in xanesnet.models.e3ee_full.layers.branch_all_atom) AllAtomEquivariantAtomAttention (class in xanesnet.models.e3ee_full.layers.branch_eq_attention) AllAtomEquivariantAtomConvolution (class in xanesnet.models.e3ee_full.layers.branch_convolution) AllAtomEquivariantHead (class in xanesnet.models.e3ee_full.layers.branch_equivariant) AllAtomPathAggregator (class in xanesnet.models.e3ee_full.layers.branch_path) AllSpectraPlotter (class in xanesnet.analysis.plotters.spectra) AnalysisResults (class in xanesnet.analysis.result) analyze() (in module xanesnet.core_analyze) angle (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) apply_decimal_tick_format() (in module xanesnet.analysis.plotters.common.formatting) as_dict() (xanesnet.serialization.config.Config method) as_float_vector() (in module xanesnet.analysis.utils) as_kwargs() (xanesnet.serialization.config.Config method) associated_legendre_polynomials() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis) atoms_to_pyscf() (in module xanesnet.descriptors.pdos) att_dist (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) att_dst (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) att_src (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) att_vec (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) auto_yes() (in module xanesnet.utils.prompts)

B

basis (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) (xanesnet.datasets.torch.envembed.EnvEmbedDataset attribute) batch (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) BatchProcessor (class in xanesnet.batchprocessors.base) BCEWithLogitsLoss (class in xanesnet.losses.bcewithlogits) BernoulliSelector (class in xanesnet.analysis.selectors.bernoulli) bessel_basis() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis) BesselBasisLayer (class in xanesnet.models.dimenet.dimenet) (class in xanesnet.models.gemnet.layers.basis)

BiasVarianceAggregator (class in xanesnet.analysis.aggregators.bias_variance) BiasVariancePlotter (class in xanesnet.analysis.plotters.bias_variance) build() (xanesnet.graphs.base.GraphBuilder method) (xanesnet.graphs.radius.CovRadiusGraphBuilder method) (xanesnet.graphs.radius.RadiusGraphBuilder method) (xanesnet.graphs.voronoi.VoronoiGraphBuilder method) build_combined_table() (in module xanesnet.analysis.plotters.common.stat_tables) build_parameter_rows() (in module xanesnet.encodings.affine) build_prediction_reader() (in module xanesnet.serialization.prediction_readers) build_ridge_operator() (in module xanesnet.utils.math.gaussian) build_single_table() (in module xanesnet.analysis.plotters.common.stat_tables) build_target_site_paths() (in module xanesnet.graphs.utils.target_site_paths)

C

c_star (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) canvas_padding() (xanesnet.analysis.plotters.common.style.PlotStyle method) cell_marks (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute) (xanesnet.analysis.plotters.common.stat_tables.SingleTable attribute) cell_marks() (in module xanesnet.analysis.plotters.common.stat_tables) cell_text (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute) (xanesnet.analysis.plotters.common.stat_tables.SingleTable attribute) cell_values (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute) (xanesnet.analysis.plotters.common.stat_tables.SingleTable attribute) ChainSelector (class in xanesnet.analysis.selectors.chain) channel_indices() (in module xanesnet.analysis.plotters.common.channels) check_preload() (xanesnet.datasets.base.base.Dataset method) Checkpoint (class in xanesnet.serialization.checkpoints) Checkpointer (class in xanesnet.checkpointing.checkpointer) close() (xanesnet.serialization.prediction_readers.HDF5Reader method) (xanesnet.serialization.prediction_readers.PredictionReader method) (xanesnet.serialization.prediction_readers.PreloadedPredictionReader method) (xanesnet.serialization.prediction_readers.StructureMatchedPredictionReader method) (xanesnet.serialization.prediction_writers.PredictionWriter method) (xanesnet.serialization.tensorboard.TensorBoardLogger method) CoeffHeadGroupedResidualPreLN (class in xanesnet.models.envembed.layers.coeff_head) col_labels (xanesnet.analysis.plotters.common.stat_tables.SingleTable attribute) collate_fn() (xanesnet.datasets.base.base.Dataset method) (xanesnet.datasets.base.torch_dataset.TorchDataset method) (xanesnet.datasets.base.torchgeometric_dataset.TorchGeometricDataset method) (xanesnet.datasets.torch.descriptor.DescriptorDataset method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadDataset method) (xanesnet.datasets.torch.envembed.EnvEmbedDataset method) (xanesnet.datasets.torchgeometric.e3ee.E3EEDataset method) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullDataset method) (xanesnet.datasets.torchgeometric.gemnet.GemNetDataset method) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphDataset method) collect_scale_factors() (in module xanesnet.models.gemnet.layers.scaling)

collect_spectral_statistics() (in module xanesnet.serialization.auto_config.statistics) collect_tables() (in module xanesnet.analysis.plotters.common.stat_tables) Collector (class in xanesnet.analysis.collectors.base) collector_results (xanesnet.analysis.result.AnalysisResults attribute) collector_stream() (xanesnet.analysis.result.AnalysisResults method) combined (xanesnet.analysis.plotters.common.stat_tables.TableSource attribute) combined_spectra_page_figure() (in module xanesnet.analysis.plotters.common.spectra_pages) combined_stem() (in module xanesnet.analysis.plotters.common.stat_tables) CombinedEncoding (class in xanesnet.encodings.combined) CombinedLoss (class in xanesnet.losses.combined) CombinedTable (class in xanesnet.analysis.plotters.common.stat_tables) compile_pdf() (in module xanesnet.analysis.plotters.common.latex) compute_id_swap() (in module xanesnet.graphs.utils.directional_indices) compute_mixed_triplets() (in module xanesnet.graphs.utils.directional_indices) compute_quadruplets() (in module xanesnet.graphs.utils.directional_indices) compute_triplets() (in module xanesnet.graphs.utils.directional_indices) compute_triplets_and_angles() (in module xanesnet.graphs.utils.triplets) ConcatEncoding (class in xanesnet.encodings.concat) Config (class in xanesnet.serialization.config) ConfigError confirm_yes_no() (in module xanesnet.utils.prompts) console_main() (in module xanesnet.cli) ConstantLRScheduler (class in xanesnet.components.lrscheduler) context() (xanesnet.analysis.plotters.common.style.PlotStyle method) copy_file() (in module xanesnet.utils.filesystem) copy_raw_config() (in module xanesnet.serialization.config) CosineCutoff (class in xanesnet.models.e3ee.layers.basic) (class in xanesnet.models.e3ee_full.layers.basic) CovRadiusGraphBuilder (class in xanesnet.graphs.radius) create() (xanesnet.utils.registry.Registry method) create_run_dir() (in module xanesnet.utils.filesystem) create_subfolders() (in module xanesnet.utils.filesystem) CriticalError CustomModule (class in xanesnet.analysis.custom_modules.base)

D

data (xanesnet.analysis.aggregators.base.AggregatorResult attribute) Dataset (class in xanesnet.datasets.base.base) DataSource (class in xanesnet.datasources.base) decode() (xanesnet.encodings.affine.AffineEncoding method) (xanesnet.encodings.base.SpectraEncoding method) (xanesnet.encodings.combined.CombinedEncoding method) (xanesnet.encodings.concat.ConcatEncoding method) (xanesnet.encodings.fourier.FourierEncoding method) (xanesnet.encodings.gaussian.GaussianEncoding method) (xanesnet.encodings.none.NoneEncoding method) decode_target() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.base.ForwardBatchProcessor method) (xanesnet.batchprocessors.inverse.base.InverseBatchProcessor method) Descriptor (class in xanesnet.descriptors.base) descriptor_features (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) descriptor_list (xanesnet.datasets.torch.descriptor.DescriptorDataset attribute) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadDataset attribute) (xanesnet.datasets.torch.envembed.EnvEmbedDataset attribute)

descriptor_matrix() (in module xanesnet.analysis.descriptor_cache) descriptor_vector() (in module xanesnet.analysis.descriptor_cache) DescriptorCollector (class in xanesnet.analysis.collectors.descriptor) DescriptorData (class in xanesnet.datasets.torch.descriptor) DescriptorDataset (class in xanesnet.datasets.torch.descriptor) DescriptorDatasetMp (class in xanesnet.datasets.torch.mp.descriptor) DescriptorMLPBatchProcessor (class in xanesnet.batchprocessors.forward.descriptor_mlp) DescriptorMultiheadBatchProcessor (class in xanesnet.batchprocessors.forward.descriptor_multihead) DescriptorMultiheadData (class in xanesnet.datasets.torch.descriptor_multihead) DescriptorMultiheadDataset (class in xanesnet.datasets.torch.descriptor_multihead) DescriptorMultiheadDatasetMp (class in xanesnet.datasets.torch.mp.descriptor_multihead) detect_prediction_format() (in module xanesnet.serialization.prediction_readers) device_copy() (xanesnet.utils.math.gaussian.SpectralBasis method) DimeNet (class in xanesnet.models.dimenet.dimenet) DimeNetPlusPlus (class in xanesnet.models.dimenet.dimenet_pp) dir_name (xanesnet.analysis.result.MethodLabel attribute) DIRECT (class in xanesnet.descriptors.direct) distance_features (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) draw_structure() (in module xanesnet.analysis.plotters.common.structures)

E

E3EE (class in xanesnet.models.e3ee.e3ee) E3EEBatch (class in xanesnet.datasets.torchgeometric.e3ee) E3EEBatchProcessor (class in xanesnet.batchprocessors.forward.e3ee) E3EEDataset (class in xanesnet.datasets.torchgeometric.e3ee) E3EEDatasetMp (class in xanesnet.datasets.torchgeometric.mp.e3ee) E3EEFull (class in xanesnet.models.e3ee_full.e3ee_full) E3EEFullBatch (class in xanesnet.datasets.torchgeometric.e3ee_full) E3EEFullBatchProcessor (class in xanesnet.batchprocessors.forward.e3ee_full) E3EEFullDataset (class in xanesnet.datasets.torchgeometric.e3ee_full) E3EEFullDatasetMp (class in xanesnet.datasets.torchgeometric.mp.e3ee_full) edge_dst (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) edge_index (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) edge_src (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) edge_vec (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) edge_weight (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) element (xanesnet.datasets.torch.descriptor.DescriptorData attribute) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData attribute) (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) element_preparation() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_mlp.DescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_multihead.DescriptorMultiheadBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee.E3EEBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee_full.E3EEFullBatchProcessor method) (xanesnet.batchprocessors.forward.envembed.EnvEmbedBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet.GemNetBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet_oc.GemNetOCBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_dimenet.GeometryGraphDimeNetBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_schnet.GeometryGraphSchNetBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_mlp.InverseDescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_multihead.InverseDescriptorMultiheadBatchProcessor method) element_preparation_single() (xanesnet.batchprocessors.base.BatchProcessor method) element_stats() (xanesnet.serialization.auto_config.statistics.SpectralStatisticsCollector method) ElementSelector (class in xanesnet.analysis.selectors.by_element) EmbeddingBlock (class in xanesnet.models.dimenet.dimenet) EMDLoss (class in xanesnet.losses.emd) enabled (xanesnet.serialization.tensorboard.TensorBoardLogger property) encode() (xanesnet.encodings.affine.AffineEncoding method) (xanesnet.encodings.base.SpectraEncoding method) (xanesnet.encodings.combined.CombinedEncoding method) (xanesnet.encodings.concat.ConcatEncoding method) (xanesnet.encodings.fourier.FourierEncoding method) (xanesnet.encodings.gaussian.GaussianEncoding method) (xanesnet.encodings.none.NoneEncoding method)

encode_input() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.base.ForwardBatchProcessor method) (xanesnet.batchprocessors.inverse.base.InverseBatchProcessor method) encode_target() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.base.ForwardBatchProcessor method) (xanesnet.batchprocessors.inverse.base.InverseBatchProcessor method) EncodingAutoResolver (in module xanesnet.serialization.auto_config.registries) EncodingResolver (in module xanesnet.serialization.auto_config.registries) energies (xanesnet.datasets.torch.descriptor.DescriptorData attribute) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData attribute) (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) EnergyConditionedAtomAttention (class in xanesnet.models.e3ee.layers.branch_attention) EnergyConditionedAtomConvolution (class in xanesnet.models.e3ee.layers.branch_convolution) EnergyConditionedEquivariantAtomAttention (class in xanesnet.models.e3ee.layers.branch_eq_attention) EnergyConditionedEquivariantAtomConvolution (class in xanesnet.models.e3ee.layers.branch_convolution) EnergyConditionedEquivariantTargetSiteHead (class in xanesnet.models.e3ee.layers.branch_equivariant) EnergyConditionedTargetSiteBranch (class in xanesnet.models.e3ee.layers.branch_target_site) EnergyIrrepModulation (class in xanesnet.models.e3ee.layers.branch_equivariant) (class in xanesnet.models.e3ee_full.layers.branch_equivariant) EnergyRBFEmbedding (class in xanesnet.models.e3ee.layers.basic) (class in xanesnet.models.e3ee_full.layers.basic) EnergyResolvedLossPlotter (class in xanesnet.analysis.plotters.energy_resolved) Envelope (class in xanesnet.models.dimenet.dimenet) (class in xanesnet.models.gemnet.layers.envelope) EnvEmbed (class in xanesnet.models.envembed.envembed) EnvEmbedBatchProcessor (class in xanesnet.batchprocessors.forward.envembed) EnvEmbedData (class in xanesnet.datasets.torch.envembed) EnvEmbedDataset (class in xanesnet.datasets.torch.envembed) EnvEmbedDatasetMp (class in xanesnet.datasets.torch.mp.envembed) epochs (xanesnet.analysis.custom_modules.tensorboard.events.ScalarSeries attribute) EquivariantAtomEncoder (class in xanesnet.models.e3ee.layers.atom_encoder) (class in xanesnet.models.e3ee_full.layers.atom_encoder) EquivariantInteractionBlock (class in xanesnet.models.e3ee.layers.interactions) (class in xanesnet.models.e3ee_full.layers.interactions) ErrorCorrelationPlotter (class in xanesnet.analysis.plotters.error_correlation) escape_latex() (in module xanesnet.analysis.plotters.common.latex) expand_selectors() (xanesnet.analysis.selectors.base.Selector method) (xanesnet.analysis.selectors.chain.ChainSelector method) (xanesnet.analysis.selectors.structure_cluster.StructureClusterSelector method) ExponentialLRScheduler (class in xanesnet.components.lrscheduler)

F

fft() (in module xanesnet.utils.math.fourier) figsize() (xanesnet.analysis.plotters.common.style.PlotStyle method) figure_scale (xanesnet.analysis.plotters.common.style.PlotStyle attribute) figure_size() (xanesnet.analysis.plotters.common.style.PlotStyle method) filter() (xanesnet.utils.logger.LevelFilter method) finish_grid() (in module xanesnet.analysis.plotters.common.layout) finish_member() (xanesnet.checkpointing.checkpointer.Checkpointer method) finish_single_panel() (in module xanesnet.analysis.plotters.common.layout) flush() (xanesnet.serialization.prediction_writers.PredictionWriter method) (xanesnet.serialization.tensorboard.TensorBoardLogger method) (xanesnet.utils.logger.TeeLogger method) font_scale (xanesnet.analysis.plotters.common.style.PlotStyle attribute) fontsize() (xanesnet.analysis.plotters.common.style.PlotStyle method) format_cell() (in module xanesnet.analysis.plotters.common.latex) format_decimal() (in module xanesnet.analysis.plotters.common.formatting) format_fixed_decimal() (in module xanesnet.analysis.plotters.common.formatting) format_label_cell() (in module xanesnet.analysis.plotters.common.latex) format_value() (in module xanesnet.serialization.auto_config.helpers) forward() (xanesnet.losses.base.Loss method) (xanesnet.losses.bcewithlogits.BCEWithLogitsLoss method) (xanesnet.losses.combined.CombinedLoss method) (xanesnet.losses.emd.EMDLoss method) (xanesnet.losses.l1.L1Loss method) (xanesnet.losses.mse.MSELoss method) (xanesnet.losses.msssim.MultiScale_SSIM method) (xanesnet.losses.specplus.SpectralLossPlus method) (xanesnet.losses.wcc.WCCLoss method) (xanesnet.models.dimenet.dimenet.BesselBasisLayer method) (xanesnet.models.dimenet.dimenet.DimeNet method) (xanesnet.models.dimenet.dimenet.EmbeddingBlock method) (xanesnet.models.dimenet.dimenet.Envelope method) (xanesnet.models.dimenet.dimenet.InteractionBlock method) (xanesnet.models.dimenet.dimenet.OutputBlock method) (xanesnet.models.dimenet.dimenet.ResidualLayer method) (xanesnet.models.dimenet.dimenet.SphericalBasisLayer method) (xanesnet.models.dimenet.dimenet_pp.InteractionBlock method) (xanesnet.models.dimenet.dimenet_pp.OutputBlock method) (xanesnet.models.dimenet.dimenet_pp.ResidualLayer method) (xanesnet.models.e3ee.e3ee.E3EE method) (xanesnet.models.e3ee.layers.atom_encoder.EquivariantAtomEncoder method) (xanesnet.models.e3ee.layers.basic.CosineCutoff method) (xanesnet.models.e3ee.layers.basic.EnergyRBFEmbedding method) (xanesnet.models.e3ee.layers.basic.GaussianRBF method) (xanesnet.models.e3ee.layers.basic.IrrepNorm method) (xanesnet.models.e3ee.layers.basic.MLP method) (xanesnet.models.e3ee.layers.basic.RadialMLP method) (xanesnet.models.e3ee.layers.branch_attention.EnergyConditionedAtomAttention method) (xanesnet.models.e3ee.layers.branch_convolution.EnergyConditionedAtomConvolution method) (xanesnet.models.e3ee.layers.branch_convolution.EnergyConditionedEquivariantAtomConvolution method) (xanesnet.models.e3ee.layers.branch_eq_attention.EnergyConditionedEquivariantAtomAttention method) (xanesnet.models.e3ee.layers.branch_equivariant.EnergyConditionedEquivariantTargetSiteHead method) (xanesnet.models.e3ee.layers.branch_equivariant.EnergyIrrepModulation method) (xanesnet.models.e3ee.layers.branch_fusion.GatedBranchFusion method) (xanesnet.models.e3ee.layers.branch_path.PairElementEnergyScattering method) (xanesnet.models.e3ee.layers.branch_path.TargetSitePathAggregator method) (xanesnet.models.e3ee.layers.branch_target_site.EnergyConditionedTargetSiteBranch method) (xanesnet.models.e3ee.layers.interactions.EquivariantInteractionBlock method) (xanesnet.models.e3ee_full.e3ee_full.E3EEFull method) (xanesnet.models.e3ee_full.layers.atom_encoder.EquivariantAtomEncoder method) (xanesnet.models.e3ee_full.layers.basic.CosineCutoff method) (xanesnet.models.e3ee_full.layers.basic.EnergyRBFEmbedding method) (xanesnet.models.e3ee_full.layers.basic.GaussianRBF method) (xanesnet.models.e3ee_full.layers.basic.IrrepNorm method) (xanesnet.models.e3ee_full.layers.basic.MLP method) (xanesnet.models.e3ee_full.layers.basic.RadialMLP method) (xanesnet.models.e3ee_full.layers.branch_all_atom.AllAtomEnergyBranch method) (xanesnet.models.e3ee_full.layers.branch_attention.AllAtomAtomAttention method) (xanesnet.models.e3ee_full.layers.branch_convolution.AllAtomAtomConvolution method) (xanesnet.models.e3ee_full.layers.branch_convolution.AllAtomEquivariantAtomConvolution method) (xanesnet.models.e3ee_full.layers.branch_eq_attention.AllAtomEquivariantAtomAttention method) (xanesnet.models.e3ee_full.layers.branch_equivariant.AllAtomEquivariantHead method) (xanesnet.models.e3ee_full.layers.branch_equivariant.EnergyIrrepModulation method) (xanesnet.models.e3ee_full.layers.branch_fusion.GatedBranchFusion method) (xanesnet.models.e3ee_full.layers.branch_path.AllAtomPathAggregator method) (xanesnet.models.e3ee_full.layers.branch_path.PairElementEnergyScattering method) (xanesnet.models.e3ee_full.layers.interactions.EquivariantInteractionBlock method) (xanesnet.models.envembed.envembed.EnvEmbed method) (xanesnet.models.envembed.layers.coeff_head.CoeffHeadGroupedResidualPreLN method) (xanesnet.models.envembed.layers.coeff_head.ResidualPreLNBlock method) (xanesnet.models.envembed.layers.encoder.SoftRadialShellsEncoder method) (xanesnet.models.gemnet.layers.basis.BesselBasisLayer method) (xanesnet.models.gemnet.layers.basis.SphericalBasisLayer method) (xanesnet.models.gemnet.layers.basis.TensorBasisLayer method) (xanesnet.models.gemnet.layers.envelope.Envelope method) (xanesnet.models.gemnet.layers.scaling.ScaleFactor method) (xanesnet.models.gemnet.layers.scaling.ScalingFactor method) (xanesnet.utils.math.gaussian.SpectralPost method)

forward_from_coeffs() (xanesnet.utils.math.gaussian.SpectralPost method) ForwardBatchProcessor (class in xanesnet.batchprocessors.forward.base) FourierEncoding (class in xanesnet.encodings.fourier) from_configs() (xanesnet.encodings.combined.CombinedEncoding class method) from_state_dict() (xanesnet.datasets.torch.descriptor.DescriptorData class method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData class method) (xanesnet.datasets.torch.envembed.EnvEmbedData class method) (xanesnet.serialization.checkpoints.Checkpoint class method)

G

GatedBranchFusion (class in xanesnet.models.e3ee.layers.branch_fusion) (class in xanesnet.models.e3ee_full.layers.branch_fusion) gaussian_blur1d() (xanesnet.losses.specplus.SpectralLossPlus method) gaussian_fit() (in module xanesnet.utils.math.gaussian) gaussian_inverse() (in module xanesnet.utils.math.gaussian) GaussianEncoding (class in xanesnet.encodings.gaussian) GaussianRBF (class in xanesnet.models.e3ee.layers.basic) (class in xanesnet.models.e3ee_full.layers.basic) GemNetBatch (class in xanesnet.datasets.torchgeometric.gemnet) GemNetBatchProcessor (class in xanesnet.batchprocessors.forward.gemnet) GemNetData (class in xanesnet.datasets.torchgeometric.gemnet) GemNetDataset (class in xanesnet.datasets.torchgeometric.gemnet) GemNetDatasetMp (class in xanesnet.datasets.torchgeometric.mp.gemnet) GemNetOCBatchProcessor (class in xanesnet.batchprocessors.forward.gemnet_oc) GeometryGraphBatch (class in xanesnet.datasets.torchgeometric.geometrygraph) GeometryGraphData (class in xanesnet.datasets.torchgeometric.geometrygraph) GeometryGraphDataset (class in xanesnet.datasets.torchgeometric.geometrygraph) GeometryGraphDatasetMp (class in xanesnet.datasets.torchgeometric.mp.geometrygraph) GeometryGraphDimeNetBatchProcessor (class in xanesnet.batchprocessors.forward.geometrygraph_dimenet) GeometryGraphSchNetBatchProcessor (class in xanesnet.batchprocessors.forward.geometrygraph_schnet) get() (xanesnet.serialization.config.Config method) (xanesnet.utils.registry.Registry method) get_all() (xanesnet.serialization.prediction_readers.HDF5Reader method) (xanesnet.serialization.prediction_readers.PredictionReader method) (xanesnet.serialization.prediction_readers.StructureMatchedPredictionReader method) get_all_subset_indices() (xanesnet.datasets.base.base.Dataset method) get_bool() (xanesnet.serialization.config.Config method)

get_config_list() (xanesnet.serialization.config.Config method) get_dataloader() (xanesnet.datasets.base.base.Dataset method) get_dataset() (xanesnet.datasets.base.base.Dataset method) get_extra_state() (xanesnet.losses.msssim.MultiScale_SSIM method) get_float() (xanesnet.serialization.config.Config method) get_hardware_info() (in module xanesnet.serialization.metadata) get_int() (xanesnet.serialization.config.Config method) get_lightning_context_path() (in module xanesnet.utils.lightning) get_optional_bool() (xanesnet.serialization.config.Config method) get_optional_float() (xanesnet.serialization.config.Config method) get_optional_int() (xanesnet.serialization.config.Config method) get_optional_str() (xanesnet.serialization.config.Config method) get_plot_style() (in module xanesnet.analysis.plotters.common.style) get_software_info() (in module xanesnet.serialization.metadata) get_str() (xanesnet.serialization.config.Config method) get_subset() (xanesnet.datasets.base.base.Dataset method) get_subset_indices() (xanesnet.datasets.base.base.Dataset method) global_maximum (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) global_mean (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) global_minimum (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) global_std (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) GraphBuilder (class in xanesnet.graphs.base) grid_cell_size() (xanesnet.analysis.plotters.common.style.PlotStyle method) grid_figsize() (xanesnet.analysis.plotters.common.style.PlotStyle method) grid_gaps() (xanesnet.analysis.plotters.common.style.PlotStyle method) grid_margins() (xanesnet.analysis.plotters.common.style.PlotStyle method) grid_shape() (in module xanesnet.analysis.plotters.common.layout) groups (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute)

H

has_split_indexfile (xanesnet.datasets.base.base.Dataset property) HDF5Reader (class in xanesnet.serialization.prediction_readers)

HDF5Writer (class in xanesnet.serialization.prediction_writers) head_idx (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData attribute) huber_loss() (xanesnet.losses.specplus.SpectralLossPlus method)

I

id3_expand_ba (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) id3_reduce_ca (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) id_a (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) id_c (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) id_swap (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) IdentitySelector (class in xanesnet.analysis.selectors.identity) idx_ji (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) idx_kj (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) IndexRangeSelector (class in xanesnet.analysis.selectors.by_range) IndexSelector (class in xanesnet.analysis.selectors.by_index) init_mlp_weights() (in module xanesnet.models.envembed.layers.encoder) init_weights() (xanesnet.models.base.Model method) (xanesnet.models.dimenet.dimenet.DimeNet method) (xanesnet.models.e3ee.e3ee.E3EE method) (xanesnet.models.e3ee_full.e3ee_full.E3EEFull method) (xanesnet.models.envembed.envembed.EnvEmbed method) InitFn (class in xanesnet.components.init) input_preparation() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_mlp.DescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_multihead.DescriptorMultiheadBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee.E3EEBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee_full.E3EEFullBatchProcessor method) (xanesnet.batchprocessors.forward.envembed.EnvEmbedBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet.GemNetBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet_oc.GemNetOCBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_dimenet.GeometryGraphDimeNetBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_schnet.GeometryGraphSchNetBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_mlp.InverseDescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_multihead.InverseDescriptorMultiheadBatchProcessor method)

input_preparation_single() (xanesnet.batchprocessors.base.BatchProcessor method) intensities (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) InteractionBlock (class in xanesnet.models.dimenet.dimenet) (class in xanesnet.models.dimenet.dimenet_pp) invariant_feature_dim() (in module xanesnet.models.e3ee.utils.invariants) (in module xanesnet.models.e3ee_full.utils.invariants) invariant_features_from_irreps() (in module xanesnet.models.e3ee.utils.invariants) (in module xanesnet.models.e3ee_full.utils.invariants) inverse_fft() (in module xanesnet.utils.math.fourier) InverseBatchProcessor (class in xanesnet.batchprocessors.inverse.base) InverseDescriptorMLPBatchProcessor (class in xanesnet.batchprocessors.inverse.descriptor_mlp) InverseDescriptorMultiheadBatchProcessor (class in xanesnet.batchprocessors.inverse.descriptor_multihead) IrrepNorm (class in xanesnet.models.e3ee.layers.basic) (class in xanesnet.models.e3ee_full.layers.basic) is_auto_yes_enabled() (in module xanesnet.utils.prompts) is_scalar_value() (in module xanesnet.analysis.utils) is_vector_value() (in module xanesnet.analysis.utils) iter_scalar_items() (in module xanesnet.analysis.utils) iter_vector_items() (in module xanesnet.analysis.utils)

J

Jn() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis) Jn_zeros() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis)

joined (xanesnet.analysis.result.MethodLabel property) json_friendly() (in module xanesnet.serialization.jsonl_stream) JSONLStream (class in xanesnet.serialization.jsonl_stream) JSONReader (class in xanesnet.serialization.prediction_readers) JSONWriter (class in xanesnet.serialization.prediction_writers)

K

Kidx3 (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute)

L

L1Loss (class in xanesnet.losses.l1) layout_scale (xanesnet.analysis.plotters.common.style.PlotStyle attribute) learning_rate (xanesnet.analysis.custom_modules.tensorboard.events.TrainingHistory attribute) legend_margin() (xanesnet.analysis.plotters.common.style.PlotStyle method) lengths (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) LevelFilter (class in xanesnet.utils.logger) line_scale (xanesnet.analysis.plotters.common.style.PlotStyle attribute) LinearLRScheduler (class in xanesnet.components.lrscheduler) lines (xanesnet.analysis.result.MethodLabel attribute) linewidth() (xanesnet.analysis.plotters.common.style.PlotStyle method) list() (xanesnet.utils.registry.Registry method) list_files() (in module xanesnet.utils.filesystem) list_filestems() (in module xanesnet.utils.filesystem) list_subdir_stems() (in module xanesnet.utils.filesystem) list_subdirs() (in module xanesnet.utils.filesystem) load() (xanesnet.datasets.torch.descriptor.DescriptorData class method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData class method) (xanesnet.datasets.torch.envembed.EnvEmbedData class method) (xanesnet.serialization.checkpoints.Checkpoint class method) load_config_schema() (in module xanesnet.serialization.schema_validation)

load_json() (xanesnet.datasources.pmgjson.PMGJSONSource static method) load_raw_config() (in module xanesnet.serialization.config) load_scales_json() (in module xanesnet.models.gemnet.layers.scaling) load_spectrum() (xanesnet.datasources.multixyzspec.MultiXYZSpecSource static method) (xanesnet.datasources.xyzspec.XYZSpecSource static method) load_splits() (in module xanesnet.serialization.splits) load_xyz() (xanesnet.datasources.multixyzspec.MultiXYZSpecSource static method) (xanesnet.datasources.xyzspec.XYZSpecSource static method) log_epoch_metrics() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_figure() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_final_metrics() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_histogram() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_learning_rate() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_model_graph() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_model_weights() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_scalar() (xanesnet.serialization.tensorboard.TensorBoardLogger method) log_text() (xanesnet.serialization.tensorboard.TensorBoardLogger method) Loss (class in xanesnet.losses.base) loss_energy_label() (in module xanesnet.analysis.plotters.common.formatting) LossCollector (class in xanesnet.analysis.collectors.loss) lr_scheduler_type (xanesnet.components.lrscheduler.Scheduler attribute)

M

MACE (class in xanesnet.descriptors.mace) main() (in module xanesnet.analyze) (in module xanesnet.cli) marker_scale (xanesnet.analysis.plotters.common.style.PlotStyle attribute) mask (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) matrix_grid() (in module xanesnet.analysis.plotters.common.layout) maximum (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) mean (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) MeanSpectrumPlotter (class in xanesnet.analysis.plotters.mean_spectrum) merge_raw_configs() (in module xanesnet.serialization.config) method_color() (in module xanesnet.analysis.plotters.common.style) method_grid() (in module xanesnet.analysis.plotters.common.layout) method_label() (xanesnet.analysis.result.AnalysisResults method) MethodLabel (class in xanesnet.analysis.result) minimum (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) minimum_validation_point() (in module xanesnet.analysis.custom_modules.tensorboard.events) MinMaxEncoding (class in xanesnet.encodings.minmax) MLP (class in xanesnet.models.e3ee.layers.basic) (class in xanesnet.models.e3ee_full.layers.basic) Model (class in xanesnet.models.base) model_states (xanesnet.serialization.checkpoints.Checkpoint attribute) ModelAutoResolver (in module xanesnet.serialization.auto_config.registries) ModelResolver (in module xanesnet.serialization.auto_config.registries) module xanesnet xanesnet.analysis xanesnet.analysis.aggregators xanesnet.analysis.aggregators.base xanesnet.analysis.aggregators.bias_variance xanesnet.analysis.aggregators.ranking xanesnet.analysis.aggregators.registry xanesnet.analysis.aggregators.scalar xanesnet.analysis.aggregators.spectrum xanesnet.analysis.aggregators.vector xanesnet.analysis.collectors xanesnet.analysis.collectors.base xanesnet.analysis.collectors.descriptor xanesnet.analysis.collectors.loss xanesnet.analysis.collectors.registry xanesnet.analysis.custom_modules xanesnet.analysis.custom_modules.base xanesnet.analysis.custom_modules.registry xanesnet.analysis.custom_modules.tensorboard xanesnet.analysis.custom_modules.tensorboard.events xanesnet.analysis.custom_modules.tensorboard.module xanesnet.analysis.custom_modules.tensorboard.plotting xanesnet.analysis.descriptor_cache xanesnet.analysis.plotters xanesnet.analysis.plotters.base xanesnet.analysis.plotters.bias_variance xanesnet.analysis.plotters.common xanesnet.analysis.plotters.common.channels xanesnet.analysis.plotters.common.formatting xanesnet.analysis.plotters.common.latex xanesnet.analysis.plotters.common.layout xanesnet.analysis.plotters.common.spectra_pages xanesnet.analysis.plotters.common.stat_tables xanesnet.analysis.plotters.common.structures xanesnet.analysis.plotters.common.style xanesnet.analysis.plotters.common.visual_constants xanesnet.analysis.plotters.energy_resolved xanesnet.analysis.plotters.error_correlation xanesnet.analysis.plotters.mean_spectrum xanesnet.analysis.plotters.parity xanesnet.analysis.plotters.pca xanesnet.analysis.plotters.registry xanesnet.analysis.plotters.scalar xanesnet.analysis.plotters.selector_overview xanesnet.analysis.plotters.spectra xanesnet.analysis.plotters.spectra_comparison xanesnet.analysis.plotters.stat_table xanesnet.analysis.plotters.stat_table_latex xanesnet.analysis.reporters xanesnet.analysis.reporters.base xanesnet.analysis.reporters.registry xanesnet.analysis.reporters.scalar xanesnet.analysis.reporters.statistics xanesnet.analysis.result xanesnet.analysis.selectors xanesnet.analysis.selectors.base xanesnet.analysis.selectors.bernoulli xanesnet.analysis.selectors.by_element xanesnet.analysis.selectors.by_index xanesnet.analysis.selectors.by_range xanesnet.analysis.selectors.chain xanesnet.analysis.selectors.identity xanesnet.analysis.selectors.registry xanesnet.analysis.selectors.structure_cluster xanesnet.analysis.utils xanesnet.analyze xanesnet.batchprocessors xanesnet.batchprocessors.base xanesnet.batchprocessors.forward xanesnet.batchprocessors.forward.base xanesnet.batchprocessors.forward.descriptor_mlp xanesnet.batchprocessors.forward.descriptor_multihead xanesnet.batchprocessors.forward.e3ee xanesnet.batchprocessors.forward.e3ee_full xanesnet.batchprocessors.forward.envembed xanesnet.batchprocessors.forward.gemnet xanesnet.batchprocessors.forward.gemnet_oc xanesnet.batchprocessors.forward.geometrygraph_dimenet xanesnet.batchprocessors.forward.geometrygraph_schnet xanesnet.batchprocessors.inverse xanesnet.batchprocessors.inverse.base xanesnet.batchprocessors.inverse.descriptor_mlp xanesnet.batchprocessors.inverse.descriptor_multihead xanesnet.batchprocessors.registry xanesnet.checkpointing xanesnet.checkpointing.checkpointer xanesnet.cli xanesnet.components xanesnet.components.activation xanesnet.components.init xanesnet.components.lrscheduler xanesnet.components.optim xanesnet.core_analyze xanesnet.datasets xanesnet.datasets.base xanesnet.datasets.base.base xanesnet.datasets.base.torch_dataset xanesnet.datasets.base.torchgeometric_dataset xanesnet.datasets.registry xanesnet.datasets.torch xanesnet.datasets.torch.descriptor xanesnet.datasets.torch.descriptor_multihead xanesnet.datasets.torch.envembed xanesnet.datasets.torch.mp xanesnet.datasets.torch.mp.descriptor xanesnet.datasets.torch.mp.descriptor_multihead xanesnet.datasets.torch.mp.envembed xanesnet.datasets.torchgeometric xanesnet.datasets.torchgeometric.e3ee xanesnet.datasets.torchgeometric.e3ee_full xanesnet.datasets.torchgeometric.gemnet xanesnet.datasets.torchgeometric.geometrygraph xanesnet.datasets.torchgeometric.mp xanesnet.datasets.torchgeometric.mp.e3ee xanesnet.datasets.torchgeometric.mp.e3ee_full xanesnet.datasets.torchgeometric.mp.gemnet xanesnet.datasets.torchgeometric.mp.geometrygraph xanesnet.datasources xanesnet.datasources.base xanesnet.datasources.multipmgjson xanesnet.datasources.multixyzspec xanesnet.datasources.pmgjson xanesnet.datasources.registry xanesnet.datasources.xyzspec xanesnet.descriptors xanesnet.descriptors.base xanesnet.descriptors.direct xanesnet.descriptors.mace xanesnet.descriptors.pdos xanesnet.descriptors.rdc xanesnet.descriptors.registry xanesnet.descriptors.soap xanesnet.descriptors.wacsf xanesnet.encodings xanesnet.encodings.affine xanesnet.encodings.base xanesnet.encodings.combined xanesnet.encodings.concat xanesnet.encodings.fourier xanesnet.encodings.gaussian xanesnet.encodings.minmax xanesnet.encodings.none xanesnet.encodings.registry xanesnet.encodings.scale xanesnet.encodings.subtract_average xanesnet.encodings.zscore xanesnet.graphs xanesnet.graphs.base xanesnet.graphs.radius xanesnet.graphs.registry xanesnet.graphs.utils xanesnet.graphs.utils.directional_indices xanesnet.graphs.utils.symmetrize xanesnet.graphs.utils.target_site_paths xanesnet.graphs.utils.triplets xanesnet.graphs.voronoi xanesnet.losses xanesnet.losses.base xanesnet.losses.bcewithlogits xanesnet.losses.combined xanesnet.losses.emd xanesnet.losses.l1 xanesnet.losses.mse xanesnet.losses.msssim xanesnet.losses.registry xanesnet.losses.specplus xanesnet.losses.wcc xanesnet.models.base xanesnet.models.dimenet xanesnet.models.dimenet.dimenet xanesnet.models.dimenet.dimenet_pp xanesnet.models.dimenet.resolver xanesnet.models.e3ee xanesnet.models.e3ee.e3ee xanesnet.models.e3ee.layers xanesnet.models.e3ee.layers.atom_encoder xanesnet.models.e3ee.layers.basic xanesnet.models.e3ee.layers.branch_attention xanesnet.models.e3ee.layers.branch_convolution xanesnet.models.e3ee.layers.branch_eq_attention xanesnet.models.e3ee.layers.branch_equivariant xanesnet.models.e3ee.layers.branch_fusion xanesnet.models.e3ee.layers.branch_path xanesnet.models.e3ee.layers.branch_target_site xanesnet.models.e3ee.layers.interactions xanesnet.models.e3ee.resolver xanesnet.models.e3ee.utils xanesnet.models.e3ee.utils.invariants xanesnet.models.e3ee_full xanesnet.models.e3ee_full.e3ee_full xanesnet.models.e3ee_full.layers xanesnet.models.e3ee_full.layers.atom_encoder xanesnet.models.e3ee_full.layers.basic xanesnet.models.e3ee_full.layers.branch_all_atom xanesnet.models.e3ee_full.layers.branch_attention xanesnet.models.e3ee_full.layers.branch_convolution xanesnet.models.e3ee_full.layers.branch_eq_attention xanesnet.models.e3ee_full.layers.branch_equivariant xanesnet.models.e3ee_full.layers.branch_fusion xanesnet.models.e3ee_full.layers.branch_path xanesnet.models.e3ee_full.layers.interactions xanesnet.models.e3ee_full.resolver xanesnet.models.e3ee_full.utils xanesnet.models.e3ee_full.utils.invariants xanesnet.models.envembed xanesnet.models.envembed.envembed xanesnet.models.envembed.layers xanesnet.models.envembed.layers.coeff_head xanesnet.models.envembed.layers.encoder xanesnet.models.envembed.resolver xanesnet.models.gemnet.layers xanesnet.models.gemnet.layers.basis xanesnet.models.gemnet.layers.envelope xanesnet.models.gemnet.layers.scaling xanesnet.models.registry xanesnet.serialization xanesnet.serialization.auto_config xanesnet.serialization.auto_config.core xanesnet.serialization.auto_config.helpers xanesnet.serialization.auto_config.registries xanesnet.serialization.auto_config.statistics xanesnet.serialization.checkpoints xanesnet.serialization.config xanesnet.serialization.jsonl_stream xanesnet.serialization.metadata xanesnet.serialization.prediction_readers xanesnet.serialization.prediction_writers xanesnet.serialization.runtime_contracts xanesnet.serialization.schema_validation xanesnet.serialization.splits xanesnet.serialization.tensorboard xanesnet.utils xanesnet.utils.exceptions xanesnet.utils.filesystem xanesnet.utils.lightning xanesnet.utils.logger xanesnet.utils.math xanesnet.utils.math.fourier xanesnet.utils.math.gaussian xanesnet.utils.prompts xanesnet.utils.random xanesnet.utils.registry

MSELoss (class in xanesnet.losses.mse) MultiPMGJSONSource (class in xanesnet.datasources.multipmgjson) MultiScale_SSIM (class in xanesnet.losses.msssim) MultiStepLRScheduler (class in xanesnet.components.lrscheduler) MultiXYZSpecSource (class in xanesnet.datasources.multixyzspec)

N

name (xanesnet.analysis.plotters.common.style.PlotStyle attribute) new_run() (xanesnet.serialization.tensorboard.TensorBoardLogger method) NoneEncoding (class in xanesnet.encodings.none) NoOpLRScheduler (class in xanesnet.components.lrscheduler)

num_heads (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadDataset property) num_points (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) NumpyReader (class in xanesnet.serialization.prediction_readers) NumpyWriter (class in xanesnet.serialization.prediction_writers)

O

one_line_label() (in module xanesnet.analysis.utils) Optimizer (class in xanesnet.components.optim) optimizer_type (xanesnet.components.optim.Optimizer attribute) optional_section() (xanesnet.serialization.config.Config method) output_size() (xanesnet.encodings.affine.AffineEncoding method) (xanesnet.encodings.base.SpectraEncoding method) (xanesnet.encodings.combined.CombinedEncoding method) (xanesnet.encodings.concat.ConcatEncoding method) (xanesnet.encodings.fourier.FourierEncoding method) (xanesnet.encodings.gaussian.GaussianEncoding method) (xanesnet.encodings.none.NoneEncoding method)

OutputBlock (class in xanesnet.models.dimenet.dimenet) (class in xanesnet.models.dimenet.dimenet_pp)

P

pad_figure() (in module xanesnet.analysis.plotters.common.layout) PairElementEnergyScattering (class in xanesnet.models.e3ee.layers.branch_path) (class in xanesnet.models.e3ee_full.layers.branch_path) panel_rect() (xanesnet.analysis.plotters.common.style.PlotStyle method) ParityPlotter (class in xanesnet.analysis.plotters.parity) parse_args() (in module xanesnet.analyze) path_batch (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) path_center (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) path_cosangle (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) path_j (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) path_k (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) path_r0j (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) path_r0k (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) path_rjk (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) PcaPlotter (class in xanesnet.analysis.plotters.pca) PDOS (class in xanesnet.descriptors.pdos) peak_weighting() (xanesnet.losses.specplus.SpectralLossPlus method) plot() (xanesnet.analysis.plotters.base.Plotter method) plot_combined_runs() (in module xanesnet.analysis.custom_modules.tensorboard.plotting) plot_single_run() (in module xanesnet.analysis.custom_modules.tensorboard.plotting) PlotStyle (class in xanesnet.analysis.plotters.common.style) Plotter (class in xanesnet.analysis.plotters.base) PMGJSONSource (class in xanesnet.datasources.pmgjson) pos (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute)

prediction (xanesnet.serialization.prediction_readers.PredictionSample attribute) (xanesnet.serialization.prediction_writers.PredictionBatch attribute) prediction_names (xanesnet.analysis.result.AnalysisResults attribute) prediction_preparation() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_multihead.DescriptorMultiheadBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee_full.E3EEFullBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet.GemNetBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet_oc.GemNetOCBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_dimenet.GeometryGraphDimeNetBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_schnet.GeometryGraphSchNetBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_multihead.InverseDescriptorMultiheadBatchProcessor method) prediction_std (xanesnet.serialization.prediction_readers.PredictionSample attribute) (xanesnet.serialization.prediction_writers.PredictionBatch attribute) PredictionBatch (class in xanesnet.serialization.prediction_writers) PredictionReader (class in xanesnet.serialization.prediction_readers) PredictionSample (class in xanesnet.serialization.prediction_readers) PredictionWriter (class in xanesnet.serialization.prediction_writers) PreloadedPredictionReader (class in xanesnet.serialization.prediction_readers) prepare() (xanesnet.datasets.base.base.Dataset method) (xanesnet.encodings.base.SpectraEncoding method) (xanesnet.encodings.combined.CombinedEncoding method) (xanesnet.encodings.concat.ConcatEncoding method) process() (xanesnet.analysis.collectors.base.Collector method) (xanesnet.analysis.collectors.descriptor.DescriptorCollector method) (xanesnet.analysis.collectors.loss.LossCollector method) processed_dir (xanesnet.datasets.base.base.Dataset property) processed_files (xanesnet.datasets.base.base.Dataset property) provides_structures() (xanesnet.serialization.prediction_readers.PredictionReader method) (xanesnet.serialization.prediction_readers.PreloadedPredictionReader method) (xanesnet.serialization.prediction_readers.StructureMatchedPredictionReader method)

R

RadialMLP (class in xanesnet.models.e3ee.layers.basic) (class in xanesnet.models.e3ee_full.layers.basic) RadiusGraphBuilder (class in xanesnet.graphs.radius) RankingAggregator (class in xanesnet.analysis.aggregators.ranking) RDC (class in xanesnet.descriptors.rdc) read_training_history() (in module xanesnet.analysis.custom_modules.tensorboard.events) real_sph_harm() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis) register() (xanesnet.utils.registry.Registry method) Registry (class in xanesnet.utils.registry) report() (xanesnet.analysis.reporters.base.Reporter method) (xanesnet.analysis.reporters.scalar.ScalarReporter method) (xanesnet.analysis.reporters.statistics.StatisticsReporter method) Reporter (class in xanesnet.analysis.reporters.base) requested_auto_fields() (in module xanesnet.serialization.auto_config.helpers) reserve_grid_headroom() (in module xanesnet.analysis.plotters.common.layout) reset_gate_logits() (xanesnet.models.e3ee.layers.branch_fusion.GatedBranchFusion method) (xanesnet.models.e3ee_full.layers.branch_fusion.GatedBranchFusion method) reset_parameters() (xanesnet.models.dimenet.dimenet.BesselBasisLayer method) (xanesnet.models.dimenet.dimenet.EmbeddingBlock method) (xanesnet.models.dimenet.dimenet.InteractionBlock method) (xanesnet.models.dimenet.dimenet.OutputBlock method) (xanesnet.models.dimenet.dimenet.ResidualLayer method) (xanesnet.models.dimenet.dimenet_pp.InteractionBlock method) (xanesnet.models.dimenet.dimenet_pp.OutputBlock method) (xanesnet.models.dimenet.dimenet_pp.ResidualLayer method) (xanesnet.models.gemnet.layers.basis.BesselBasisLayer method)

ResidualLayer (class in xanesnet.models.dimenet.dimenet) (class in xanesnet.models.dimenet.dimenet_pp) ResidualPreLNBlock (class in xanesnet.models.envembed.layers.coeff_head) resolve_auto_encoding_config() (in module xanesnet.serialization.auto_config.core) resolve_auto_model_config() (in module xanesnet.serialization.auto_config.core) resolve_dimenet() (in module xanesnet.models.dimenet.resolver) resolve_dimenet_pp() (in module xanesnet.models.dimenet.resolver) resolve_e3ee() (in module xanesnet.models.e3ee.resolver) resolve_e3ee_full() (in module xanesnet.models.e3ee_full.resolver) resolve_envembed() (in module xanesnet.models.envembed.resolver) resolve_gaussian_encoding() (in module xanesnet.encodings.gaussian) resolve_minmax_encoding() (in module xanesnet.encodings.minmax) resolve_scale_encoding() (in module xanesnet.encodings.scale) resolve_subtract_average_encoding() (in module xanesnet.encodings.subtract_average) resolve_zscore_encoding() (in module xanesnet.encodings.zscore) ResourceError RMSpropOptimizer (class in xanesnet.components.optim) row_label_lines (xanesnet.analysis.plotters.common.stat_tables.TableSource attribute) row_labels (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute) (xanesnet.analysis.plotters.common.stat_tables.SingleTable attribute) row_order (xanesnet.analysis.plotters.common.stat_tables.TableSource attribute) run() (xanesnet.analysis.custom_modules.base.CustomModule method) (xanesnet.analysis.custom_modules.tensorboard.module.TensorBoardModule method)

S

sample_id (xanesnet.datasets.torch.descriptor.DescriptorData attribute) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData attribute) (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) (xanesnet.serialization.prediction_readers.PredictionSample attribute) (xanesnet.serialization.prediction_writers.PredictionBatch attribute) sample_id_preparation() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_mlp.DescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_multihead.DescriptorMultiheadBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee.E3EEBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee_full.E3EEFullBatchProcessor method) (xanesnet.batchprocessors.forward.envembed.EnvEmbedBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet.GemNetBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet_oc.GemNetOCBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_dimenet.GeometryGraphDimeNetBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_schnet.GeometryGraphSchNetBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_mlp.InverseDescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_multihead.InverseDescriptorMultiheadBatchProcessor method) sample_key() (in module xanesnet.analysis.utils) sample_key_sort_key() (in module xanesnet.analysis.utils) sample_label() (in module xanesnet.analysis.utils) sanitize_label() (in module xanesnet.analysis.plotters.common.latex) save() (xanesnet.checkpointing.checkpointer.Checkpointer method) (xanesnet.datasets.torch.descriptor.DescriptorData method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData method) (xanesnet.datasets.torch.envembed.EnvEmbedData method) (xanesnet.serialization.checkpoints.Checkpoint method) (xanesnet.serialization.config.Config method) save_figure() (in module xanesnet.analysis.plotters.common.layout) save_raw_config() (in module xanesnet.serialization.config) save_separate() (xanesnet.serialization.checkpoints.Checkpoint method) save_separate_splits() (in module xanesnet.serialization.splits) save_splits() (in module xanesnet.serialization.splits) savefig_dpi (xanesnet.analysis.plotters.common.style.PlotStyle attribute) ScalarAggregator (class in xanesnet.analysis.aggregators.scalar) ScalarPlotter (class in xanesnet.analysis.plotters.scalar) ScalarReporter (class in xanesnet.analysis.reporters.scalar) ScalarSeries (class in xanesnet.analysis.custom_modules.tensorboard.events) scale_factor (xanesnet.models.gemnet.layers.scaling.ScaleFactor attribute) ScaleEncoding (class in xanesnet.encodings.scale) ScaleFactor (class in xanesnet.models.gemnet.layers.scaling) ScalingFactor (class in xanesnet.models.gemnet.layers.scaling) scatter_size() (xanesnet.analysis.plotters.common.style.PlotStyle method) Scheduler (class in xanesnet.components.lrscheduler) section() (xanesnet.serialization.config.Config method) Selector (class in xanesnet.analysis.selectors.base) SelectorOverviewPlotter (class in xanesnet.analysis.plotters.selector_overview) selectors (xanesnet.analysis.result.AnalysisResults attribute) set_auto_yes() (in module xanesnet.utils.prompts) set_config() (xanesnet.serialization.tensorboard.TensorBoardLogger method) set_context_title() (in module xanesnet.analysis.plotters.common.style) set_extra_state() (xanesnet.losses.msssim.MultiScale_SSIM method) set_global_seed() (in module xanesnet.utils.random) set_log_weights() (xanesnet.serialization.tensorboard.TensorBoardLogger method) set_splits() (xanesnet.datasets.base.base.Dataset method) setup_file_logging() (in module xanesnet.utils.logger) setup_logging() (in module xanesnet.utils.logger) setup_splits() (xanesnet.datasets.base.base.Dataset method) SGDOptimizer (class in xanesnet.components.optim) shorten_label() (in module xanesnet.analysis.plotters.common.formatting) signature (xanesnet.analysis.aggregators.base.Aggregator property) (xanesnet.analysis.aggregators.ranking.RankingAggregator property) (xanesnet.analysis.aggregators.scalar.ScalarAggregator property) (xanesnet.analysis.aggregators.spectrum.SpectrumAggregator property) (xanesnet.analysis.aggregators.vector.VectorAggregator property) (xanesnet.analysis.collectors.base.Collector property) (xanesnet.analysis.collectors.descriptor.DescriptorCollector property) (xanesnet.analysis.collectors.loss.LossCollector property) (xanesnet.analysis.custom_modules.base.CustomModule property) (xanesnet.analysis.custom_modules.tensorboard.module.TensorBoardModule property) (xanesnet.analysis.plotters.base.Plotter property) (xanesnet.analysis.plotters.bias_variance.BiasVariancePlotter property) (xanesnet.analysis.plotters.energy_resolved.EnergyResolvedLossPlotter property) (xanesnet.analysis.plotters.error_correlation.ErrorCorrelationPlotter property) (xanesnet.analysis.plotters.mean_spectrum.MeanSpectrumPlotter property) (xanesnet.analysis.plotters.pca.PcaPlotter property) (xanesnet.analysis.plotters.scalar.ScalarPlotter property) (xanesnet.analysis.plotters.selector_overview.SelectorOverviewPlotter property) (xanesnet.analysis.plotters.spectra.AllSpectraPlotter property) (xanesnet.analysis.plotters.spectra_comparison.SpectraComparisonPlotter property) (xanesnet.analysis.plotters.stat_table.StatTablePlotter property) (xanesnet.analysis.plotters.stat_table_latex.StatTableLatexPlotter property) (xanesnet.analysis.reporters.base.Reporter property) (xanesnet.analysis.reporters.statistics.StatisticsReporter property) (xanesnet.analysis.selectors.base.Selector property) (xanesnet.analysis.selectors.bernoulli.BernoulliSelector property) (xanesnet.analysis.selectors.by_element.ElementSelector property) (xanesnet.analysis.selectors.by_index.IndexSelector property) (xanesnet.analysis.selectors.by_range.IndexRangeSelector property) (xanesnet.analysis.selectors.chain.ChainSelector property) (xanesnet.analysis.selectors.structure_cluster.StructureClusterSelector property) (xanesnet.components.lrscheduler.Scheduler property) (xanesnet.components.optim.Optimizer property) (xanesnet.datasets.base.base.Dataset property) (xanesnet.datasets.torch.descriptor.DescriptorDataset property) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadDataset property) (xanesnet.datasets.torch.envembed.EnvEmbedDataset property) (xanesnet.datasets.torchgeometric.e3ee.E3EEDataset property) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullDataset property) (xanesnet.datasets.torchgeometric.gemnet.GemNetDataset property) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphDataset property) (xanesnet.encodings.base.SpectraEncoding property) (xanesnet.encodings.combined.CombinedEncoding property) (xanesnet.encodings.concat.ConcatEncoding property) (xanesnet.encodings.fourier.FourierEncoding property) (xanesnet.encodings.gaussian.GaussianEncoding property) (xanesnet.encodings.minmax.MinMaxEncoding property) (xanesnet.encodings.none.NoneEncoding property) (xanesnet.encodings.scale.ScaleEncoding property) (xanesnet.encodings.subtract_average.SubtractAverageEncoding property) (xanesnet.encodings.zscore.ZScoreEncoding property) (xanesnet.models.base.Model property) (xanesnet.models.dimenet.dimenet.DimeNet property) (xanesnet.models.dimenet.dimenet_pp.DimeNetPlusPlus property) (xanesnet.models.e3ee.e3ee.E3EE property) (xanesnet.models.e3ee_full.e3ee_full.E3EEFull property) (xanesnet.models.envembed.envembed.EnvEmbed property) (xanesnet.serialization.checkpoints.Checkpoint attribute)

single (xanesnet.analysis.plotters.common.stat_tables.TableSource attribute) single_panel() (in module xanesnet.analysis.plotters.common.layout) SingleTable (class in xanesnet.analysis.plotters.common.stat_tables) slice_channels() (in module xanesnet.analysis.plotters.common.channels) snapshot() (xanesnet.checkpointing.checkpointer.Checkpointer method) SOAP (class in xanesnet.descriptors.soap) SoftRadialShellsEncoder (class in xanesnet.models.envembed.layers.encoder) sort_col (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute) (xanesnet.analysis.plotters.common.stat_tables.SingleTable attribute) sorted_elements() (xanesnet.serialization.auto_config.statistics.SpectralStatisticsCollector method) spacing() (xanesnet.analysis.plotters.common.style.PlotStyle method) spectra_input_key (xanesnet.batchprocessors.inverse.base.InverseBatchProcessor attribute) spectra_page_figure() (in module xanesnet.analysis.plotters.common.spectra_pages) spectra_structure_page_figure() (in module xanesnet.analysis.plotters.common.spectra_pages) SpectraComparisonPlotter (class in xanesnet.analysis.plotters.spectra_comparison) SpectraEncoding (class in xanesnet.encodings.base) SpectralBasis (class in xanesnet.utils.math.gaussian) SpectralLossPlus (class in xanesnet.losses.specplus) SpectralPost (class in xanesnet.utils.math.gaussian) SpectralStatistics (class in xanesnet.serialization.auto_config.statistics) SpectralStatisticsCollector (class in xanesnet.serialization.auto_config.statistics) spectrum() (in module xanesnet.descriptors.pdos) SpectrumAggregator (class in xanesnet.analysis.aggregators.spectrum) sph_harm_prefactor() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis) spherical_bessel_formulas() (in module xanesnet.models.dimenet.dimenet) (in module xanesnet.models.gemnet.layers.basis) SphericalBasisLayer (class in xanesnet.models.dimenet.dimenet) (class in xanesnet.models.gemnet.layers.basis) state_dict() (xanesnet.components.lrscheduler.Scheduler method) (xanesnet.components.optim.Optimizer method) state_to_cpu() (in module xanesnet.checkpointing.checkpointer) StatisticsReporter (class in xanesnet.analysis.reporters.statistics) StatTableLatexPlotter (class in xanesnet.analysis.plotters.stat_table_latex) StatTablePlotter (class in xanesnet.analysis.plotters.stat_table) std (xanesnet.serialization.auto_config.statistics.SpectralStatistics property) step() (xanesnet.checkpointing.checkpointer.Checkpointer method) StepLRScheduler (class in xanesnet.components.lrscheduler) structure (xanesnet.serialization.prediction_readers.PredictionSample attribute) StructureClusterSelector (class in xanesnet.analysis.selectors.structure_cluster) StructureMatchedPredictionReader (class in xanesnet.serialization.prediction_readers) style_axis() (in module xanesnet.analysis.plotters.common.style) style_grid_cell() (in module xanesnet.analysis.plotters.common.layout) subsets (xanesnet.datasets.base.base.Dataset property) SubtractAverageEncoding (class in xanesnet.encodings.subtract_average) symmetrize_directed_edges() (in module xanesnet.graphs.utils.symmetrize) synthesize() (xanesnet.utils.math.gaussian.SpectralBasis method)

T

table_label_width() (xanesnet.analysis.plotters.common.style.PlotStyle method) table_tight_layout_pad (xanesnet.analysis.plotters.common.style.PlotStyle attribute) TableSource (class in xanesnet.analysis.plotters.common.stat_tables) target (xanesnet.serialization.prediction_readers.PredictionSample attribute) (xanesnet.serialization.prediction_writers.PredictionBatch attribute) target_preparation() (xanesnet.batchprocessors.base.BatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_mlp.DescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.forward.descriptor_multihead.DescriptorMultiheadBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee.E3EEBatchProcessor method) (xanesnet.batchprocessors.forward.e3ee_full.E3EEFullBatchProcessor method) (xanesnet.batchprocessors.forward.envembed.EnvEmbedBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet.GemNetBatchProcessor method) (xanesnet.batchprocessors.forward.gemnet_oc.GemNetOCBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_dimenet.GeometryGraphDimeNetBatchProcessor method) (xanesnet.batchprocessors.forward.geometrygraph_schnet.GeometryGraphSchNetBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_mlp.InverseDescriptorMLPBatchProcessor method) (xanesnet.batchprocessors.inverse.descriptor_multihead.InverseDescriptorMultiheadBatchProcessor method) target_preparation_single() (xanesnet.batchprocessors.base.BatchProcessor method) target_site_index (xanesnet.datasets.torch.descriptor.DescriptorData attribute) (xanesnet.datasets.torch.envembed.EnvEmbedData attribute) (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) (xanesnet.serialization.prediction_readers.PredictionSample attribute) (xanesnet.serialization.prediction_writers.PredictionBatch attribute) target_site_index_preparation() (xanesnet.batchprocessors.base.BatchProcessor method) target_site_mask (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) TargetSitePathAggregator (class in xanesnet.models.e3ee.layers.branch_path)

TeeLogger (class in xanesnet.utils.logger) TensorBasisLayer (class in xanesnet.models.gemnet.layers.basis) TensorBoardLogger (class in xanesnet.serialization.tensorboard) TensorBoardModule (class in xanesnet.analysis.custom_modules.tensorboard.module) time_per_spectrum (xanesnet.serialization.prediction_readers.PredictionSample attribute) (xanesnet.serialization.prediction_writers.PredictionBatch attribute) to() (xanesnet.datasets.torch.descriptor.DescriptorData method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData method) (xanesnet.datasets.torch.envembed.EnvEmbedData method) to_state_dict() (xanesnet.datasets.torch.descriptor.DescriptorData method) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData method) (xanesnet.datasets.torch.envembed.EnvEmbedData method) (xanesnet.serialization.checkpoints.Checkpoint method) torch_optimizer (xanesnet.components.optim.Optimizer property) torch_scheduler (xanesnet.components.lrscheduler.Scheduler property) TorchDataset (class in xanesnet.datasets.base.torch_dataset) TorchGeometricDataset (class in xanesnet.datasets.base.torchgeometric_dataset) train_subset (xanesnet.datasets.base.base.Dataset property) training_loss (xanesnet.analysis.custom_modules.tensorboard.events.TrainingHistory attribute) training_state (xanesnet.serialization.checkpoints.Checkpoint attribute) TrainingHistory (class in xanesnet.analysis.custom_modules.tensorboard.events) transform() (xanesnet.descriptors.base.Descriptor method) (xanesnet.descriptors.direct.DIRECT method) (xanesnet.descriptors.mace.MACE method) (xanesnet.descriptors.pdos.PDOS method) (xanesnet.descriptors.rdc.RDC method) (xanesnet.descriptors.soap.SOAP method) (xanesnet.descriptors.wacsf.WACSF method) transform_pmg() (xanesnet.descriptors.base.Descriptor method) truncate_per_source() (in module xanesnet.graphs.utils.symmetrize) truncate_text() (in module xanesnet.analysis.plotters.common.formatting)

U

update() (xanesnet.serialization.auto_config.statistics.SpectralStatistics method) (xanesnet.serialization.auto_config.statistics.SpectralStatisticsCollector method) (xanesnet.serialization.config.Config method)

update_with_dict() (xanesnet.serialization.config.Config method)

V

valid_subset (xanesnet.datasets.base.base.Dataset property) validate_config_schema() (in module xanesnet.serialization.schema_validation) validate_runtime_contracts() (in module xanesnet.serialization.runtime_contracts) validation_loss (xanesnet.analysis.custom_modules.tensorboard.events.TrainingHistory attribute) value_cols (xanesnet.analysis.plotters.common.stat_tables.CombinedTable attribute)

value_display_label() (in module xanesnet.analysis.plotters.common.stat_tables) value_display_unit() (in module xanesnet.analysis.plotters.common.stat_tables) value_order (xanesnet.analysis.plotters.common.stat_tables.TableSource attribute) values (xanesnet.analysis.custom_modules.tensorboard.events.ScalarSeries attribute) VectorAggregator (class in xanesnet.analysis.aggregators.vector) VoronoiGraphBuilder (class in xanesnet.graphs.voronoi)

W

WACSF (class in xanesnet.descriptors.wacsf) WCCLoss (class in xanesnet.losses.wcc) write() (xanesnet.utils.logger.TeeLogger method)

write_document() (in module xanesnet.analysis.plotters.common.latex) write_run_metadata() (in module xanesnet.serialization.metadata) writer (xanesnet.serialization.tensorboard.TensorBoardLogger property)

X

x (xanesnet.datasets.torch.descriptor.DescriptorData attribute) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData attribute) (xanesnet.datasets.torchgeometric.e3ee.E3EEBatch attribute) (xanesnet.datasets.torchgeometric.e3ee_full.E3EEFullBatch attribute) (xanesnet.datasets.torchgeometric.gemnet.GemNetBatch attribute) (xanesnet.datasets.torchgeometric.geometrygraph.GeometryGraphBatch attribute) xanesnet module xanesnet.analysis module xanesnet.analysis.aggregators module xanesnet.analysis.aggregators.base module xanesnet.analysis.aggregators.bias_variance module xanesnet.analysis.aggregators.ranking module xanesnet.analysis.aggregators.registry module xanesnet.analysis.aggregators.scalar module xanesnet.analysis.aggregators.spectrum module xanesnet.analysis.aggregators.vector module xanesnet.analysis.collectors module xanesnet.analysis.collectors.base module xanesnet.analysis.collectors.descriptor module xanesnet.analysis.collectors.loss module xanesnet.analysis.collectors.registry module xanesnet.analysis.custom_modules module xanesnet.analysis.custom_modules.base module xanesnet.analysis.custom_modules.registry module xanesnet.analysis.custom_modules.tensorboard module xanesnet.analysis.custom_modules.tensorboard.events module xanesnet.analysis.custom_modules.tensorboard.module module xanesnet.analysis.custom_modules.tensorboard.plotting module xanesnet.analysis.descriptor_cache module xanesnet.analysis.plotters module xanesnet.analysis.plotters.base module xanesnet.analysis.plotters.bias_variance module xanesnet.analysis.plotters.common module xanesnet.analysis.plotters.common.channels module xanesnet.analysis.plotters.common.formatting module xanesnet.analysis.plotters.common.latex module xanesnet.analysis.plotters.common.layout module xanesnet.analysis.plotters.common.spectra_pages module xanesnet.analysis.plotters.common.stat_tables module xanesnet.analysis.plotters.common.structures module xanesnet.analysis.plotters.common.style module xanesnet.analysis.plotters.common.visual_constants module xanesnet.analysis.plotters.energy_resolved module xanesnet.analysis.plotters.error_correlation module xanesnet.analysis.plotters.mean_spectrum module xanesnet.analysis.plotters.parity module xanesnet.analysis.plotters.pca module xanesnet.analysis.plotters.registry module xanesnet.analysis.plotters.scalar module xanesnet.analysis.plotters.selector_overview module xanesnet.analysis.plotters.spectra module xanesnet.analysis.plotters.spectra_comparison module xanesnet.analysis.plotters.stat_table module xanesnet.analysis.plotters.stat_table_latex module xanesnet.analysis.reporters module xanesnet.analysis.reporters.base module xanesnet.analysis.reporters.registry module xanesnet.analysis.reporters.scalar module xanesnet.analysis.reporters.statistics module xanesnet.analysis.result module xanesnet.analysis.selectors module xanesnet.analysis.selectors.base module xanesnet.analysis.selectors.bernoulli module xanesnet.analysis.selectors.by_element module xanesnet.analysis.selectors.by_index module xanesnet.analysis.selectors.by_range module xanesnet.analysis.selectors.chain module xanesnet.analysis.selectors.identity module xanesnet.analysis.selectors.registry module xanesnet.analysis.selectors.structure_cluster module xanesnet.analysis.utils module xanesnet.analyze module xanesnet.batchprocessors module xanesnet.batchprocessors.base module xanesnet.batchprocessors.forward module xanesnet.batchprocessors.forward.base module xanesnet.batchprocessors.forward.descriptor_mlp module xanesnet.batchprocessors.forward.descriptor_multihead module xanesnet.batchprocessors.forward.e3ee module xanesnet.batchprocessors.forward.e3ee_full module xanesnet.batchprocessors.forward.envembed module xanesnet.batchprocessors.forward.gemnet module xanesnet.batchprocessors.forward.gemnet_oc module xanesnet.batchprocessors.forward.geometrygraph_dimenet module xanesnet.batchprocessors.forward.geometrygraph_schnet module xanesnet.batchprocessors.inverse module xanesnet.batchprocessors.inverse.base module xanesnet.batchprocessors.inverse.descriptor_mlp module xanesnet.batchprocessors.inverse.descriptor_multihead module xanesnet.batchprocessors.registry module xanesnet.checkpointing module xanesnet.checkpointing.checkpointer module xanesnet.cli module xanesnet.components module xanesnet.components.activation module xanesnet.components.init module xanesnet.components.lrscheduler module xanesnet.components.optim module xanesnet.core_analyze module xanesnet.datasets module xanesnet.datasets.base module xanesnet.datasets.base.base module xanesnet.datasets.base.torch_dataset module xanesnet.datasets.base.torchgeometric_dataset module xanesnet.datasets.registry module xanesnet.datasets.torch module xanesnet.datasets.torch.descriptor module xanesnet.datasets.torch.descriptor_multihead module xanesnet.datasets.torch.envembed module xanesnet.datasets.torch.mp module xanesnet.datasets.torch.mp.descriptor module xanesnet.datasets.torch.mp.descriptor_multihead module xanesnet.datasets.torch.mp.envembed module xanesnet.datasets.torchgeometric module xanesnet.datasets.torchgeometric.e3ee module xanesnet.datasets.torchgeometric.e3ee_full module xanesnet.datasets.torchgeometric.gemnet module xanesnet.datasets.torchgeometric.geometrygraph module xanesnet.datasets.torchgeometric.mp module xanesnet.datasets.torchgeometric.mp.e3ee module xanesnet.datasets.torchgeometric.mp.e3ee_full module xanesnet.datasets.torchgeometric.mp.gemnet module xanesnet.datasets.torchgeometric.mp.geometrygraph module xanesnet.datasources module xanesnet.datasources.base module xanesnet.datasources.multipmgjson module

xanesnet.datasources.multixyzspec module xanesnet.datasources.pmgjson module xanesnet.datasources.registry module xanesnet.datasources.xyzspec module xanesnet.descriptors module xanesnet.descriptors.base module xanesnet.descriptors.direct module xanesnet.descriptors.mace module xanesnet.descriptors.pdos module xanesnet.descriptors.rdc module xanesnet.descriptors.registry module xanesnet.descriptors.soap module xanesnet.descriptors.wacsf module xanesnet.encodings module xanesnet.encodings.affine module xanesnet.encodings.base module xanesnet.encodings.combined module xanesnet.encodings.concat module xanesnet.encodings.fourier module xanesnet.encodings.gaussian module xanesnet.encodings.minmax module xanesnet.encodings.none module xanesnet.encodings.registry module xanesnet.encodings.scale module xanesnet.encodings.subtract_average module xanesnet.encodings.zscore module xanesnet.graphs module xanesnet.graphs.base module xanesnet.graphs.radius module xanesnet.graphs.registry module xanesnet.graphs.utils module xanesnet.graphs.utils.directional_indices module xanesnet.graphs.utils.symmetrize module xanesnet.graphs.utils.target_site_paths module xanesnet.graphs.utils.triplets module xanesnet.graphs.voronoi module xanesnet.losses module xanesnet.losses.base module xanesnet.losses.bcewithlogits module xanesnet.losses.combined module xanesnet.losses.emd module xanesnet.losses.l1 module xanesnet.losses.mse module xanesnet.losses.msssim module xanesnet.losses.registry module xanesnet.losses.specplus module xanesnet.losses.wcc module xanesnet.models.base module xanesnet.models.dimenet module xanesnet.models.dimenet.dimenet module xanesnet.models.dimenet.dimenet_pp module xanesnet.models.dimenet.resolver module xanesnet.models.e3ee module xanesnet.models.e3ee.e3ee module xanesnet.models.e3ee.layers module xanesnet.models.e3ee.layers.atom_encoder module xanesnet.models.e3ee.layers.basic module xanesnet.models.e3ee.layers.branch_attention module xanesnet.models.e3ee.layers.branch_convolution module xanesnet.models.e3ee.layers.branch_eq_attention module xanesnet.models.e3ee.layers.branch_equivariant module xanesnet.models.e3ee.layers.branch_fusion module xanesnet.models.e3ee.layers.branch_path module xanesnet.models.e3ee.layers.branch_target_site module xanesnet.models.e3ee.layers.interactions module xanesnet.models.e3ee.resolver module xanesnet.models.e3ee.utils module xanesnet.models.e3ee.utils.invariants module xanesnet.models.e3ee_full module xanesnet.models.e3ee_full.e3ee_full module xanesnet.models.e3ee_full.layers module xanesnet.models.e3ee_full.layers.atom_encoder module xanesnet.models.e3ee_full.layers.basic module xanesnet.models.e3ee_full.layers.branch_all_atom module xanesnet.models.e3ee_full.layers.branch_attention module xanesnet.models.e3ee_full.layers.branch_convolution module xanesnet.models.e3ee_full.layers.branch_eq_attention module xanesnet.models.e3ee_full.layers.branch_equivariant module xanesnet.models.e3ee_full.layers.branch_fusion module xanesnet.models.e3ee_full.layers.branch_path module xanesnet.models.e3ee_full.layers.interactions module xanesnet.models.e3ee_full.resolver module xanesnet.models.e3ee_full.utils module xanesnet.models.e3ee_full.utils.invariants module xanesnet.models.envembed module xanesnet.models.envembed.envembed module xanesnet.models.envembed.layers module xanesnet.models.envembed.layers.coeff_head module xanesnet.models.envembed.layers.encoder module xanesnet.models.envembed.resolver module xanesnet.models.gemnet.layers module xanesnet.models.gemnet.layers.basis module xanesnet.models.gemnet.layers.envelope module xanesnet.models.gemnet.layers.scaling module xanesnet.models.registry module xanesnet.serialization module xanesnet.serialization.auto_config module xanesnet.serialization.auto_config.core module xanesnet.serialization.auto_config.helpers module xanesnet.serialization.auto_config.registries module xanesnet.serialization.auto_config.statistics module xanesnet.serialization.checkpoints module xanesnet.serialization.config module xanesnet.serialization.jsonl_stream module xanesnet.serialization.metadata module xanesnet.serialization.prediction_readers module xanesnet.serialization.prediction_writers module xanesnet.serialization.runtime_contracts module xanesnet.serialization.schema_validation module xanesnet.serialization.splits module xanesnet.serialization.tensorboard module xanesnet.utils module xanesnet.utils.exceptions module xanesnet.utils.filesystem module xanesnet.utils.lightning module xanesnet.utils.logger module xanesnet.utils.math module xanesnet.utils.math.fourier module xanesnet.utils.math.gaussian module xanesnet.utils.prompts module xanesnet.utils.random module xanesnet.utils.registry module XYZSpecSource (class in xanesnet.datasources.xyzspec)

Y

y (xanesnet.datasets.torch.descriptor.DescriptorData attribute) (xanesnet.datasets.torch.descriptor_multihead.DescriptorMultiheadData attribute)

Z

ZScoreEncoding (class in xanesnet.encodings.zscore)