Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | V | Z _ __init__() (mlcolvar.core.loss.AutocorrelationLoss method) (mlcolvar.core.loss.CommittorLoss method) (mlcolvar.core.loss.ELBOGaussiansLoss method) (mlcolvar.core.loss.FisherDiscriminantLoss method) (mlcolvar.core.loss.GeneratorLoss method) (mlcolvar.core.loss.MSELoss method) (mlcolvar.core.loss.ReduceEigenvaluesLoss method) (mlcolvar.core.loss.SmartDerivatives method) (mlcolvar.core.loss.TDALoss method) (mlcolvar.core.nn.FeedForward method) (mlcolvar.core.nn.graph.BaseGNN method) (mlcolvar.core.nn.graph.GVPModel method) (mlcolvar.core.nn.graph.radial.RadialEmbeddingBlock method) (mlcolvar.core.nn.graph.SchNetModel method) (mlcolvar.core.stats.LDA method) (mlcolvar.core.stats.PCA method) (mlcolvar.core.stats.Stats method) (mlcolvar.core.stats.TICA method) (mlcolvar.core.transform.descriptors.CoordinationNumbers method) (mlcolvar.core.transform.descriptors.EigsAdjMat method) (mlcolvar.core.transform.descriptors.MultipleDescriptors method) (mlcolvar.core.transform.descriptors.PairwiseDistances method) (mlcolvar.core.transform.descriptors.TorsionalAngle method) (mlcolvar.core.transform.descriptors.TorsionalAngles method) (mlcolvar.core.transform.Normalization method) (mlcolvar.core.transform.tools.ContinuousHistogram method) (mlcolvar.core.transform.tools.Normalization method) (mlcolvar.core.transform.tools.SwitchingFunctions method) (mlcolvar.core.transform.Transform method) (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.MultiTaskCV method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictDataset method) (mlcolvar.data.DictLoader method) (mlcolvar.data.DictModule method) (mlcolvar.data.graph.AtomicNumberTable method) (mlcolvar.data.graph.Configuration method) (mlcolvar.data.graph.create_dataset_from_configurations method) (mlcolvar.data.graph.get_neighborhood method) (mlcolvar.explain.graph_sensitivity.graph_node_sensitivity method) (mlcolvar.explain.lasso.lasso_classification method) (mlcolvar.explain.lasso.lasso_regression method) (mlcolvar.explain.lasso.plot_lasso_classification method) (mlcolvar.explain.lasso.plot_lasso_regression method) (mlcolvar.explain.sensitivity.plot_sensitivity method) (mlcolvar.explain.sensitivity.sensitivity_analysis method) (mlcolvar.io.create_dataset_from_files method), [1] (mlcolvar.io.load_dataframe method), [1] (mlcolvar.utils.fes.compute_fes method) (mlcolvar.utils.plot.plot_features_distribution method) (mlcolvar.utils.plot.plot_metrics method) (mlcolvar.utils.timelagged.create_timelagged_dataset method) (mlcolvar.utils.trainer.MetricsCallback method) A AtomicNumberTable (class in mlcolvar.data.graph) AutocorrelationLoss (class in mlcolvar.core.loss) AutoEncoderCV (class in mlcolvar.cvs) B BaseCV (class in mlcolvar.cvs) BaseGNN (class in mlcolvar.core.nn.graph) batch_size (mlcolvar.data.DictLoader property) C Committor (class in mlcolvar.cvs) CommittorLoss (class in mlcolvar.core.loss) compute() (mlcolvar.core.stats.LDA method) (mlcolvar.core.stats.PCA method) (mlcolvar.core.stats.Stats method) (mlcolvar.core.stats.TICA method) compute_fes (class in mlcolvar.utils.fes) compute_scatter_matrices() (mlcolvar.core.stats.LDA method) Configuration (class in mlcolvar.data.graph) configure_model() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) configure_optimizers() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) configure_sharded_model() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) ContinuousHistogram (class in mlcolvar.core.transform.tools) CoordinationNumbers (class in mlcolvar.core.transform.descriptors) cpu() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) create_dataset_from_configurations (class in mlcolvar.data.graph) create_dataset_from_files (class in mlcolvar.io), [1] create_timelagged_dataset (class in mlcolvar.utils.timelagged) cuda() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) cumulative_explained_variance (mlcolvar.core.stats.PCA property) D dataset (mlcolvar.data.DictLoader property) dataset_len (mlcolvar.data.DictLoader property) DeepLDA (class in mlcolvar.cvs) DeepTDA (class in mlcolvar.cvs) DeepTICA (class in mlcolvar.cvs) device (mlcolvar.core.transform.descriptors.MultipleDescriptors property) DictDataset (class in mlcolvar.data) DictLoader (class in mlcolvar.data) DictModule (class in mlcolvar.data) double() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) E EigsAdjMat (class in mlcolvar.core.transform.descriptors) ELBOGaussiansLoss (class in mlcolvar.core.loss) embed_edge() (mlcolvar.core.nn.graph.BaseGNN method) (mlcolvar.core.nn.graph.GVPModel method) (mlcolvar.core.nn.graph.SchNetModel method) encode_decode() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) example_input_array (mlcolvar.cvs.AutoEncoderCV property) (mlcolvar.cvs.BaseCV property) (mlcolvar.cvs.Committor property) (mlcolvar.cvs.DeepLDA property) (mlcolvar.cvs.DeepTDA property) (mlcolvar.cvs.DeepTICA property) (mlcolvar.cvs.RegressionCV property) (mlcolvar.cvs.VariationalAutoEncoderCV property) explained_variance (mlcolvar.core.stats.PCA property) extra_repr() (mlcolvar.core.stats.LDA method) (mlcolvar.core.stats.PCA method) (mlcolvar.core.stats.TICA method) (mlcolvar.core.transform.Normalization method) (mlcolvar.core.transform.tools.Normalization method) F feature_names (mlcolvar.data.DictDataset property) FeedForward (class in mlcolvar.core.nn) FisherDiscriminantLoss (class in mlcolvar.core.loss) float() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) forward() (mlcolvar.core.loss.AutocorrelationLoss method) (mlcolvar.core.loss.CommittorLoss method) (mlcolvar.core.loss.ELBOGaussiansLoss method) (mlcolvar.core.loss.FisherDiscriminantLoss method) (mlcolvar.core.loss.GeneratorLoss method) (mlcolvar.core.loss.MSELoss method) (mlcolvar.core.loss.ReduceEigenvaluesLoss method) (mlcolvar.core.loss.SmartDerivatives method) (mlcolvar.core.loss.TDALoss method) (mlcolvar.core.nn.FeedForward method) (mlcolvar.core.nn.graph.GVPModel method) (mlcolvar.core.nn.graph.radial.RadialEmbeddingBlock method) (mlcolvar.core.nn.graph.SchNetModel method) (mlcolvar.core.stats.LDA method) (mlcolvar.core.stats.PCA method) (mlcolvar.core.stats.Stats method) (mlcolvar.core.stats.TICA method) (mlcolvar.core.transform.descriptors.CoordinationNumbers method) (mlcolvar.core.transform.descriptors.EigsAdjMat method) (mlcolvar.core.transform.descriptors.MultipleDescriptors method) (mlcolvar.core.transform.descriptors.PairwiseDistances method) (mlcolvar.core.transform.descriptors.TorsionalAngles method) (mlcolvar.core.transform.Normalization method) (mlcolvar.core.transform.tools.ContinuousHistogram method) (mlcolvar.core.transform.tools.Normalization method) (mlcolvar.core.transform.tools.SwitchingFunctions method) (mlcolvar.core.transform.Transform method) (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) forward_cv() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) from_datasets() (mlcolvar.data.DictModule class method) from_zs() (mlcolvar.data.graph.AtomicNumberTable class method) G GeneratorLoss (class in mlcolvar.core.loss) get_decoder() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) get_graph_inputs() (mlcolvar.data.DictDataset method) (mlcolvar.data.DictModule method) get_neighborhood (class in mlcolvar.data.graph) get_stats() (mlcolvar.data.DictDataset method) (mlcolvar.data.DictLoader method) graph_node_sensitivity (class in mlcolvar.explain.graph_sensitivity) GVPModel (class in mlcolvar.core.nn.graph) H half() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) hparams (mlcolvar.cvs.AutoEncoderCV property) (mlcolvar.cvs.BaseCV property) (mlcolvar.cvs.Committor property) (mlcolvar.cvs.DeepLDA property) (mlcolvar.cvs.DeepTDA property) (mlcolvar.cvs.DeepTICA property) (mlcolvar.cvs.RegressionCV property) (mlcolvar.cvs.VariationalAutoEncoderCV property) (mlcolvar.data.DictModule property) hparams_initial (mlcolvar.cvs.AutoEncoderCV property) (mlcolvar.cvs.BaseCV property) (mlcolvar.cvs.Committor property) (mlcolvar.cvs.DeepLDA property) (mlcolvar.cvs.DeepTDA property) (mlcolvar.cvs.DeepTICA property) (mlcolvar.cvs.RegressionCV property) (mlcolvar.cvs.VariationalAutoEncoderCV property) (mlcolvar.data.DictModule property) I index_to_symbol() (mlcolvar.data.graph.AtomicNumberTable method) index_to_z() (mlcolvar.data.graph.AtomicNumberTable method) initialize_blocks() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) inverse() (mlcolvar.core.transform.Normalization method) (mlcolvar.core.transform.tools.Normalization method) K keys (mlcolvar.data.DictLoader property) L lasso_classification (class in mlcolvar.explain.lasso) lasso_regression (class in mlcolvar.explain.lasso) LDA (class in mlcolvar.core.stats) load_dataframe (class in mlcolvar.io), [1] load_from_checkpoint() (mlcolvar.data.DictModule method) load_state_dict() (mlcolvar.data.DictModule method) (mlcolvar.utils.trainer.MetricsCallback method) M MetricsCallback (class in mlcolvar.utils.trainer) move_to_cpu() (mlcolvar.core.loss.SmartDerivatives method) MSELoss (class in mlcolvar.core.loss) MultipleDescriptors (class in mlcolvar.core.transform.descriptors) MultiTaskCV (class in mlcolvar.cvs) N n_cvs (mlcolvar.cvs.AutoEncoderCV property) (mlcolvar.cvs.BaseCV property) (mlcolvar.cvs.Committor property) (mlcolvar.cvs.DeepLDA property) (mlcolvar.cvs.DeepTDA property) (mlcolvar.cvs.DeepTICA property) (mlcolvar.cvs.RegressionCV property) (mlcolvar.cvs.VariationalAutoEncoderCV property) Normalization (class in mlcolvar.core.transform) (class in mlcolvar.core.transform.tools) O on_after_backward() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_after_batch_transfer() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) on_before_backward() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_before_batch_transfer() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) on_before_optimizer_step() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_before_zero_grad() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_exception() (mlcolvar.data.DictModule method) (mlcolvar.utils.trainer.MetricsCallback method) on_fit_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_fit_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_load_checkpoint() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_predict_batch_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_predict_batch_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_predict_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_predict_epoch_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_predict_epoch_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_predict_model_eval() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) on_predict_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_sanity_check_end() (mlcolvar.utils.trainer.MetricsCallback method) on_sanity_check_start() (mlcolvar.utils.trainer.MetricsCallback method) on_save_checkpoint() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_test_batch_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_test_batch_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_test_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_test_epoch_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_test_epoch_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_test_model_eval() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) on_test_model_train() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) on_test_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_train_batch_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_train_batch_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_train_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_train_epoch_end() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_train_epoch_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_train_start() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.utils.trainer.MetricsCallback method) on_validation_batch_end() 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(mlcolvar.cvs.BaseCV property) (mlcolvar.cvs.Committor property) (mlcolvar.cvs.DeepLDA property) (mlcolvar.cvs.DeepTDA property) (mlcolvar.cvs.DeepTICA property) (mlcolvar.cvs.RegressionCV property) (mlcolvar.cvs.VariationalAutoEncoderCV property) P PairwiseDistances (class in mlcolvar.core.transform.descriptors) parse_options() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) PCA (class in mlcolvar.core.stats) plot_features_distribution (class in mlcolvar.utils.plot) plot_lasso_classification (class in mlcolvar.explain.lasso) plot_lasso_regression (class in mlcolvar.explain.lasso) plot_metrics (class in mlcolvar.utils.plot) plot_sensitivity (class in mlcolvar.explain.sensitivity) pooling() (mlcolvar.core.nn.graph.BaseGNN method) (mlcolvar.core.nn.graph.GVPModel 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(mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) reset_parameters() (mlcolvar.core.nn.graph.SchNetModel method) S save_hyperparameters() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) SchNetModel (class in mlcolvar.core.nn.graph) sensitivity_analysis (class in mlcolvar.explain.sensitivity) set_custom() (mlcolvar.core.transform.Normalization method) (mlcolvar.core.transform.tools.Normalization method) set_dataset_and_batch_size() (mlcolvar.data.DictLoader method) set_from_stats() (mlcolvar.core.transform.Normalization method) 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(mlcolvar.core.transform.tools.SwitchingFunctions method) (mlcolvar.core.transform.Transform method) SmartDerivatives (class in mlcolvar.core.loss) state_dict() (mlcolvar.data.DictModule method) (mlcolvar.utils.trainer.MetricsCallback method) state_key (mlcolvar.utils.trainer.MetricsCallback property) Stats (class in mlcolvar.core.stats) SwitchingFunctions (class in mlcolvar.core.transform.tools) T TDALoss (class in mlcolvar.core.loss) teardown() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) (mlcolvar.utils.trainer.MetricsCallback method) test_dataloader() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA 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(mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) Transform (class in mlcolvar.core.transform) type() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) V val_dataloader() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) (mlcolvar.data.DictModule method) validation_step() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.BaseCV method) (mlcolvar.cvs.Committor method) (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTDA method) (mlcolvar.cvs.DeepTICA method) (mlcolvar.cvs.RegressionCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) VariationalAutoEncoderCV (class in mlcolvar.cvs) Z z_to_index() (mlcolvar.data.graph.AtomicNumberTable method) zs_to_indices() (mlcolvar.data.graph.AtomicNumberTable method)