Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | V _ __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.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.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.utils.fes.compute_fes method) (mlcolvar.utils.io.create_dataset_from_files method) (mlcolvar.utils.io.load_dataframe 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 AutocorrelationLoss (class in mlcolvar.core.loss) AutoEncoderCV (class in mlcolvar.cvs) B BaseCV (class in mlcolvar.cvs) 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) configure_model() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_files (class in mlcolvar.utils.io) create_timelagged_dataset (class in mlcolvar.utils.timelagged) cuda() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) encode_decode() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) example_input_array (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.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) G GeneratorLoss (class in mlcolvar.core.loss) get_decoder() (mlcolvar.cvs.AutoEncoderCV method) (mlcolvar.cvs.VariationalAutoEncoderCV method) get_stats() (mlcolvar.data.DictDataset method) (mlcolvar.data.DictLoader method) H half() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward property) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward property) (mlcolvar.cvs.AutoEncoderCV 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 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.utils.io) 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_start() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_end() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_epoch_end() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_epoch_start() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_model_eval() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_validation_model_train() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_validation_model_zero_grad() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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_validation_start() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) optimizer_name (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) 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) predict_dataloader() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) prepare_data() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) R ReduceEigenvaluesLoss (class in mlcolvar.core.loss) RegressionCV (class in mlcolvar.cvs) regularization_lorentzian() (mlcolvar.cvs.DeepLDA method) remove_ignored_hparams() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) S save_hyperparameters() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) 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) (mlcolvar.core.transform.tools.Normalization method) set_regularization() (mlcolvar.cvs.DeepLDA method) (mlcolvar.cvs.DeepTICA method) setup() (mlcolvar.core.loss.SmartDerivatives method) (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) setup_from_datamodule() (mlcolvar.core.transform.descriptors.CoordinationNumbers method) (mlcolvar.core.transform.descriptors.EigsAdjMat 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) 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) test_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) TICA (class in mlcolvar.core.stats) timescales() (mlcolvar.core.stats.TICA method) to() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) TorsionalAngle (class in mlcolvar.core.transform.descriptors) TorsionalAngles (class in mlcolvar.core.transform.descriptors) train_dataloader() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) training_step() (mlcolvar.cvs.AutoEncoderCV 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) transfer_batch_to_device() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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) Transform (class in mlcolvar.core.transform) type() (mlcolvar.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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.core.nn.FeedForward method) (mlcolvar.cvs.AutoEncoderCV 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)