Index

_

__add__() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] (encodermap.trajinfo.info_single.SingleTraj method), [1] __enter__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __eq__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __exit__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __getattr__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __getitem__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __init__() (encodermap.ADCParameters method) (encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.Autoencoder method) (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1] (encodermap.callbacks.callbacks.EarlyStop method) (encodermap.callbacks.callbacks.IncreaseCartesianCost method) (encodermap.callbacks.callbacks.TensorboardWriteBool method) (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.encodermap_tf1.autoencoder.Autoencoder method) (encodermap.encodermap_tf1.moldata.MolData method) (encodermap.encodermap_tf1.plot.ManualPath method) (encodermap.encodermap_tf1.plot.PathGenerateCartesians method) (encodermap.encodermap_tf1.plot.PathGenerateDihedrals method) (encodermap.encodermap_tf1.plot.PathSelect method) (encodermap.EncoderMapBaseCallback method) (encodermap.InteractivePlotting method) (encodermap.loading.features.AllCartesians method), [1] (encodermap.loading.features.CentralDihedrals method), [1] (encodermap.models.layers.BackMapLayer method), [1] (encodermap.models.layers.MeanAngles method), [1] (encodermap.models.layers.PairwiseDistances method) (encodermap.models.layers.PeriodicInput method), [1] (encodermap.models.layers.PeriodicOutput method), [1] (encodermap.MolData method) (encodermap.moldata.moldata.NewMolData method) (encodermap.Parameters method) (encodermap.parameters.parameters.ADCParameters method), [1] (encodermap.parameters.parameters.Parameters method), [1] (encodermap.plot.interactive_plotting.InteractivePlotting method) (encodermap.plot.utils.BezierBuilder method) (encodermap.plot.utils.Props method) (encodermap.Repository method) (encodermap.trajinfo.info_all.TrajEnsemble method), [1] (encodermap.trajinfo.info_single.SingleTraj method), [1] (encodermap.trajinfo.repository.Repository method) __iter__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __reversed__() (encodermap.trajinfo.info_single.SingleTraj method), [1] __serialize_fields (encodermap.loading.features.AllBondDistances attribute), [1] (encodermap.loading.features.AllCartesians attribute), [1] (encodermap.loading.features.CentralAngles attribute), [1] (encodermap.loading.features.CentralBondDistances attribute), [1] (encodermap.loading.features.CentralCartesians attribute), [1] (encodermap.loading.features.CentralDihedrals attribute), [1] (encodermap.loading.features.SideChainAngles attribute), [1] (encodermap.loading.features.SideChainBondDistances attribute), [1] (encodermap.loading.features.SideChainCartesians attribute), [1] (encodermap.loading.features.SideChainDihedrals attribute), [1] __serialize_version (encodermap.loading.features.AllBondDistances attribute), [1] (encodermap.loading.features.AllCartesians attribute), [1] (encodermap.loading.features.CentralAngles attribute), [1] (encodermap.loading.features.CentralBondDistances attribute), [1] (encodermap.loading.features.CentralCartesians attribute), [1] (encodermap.loading.features.CentralDihedrals attribute), [1] (encodermap.loading.features.SideChainAngles attribute), [1] (encodermap.loading.features.SideChainBondDistances attribute), [1] (encodermap.loading.features.SideChainCartesians attribute), [1] (encodermap.loading.features.SideChainDihedrals attribute), [1] _add_along_traj() (encodermap.trajinfo.info_single.SingleTraj method), [1] _add_point_interp() (encodermap.encodermap_tf1.plot.ManualPath method) _angle_cost() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) _auto_cost() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _build_bezier() (encodermap.plot.utils.BezierBuilder method) _can_be_feature() (in module encodermap.misc.misc) (in module encodermap.trajinfo.info_all) _cartesian_cost() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) _cartesian_distance_cost() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) _center_cost() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _check_all_templates_defined() (in module encodermap.plot.utils) _conclude() (encodermap.encodermap_tf1.moldata.Angles method) (encodermap.encodermap_tf1.moldata.Positions method) _create_readme() (in module encodermap.plot.utils) _CVs (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] _datetime_windows_and_linux_compatible() (in module encodermap.misc.misc) (in module encodermap.parameters.parameters) (in module encodermap.trajinfo.info_all)

_dihedral() (in module encodermap.misc.backmapping) _dihedral_cost() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) _displacement() (in module encodermap.misc.backmapping) _distance_cost() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.encodermap_tf1.encodermap.EncoderMap method) _do_nothing() (in module encodermap.loss_functions.loss_functions), [1] _encode() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _expand_universe() (in module encodermap.encodermap_tf1.backmapping) _flatten_model() (in module encodermap.misc.misc) _free_draw() (encodermap.encodermap_tf1.plot.ManualPath method) _free_draw_callback() (encodermap.encodermap_tf1.plot.ManualPath method) _gen_dummy_traj_single() (in module encodermap.misc.clustering) _gen_ensemble() (encodermap.trajinfo.info_single.SingleTraj method), [1] _gen_hist() (in module encodermap.misc.summaries) _gen_nan_image() (in module encodermap.misc.summaries) _gen_scatter() (in module encodermap.misc.summaries) _generate() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _get_connection() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) _get_far_and_near_networkx() (in module encodermap.misc.backmapping) _get_scheduler() (in module encodermap.misc.xarray_save_wrong_hdf5) _get_system_info() (in module encodermap.plot.utils) _grab_background() (encodermap.encodermap_tf1.plot.ManualPath method) _import_module() (in module encodermap.misc.transformations) _interpolate() (encodermap.encodermap_tf1.plot.ManualPath method) _l2_reg_cost() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _load_traj() (in module encodermap.trajinfo.info_single) (in module encodermap.trajinfo.load_traj) _load_traj_and_top() (in module encodermap.trajinfo.load_traj) _match_tops_and_trajs() (in module encodermap.plot.utils) _mdtraj_attr (encodermap.trajinfo.info_single.SingleTraj attribute), [1] _n_frames_base_h5_file (encodermap.trajinfo.info_single.SingleTraj property), [1] _on_click() (encodermap.encodermap_tf1.plot.ManualPath method) _on_key() (encodermap.encodermap_tf1.plot.ManualPath method) _on_select_rotation() (encodermap.plot.utils.ModeButton method) _optional_import() (in module encodermap._optional_imports) _original_frame_indices (encodermap.trajinfo.info_single.SingleTraj property), [1] _prepare() (encodermap.encodermap_tf1.moldata.Angles method) (encodermap.encodermap_tf1.moldata.Positions method) _prepare_data() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _pyemma_indexing() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] _random_batch() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _reset_lines() (encodermap.encodermap_tf1.plot.ManualPath method) _return_trajs_by_index() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] _set_dihedral() (in module encodermap.encodermap_tf1.backmapping) _setattr() (encodermap.plot.utils.Props method) _setattrs() (encodermap.encodermap_tf1.parameters.ParametersFramework method) _setup_callbacks() (encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.Autoencoder method) (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1] _setup_cost() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.encodermap_tf1.autoencoder.Autoencoder method) (encodermap.encodermap_tf1.encodermap.EncoderMap method) _setup_data_iterator() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _setup_network() (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMapDummy method) (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _single_frame() (encodermap.encodermap_tf1.moldata.Angles method) (encodermap.encodermap_tf1.moldata.Positions method) _split_proj_filetype() (encodermap.Repository static method) (encodermap.trajinfo.repository.Repository static method) _step() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) _string_summary() (encodermap.plot.utils.Props method) (encodermap.plot.utils.SelectFromCollection method) (encodermap.trajinfo.info_all.TrajEnsemble method), [1] (encodermap.trajinfo.info_single.SingleTraj method), [1] _summary_cost() (in module encodermap.loss_functions.loss_functions), [1] _to_netcdf() (in module encodermap.misc.xarray_save_wrong_hdf5) _traj (encodermap.trajinfo.info_single.SingleTraj property), [1] _unpack_cluster_info() (in module encodermap.plot.utils) _unpack_path_info() (in module encodermap.plot.utils) _update_bernstein() (encodermap.plot.utils.BezierBuilder method) _update_bezier() (encodermap.plot.utils.BezierBuilder method) _update_interp() (encodermap.encodermap_tf1.plot.ManualPath method) _update_lines() (encodermap.encodermap_tf1.plot.ManualPath method) _validate_attrs() (in module encodermap.misc.xarray_save_wrong_hdf5) _validate_dataset_names() (in module encodermap.misc.xarray_save_wrong_hdf5) _validate_uri() (encodermap.trajinfo.info_single.SingleTraj method), [1] (in module encodermap.loading.featurizer) (in module encodermap.misc.misc) (in module encodermap.misc.xarray) (in module encodermap.trajinfo.load_traj) _zoomingBoxManual() (in module encodermap.plot.plotting)

A

abc_to_rgb() (in module encodermap.plot.utils) accept() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) activation_functions (encodermap.ADCParameters attribute) (encodermap.Parameters attribute), [1] (encodermap.parameters.parameters.ADCParameters attribute), [1] (encodermap.parameters.parameters.Parameters attribute), [1], [2], [3] ADCParameters (class in encodermap) (class in encodermap.encodermap_tf1.parameters) (class in encodermap.parameters.parameters), [1] ADCSequentialModel (class in encodermap.models.models) add_images_to_tensorboard() (encodermap.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1], [2], [3] add_items() (encodermap.plot.utils.Menu method) (encodermap.plot.utils.StatusMenu method) add_KAC_backbone_bonds() (in module encodermap.loading.features) add_KAC_sidechain_bonds() (in module encodermap.loading.features) add_layer_summaries() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.summaries) AllBondDistances (class in encodermap.loading.features), [1] AllCartesians (class in encodermap.loading.features), [1] alpha (encodermap.plot.utils.Props attribute) analysis_path (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1]

angle_cost_reference (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] angle_cost_scale (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] angle_cost_variant (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] angle_loss() (in module encodermap.loss_functions.loss_functions), [1] AngleDihedralCartesianEncoderMap (class in encodermap) (class in encodermap.autoencoder.autoencoder), [1] (class in encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap) AngleDihedralCartesianEncoderMapDummy (class in encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap) Angles (class in encodermap.encodermap_tf1.moldata) atom_slice() (encodermap.trajinfo.info_single.SingleTraj method), [1] atoms (encodermap.trajinfo.info_single.SingleTraj attribute), [1] auto_cost_scale (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] auto_cost_variant (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] auto_loss() (in module encodermap.loss_functions.loss_functions), [1] Autoencoder (class in encodermap) (class in encodermap.autoencoder.autoencoder), [1] (class in encodermap.encodermap_tf1.autoencoder) ax (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute)

B

backbone_hydrogen_oxygen_crossproduct() (in module encodermap.misc.backmapping) backend (encodermap.trajinfo.info_single.SingleTraj attribute), [1] BackMapLayer (class in encodermap.models.layers), [1] BadError basename (encodermap.trajinfo.info_single.SingleTraj property), [1] basenames (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] basic_loss_combinator() (in module encodermap.loss_functions.loss_functions) batch_size (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] batched (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1]

Bernstein() (in module encodermap.plot.utils) bezier() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) Bezier() (in module encodermap.plot.utils) BezierBuilder (class in encodermap.plot.utils) bgcolor (encodermap.plot.utils.Props attribute) bgcolor_rgb (encodermap.plot.utils.Props attribute) (encodermap.plot.utils.Props property) bonds (encodermap.trajinfo.info_single.SingleTraj attribute), [1] build() (encodermap.models.models.SequentialModel method)

C

calc_current_cartesian_cost_scale() (encodermap.callbacks.callbacks.IncreaseCartesianCost method) calculate_dssps() (in module encodermap.plot.utils) call() (encodermap.models.layers.BackMapLayer method), [1] (encodermap.models.layers.MeanAngles method), [1] (encodermap.models.layers.PairwiseDistances method) (encodermap.models.layers.PeriodicInput method), [1] (encodermap.models.layers.PeriodicOutput method), [1] (encodermap.models.layers.Sparse method), [1] (encodermap.models.layers.SparseReshape method) (encodermap.models.models.ADCSequentialModel method) (encodermap.models.models.SequentialModel method) (encodermap.models.models.Sparse method) (encodermap.models.models.SparseModel method) call_and_map_back() (encodermap.models.models.ADCSequentialModel method) callbacks (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] cartesian_cost_reference (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_cost_scale (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_cost_scale_soft_start (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_cost_variant (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_dist_sig_parameters (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_distance_cost_scale (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_distance_loss() (in module encodermap.loss_functions.loss_functions), [1] cartesian_loss() (in module encodermap.loss_functions.loss_functions), [1] cartesian_pwd_start (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_pwd_step (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] cartesian_pwd_stop (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1]

catalogue (encodermap.Repository property) (encodermap.trajinfo.repository.Repository property) center_cost_scale (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] center_loss() (in module encodermap.loss_functions.loss_functions), [1] CentralAngles (class in encodermap.loading.features), [1] CentralBondDistances (class in encodermap.loading.features), [1] CentralCartesians (class in encodermap.loading.features), [1] CentralDihedrals (class in encodermap.loading.features), [1] chain_in_plane() (in module encodermap.encodermap_tf1.backmapping) chains (encodermap.trajinfo.info_single.SingleTraj attribute), [1] check_select() (encodermap.plot.utils.MenuItem method) (encodermap.plot.utils.ModeButton method) checkpoint_step (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] CheckpointSaver (class in encodermap.callbacks.callbacks) close() (encodermap.Autoencoder method) (encodermap.autoencoder.autoencoder.Autoencoder method), [1] (encodermap.encodermap_tf1.autoencoder.Autoencoder method) cluster_zoomed (encodermap.InteractivePlotting property) (encodermap.plot.interactive_plotting.InteractivePlotting property) common_str (encodermap.trajinfo.info_single.SingleTraj attribute), [1] compile() (encodermap.models.models.FunctionalModel method) (encodermap.models.models.SequentialModel method) construct_xarray_from_numpy() (in module encodermap.misc.xarray) correct_missing_uniques() (in module encodermap.plot.utils) create_dir() (in module encodermap.encodermap_tf1.misc) create_n_cube() (in module encodermap.misc.misc) current_path (encodermap.Repository attribute) (encodermap.trajinfo.repository.Repository attribute) CVs (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] CVs_in_file (encodermap.trajinfo.info_all.TrajEnsemble property), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1]

D

dask_transform (encodermap.loading.features.CentralDihedrals property), [1] data (encodermap.Repository attribute) (encodermap.trajinfo.repository.Repository attribute) dataset (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] datasets (encodermap.Repository property) (encodermap.trajinfo.repository.Repository property) decode() (encodermap.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1], [2], [3] decoder (encodermap.Autoencoder attribute) (encodermap.Autoencoder property) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] (encodermap.autoencoder.autoencoder.Autoencoder property), [1] decoder() (encodermap.models.models.FunctionalModel method) (encodermap.models.models.SequentialModel method) defaults (encodermap.ADCParameters attribute) (encodermap.Parameters attribute), [1] (encodermap.parameters.parameters.ADCParameters attribute), [1] (encodermap.parameters.parameters.Parameters attribute), [1], [2], [3] (encodermap.plot.utils.Props attribute), [1] defaults_description() (encodermap.ADCParameters class method) (encodermap.Parameters class method) (encodermap.parameters.parameters.ADCParameters class method), [1] (encodermap.parameters.parameters.Parameters class method), [1] describe() (encodermap.loading.features.AllBondDistances method), [1] (encodermap.loading.features.AllCartesians method), [1] (encodermap.loading.features.CentralAngles method), [1] (encodermap.loading.features.CentralCartesians method), [1] (encodermap.loading.features.CentralDihedrals method), [1] (encodermap.loading.features.SideChainAngles method), [1] (encodermap.loading.features.SideChainDihedrals method), [1]

describe_last_feats() (in module encodermap.loading.features) digitize_dssp() (in module encodermap.plot.utils) dihedral_backmapping() (in module encodermap.encodermap_tf1.backmapping) dihedral_cost_reference (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] dihedral_cost_scale (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] dihedral_cost_variant (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] dihedral_loss() (in module encodermap.loss_functions.loss_functions), [1] dihedral_to_cartesian_tf_one_way() (in module encodermap.encodermap_tf1.backmapping) DihedralEncoderMap (class in encodermap.autoencoder.autoencoder) dihedrals_to_cartesian_tf() (in module encodermap.encodermap_tf1.backmapping) dihedrals_to_cartesian_tf_old() (in module encodermap.encodermap_tf1.backmapping) disconnect() (encodermap.plot.utils.BezierBuilder method) (encodermap.plot.utils.DummyTool method) (encodermap.plot.utils.SelectFromCollection method) dist_sig_parameters (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] distance_cost() (in module encodermap.encodermap_tf1.misc) distance_cost_scale (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] distance_histogram() (in module encodermap.encodermap_tf1.plot) (in module encodermap.plot.plotting) distance_loss() (in module encodermap.loss_functions.loss_functions), [1] draw() (encodermap.plot.utils.MenuItem method) DummyTool (class in encodermap.plot.utils)

E

EarlyStop (class in encodermap.callbacks.callbacks) ellipse() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) encode() (encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1], [2], [3] (encodermap.encodermap_tf1.autoencoder.Autoencoder method) encoder (encodermap.Autoencoder attribute) (encodermap.Autoencoder property) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] (encodermap.autoencoder.autoencoder.Autoencoder property), [1] encoder() (encodermap.models.models.FunctionalModel method) (encodermap.models.models.SequentialModel method) encodermap module EncoderMap (class in encodermap) (class in encodermap.autoencoder.autoencoder), [1] (class in encodermap.encodermap_tf1.encodermap) encodermap._optional_imports module encodermap._typing module encodermap._version module encodermap.autoencoder module encodermap.autoencoder.autoencoder module encodermap.callbacks module encodermap.callbacks.callbacks module encodermap.callbacks.metrics module encodermap.encodermap_tf1 module encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap module encodermap.encodermap_tf1.autoencoder module encodermap.encodermap_tf1.backmapping module encodermap.encodermap_tf1.encodermap module encodermap.encodermap_tf1.misc module encodermap.encodermap_tf1.moldata module encodermap.encodermap_tf1.parameters module encodermap.encodermap_tf1.plot module encodermap.loading module encodermap.loading.features module, [1] encodermap.loading.featurizer module encodermap.loading.pipeline module encodermap.loading.utils module encodermap.loss_functions module

encodermap.loss_functions.loss_functions module, [1] encodermap.misc module encodermap.misc.backmapping module encodermap.misc.clustering module encodermap.misc.distances module encodermap.misc.errors module encodermap.misc.function_def module encodermap.misc.misc module encodermap.misc.saving_loading_models module encodermap.misc.summaries module encodermap.misc.transformations module encodermap.misc.xarray module encodermap.misc.xarray_save_wrong_hdf5 module encodermap.models module encodermap.models.layers module, [1] encodermap.models.models module, [1] encodermap.moldata module encodermap.moldata.moldata module encodermap.parameters module encodermap.parameters.parameters module encodermap.plot module encodermap.plot.interactive_plotting module encodermap.plot.jinja_template module encodermap.plot.plotting module encodermap.plot.utils module encodermap.trajinfo module encodermap.trajinfo.hash_files module encodermap.trajinfo.info_all module encodermap.trajinfo.info_single module encodermap.trajinfo.load_traj module encodermap.trajinfo.repository module encodermap.trajinfo.trajinfo_utils module EncoderMapBaseCallback (class in encodermap) extension (encodermap.trajinfo.info_single.SingleTraj property), [1]

F

Featurizer (class in encodermap) (class in encodermap.loading.featurizer) fetch() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) fig (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) files (encodermap.Repository attribute) (encodermap.trajinfo.repository.Repository attribute) files_dict (encodermap.Repository attribute) (encodermap.trajinfo.repository.Repository attribute) fontsize (encodermap.plot.utils.Props attribute) frames (encodermap.trajinfo.info_all.TrajEnsemble property), [1] from_checkpoint() (encodermap.AngleDihedralCartesianEncoderMap class method) (encodermap.Autoencoder class method) (encodermap.Autoencoder method) (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap class method), [1] (encodermap.autoencoder.autoencoder.Autoencoder class method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.EncoderMap class method), [1] (encodermap.EncoderMap class method)

from_pdb_id() (encodermap.trajinfo.info_single.SingleTraj class method), [1] from_textfile() (encodermap.trajinfo.info_all.TrajEnsemble class method), [1] from_xarray() (encodermap.trajinfo.info_all.TrajEnsemble class method), [1] function() (in module encodermap) (in module encodermap.misc.function_def) FunctionalModel (class in encodermap.models.models)

G

gen_dummy_traj() (in module encodermap.misc.clustering) gen_functional_model() (in module encodermap.models.models), [1] gen_sequential_model() (in module encodermap.models.models), [1] generate() (encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1], [2], [3] (encodermap.autoencoder.autoencoder.DihedralEncoderMap method) (encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.encodermap_tf1.autoencoder.Autoencoder method) generic_describe() (encodermap.loading.features.AllBondDistances method), [1] (encodermap.loading.features.CentralAngles method), [1] (encodermap.loading.features.CentralCartesians method), [1] (encodermap.loading.features.CentralDihedrals method), [1] (encodermap.loading.features.SideChainDihedrals method), [1]

get_cluster_frames() (in module encodermap.misc.clustering) get_coords() (encodermap.plot.utils.Menu method) get_full_common_str_and_ref() (in module encodermap.misc.misc) get_loss() (encodermap.models.models.FunctionalModel method) (encodermap.models.models.SparseFunctionalModel method) get_single_frame() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] (encodermap.trajinfo.info_single.SingleTraj method), [1] get_sizes() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) get_train_data_from_trajs() (encodermap.AngleDihedralCartesianEncoderMap static method) (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap static method), [1] gpu_memory_fraction (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] guess_amide_H() (in module encodermap.encodermap_tf1.backmapping) guess_amide_O() (in module encodermap.encodermap_tf1.backmapping) guess_sp2_atom() (in module encodermap.encodermap_tf1.backmapping)

H

hash_files() (in module encodermap.trajinfo.hash_files)

I

id (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] image_summary() (in module encodermap.misc.summaries) IncreaseCartesianCost (class in encodermap.callbacks.callbacks) ind (encodermap.plot.utils.BezierBuilder property) index (encodermap.trajinfo.info_single.SingleTraj attribute), [1] index_arr (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] indexes (encodermap.loading.features.AllBondDistances attribute), [1] (encodermap.loading.features.AllBondDistances property), [1] (encodermap.loading.features.AllCartesians attribute), [1] (encodermap.loading.features.CentralAngles attribute), [1] (encodermap.loading.features.CentralAngles property), [1] (encodermap.loading.features.CentralBondDistances attribute), [1] (encodermap.loading.features.CentralBondDistances property), [1] (encodermap.loading.features.CentralCartesians attribute), [1] (encodermap.loading.features.CentralDihedrals attribute), [1] (encodermap.loading.features.CentralDihedrals property), [1] (encodermap.loading.features.SideChainAngles attribute), [1] (encodermap.loading.features.SideChainAngles property), [1] (encodermap.loading.features.SideChainBondDistances attribute), [1] (encodermap.loading.features.SideChainBondDistances property), [1] (encodermap.loading.features.SideChainCartesians attribute), [1] (encodermap.loading.features.SideChainDihedrals attribute), [1] (encodermap.loading.features.SideChainDihedrals property), [1]

InteractivePlotting (class in encodermap) (class in encodermap.plot.interactive_plotting) iterframes() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] itertrajs() (encodermap.trajinfo.info_all.TrajEnsemble method), [1]

J

join() (encodermap.trajinfo.info_single.SingleTraj method), [1]

L

l2_reg_constant (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] labelcolor (encodermap.plot.utils.Props attribute) labelcolor_rgb (encodermap.plot.utils.Props attribute) (encodermap.plot.utils.Props property) lasso() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) learning_rate (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] load() (encodermap.encodermap_tf1.parameters.ParametersFramework class method) (in module encodermap) load_CV() (encodermap.trajinfo.info_single.SingleTraj method), [1] load_CVs() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] load_CVs_ensembletraj() (in module encodermap.trajinfo.trajinfo_utils) load_CVs_singletraj() (in module encodermap.trajinfo.trajinfo_utils) load_list_of_models() (in module encodermap.misc.saving_loading_models) load_model() (in module encodermap.misc.saving_loading_models)

load_project() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) load_traj() (encodermap.trajinfo.info_single.SingleTraj method), [1] load_trajs() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] locations (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] lookup() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) loss (encodermap.AngleDihedralCartesianEncoderMap property) (encodermap.Autoencoder property) (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap property), [1] (encodermap.autoencoder.autoencoder.Autoencoder property), [1] (encodermap.autoencoder.autoencoder.EncoderMap property), [1] (encodermap.EncoderMap property) (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] loss_combinator() (in module encodermap.loss_functions.loss_functions), [1]

M

main_path (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] maintainer (encodermap.Repository attribute) (encodermap.trajinfo.repository.Repository attribute) ManualPath (class in encodermap.encodermap_tf1.plot) MeanAngles (class in encodermap.models.layers), [1] Menu (class in encodermap.plot.utils) menu (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) menu_ax (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) MenuItem (class in encodermap.plot.utils) merge_cartesians() (in module encodermap.encodermap_tf1.backmapping) metrics (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] mode (encodermap.InteractivePlotting attribute) (encodermap.InteractivePlotting property) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting property) ModeButton (class in encodermap.plot.utils) model (encodermap.Autoencoder property) (encodermap.autoencoder.autoencoder.Autoencoder property), [1] model_api (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] model_sort_key() (in module encodermap.misc.saving_loading_models) module encodermap encodermap._optional_imports encodermap._typing encodermap._version encodermap.autoencoder encodermap.autoencoder.autoencoder encodermap.callbacks encodermap.callbacks.callbacks encodermap.callbacks.metrics encodermap.encodermap_tf1 encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap encodermap.encodermap_tf1.autoencoder encodermap.encodermap_tf1.backmapping encodermap.encodermap_tf1.encodermap encodermap.encodermap_tf1.misc encodermap.encodermap_tf1.moldata encodermap.encodermap_tf1.parameters encodermap.encodermap_tf1.plot encodermap.loading encodermap.loading.features, [1] encodermap.loading.featurizer encodermap.loading.pipeline encodermap.loading.utils encodermap.loss_functions encodermap.loss_functions.loss_functions, [1] encodermap.misc encodermap.misc.backmapping encodermap.misc.clustering encodermap.misc.distances encodermap.misc.errors encodermap.misc.function_def encodermap.misc.misc encodermap.misc.saving_loading_models encodermap.misc.summaries encodermap.misc.transformations encodermap.misc.xarray encodermap.misc.xarray_save_wrong_hdf5 encodermap.models encodermap.models.layers, [1] encodermap.models.models, [1] encodermap.moldata encodermap.moldata.moldata encodermap.parameters encodermap.parameters.parameters encodermap.plot encodermap.plot.interactive_plotting encodermap.plot.jinja_template encodermap.plot.plotting encodermap.plot.utils encodermap.trajinfo encodermap.trajinfo.hash_files encodermap.trajinfo.info_all encodermap.trajinfo.info_single encodermap.trajinfo.load_traj encodermap.trajinfo.repository encodermap.trajinfo.trajinfo_utils

MolData (class in encodermap) (class in encodermap.encodermap_tf1.moldata)

N

n_atoms (encodermap.trajinfo.info_single.SingleTraj property), [1] n_chains (encodermap.trajinfo.info_single.SingleTraj property), [1] n_frames (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] n_neurons (encodermap.ADCParameters attribute) (encodermap.Parameters attribute), [1] (encodermap.parameters.parameters.ADCParameters attribute), [1] (encodermap.parameters.parameters.Parameters attribute), [1], [2], [3] n_residues (encodermap.trajinfo.info_all.TrajEnsemble property), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] n_steps (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] n_trajs (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1]

name (encodermap.loading.features.AllBondDistances property), [1] (encodermap.loading.features.AllCartesians property), [1] (encodermap.loading.features.CentralAngles property), [1] (encodermap.loading.features.CentralBondDistances property), [1] (encodermap.loading.features.CentralCartesians property), [1] (encodermap.loading.features.CentralDihedrals property), [1] (encodermap.loading.features.SideChainAngles property), [1] (encodermap.loading.features.SideChainBondDistances property), [1] (encodermap.loading.features.SideChainCartesians property), [1] (encodermap.loading.features.SideChainDihedrals property), [1] name_arr (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] NewMolData (class in encodermap.moldata.moldata)

O

old_distance_loss() (in module encodermap.loss_functions.loss_functions) on_checkpoint_step() (encodermap.callbacks.callbacks.CheckpointSaver method) (encodermap.EncoderMapBaseCallback method) on_click() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) (encodermap.plot.utils.StatusMenu method) on_click_menu() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) on_click_tool() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) on_enter_ax() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) on_leave_ax() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) on_move() (encodermap.plot.utils.Menu method)

on_summary_step() (encodermap.callbacks.callbacks.ProgressBar method) (encodermap.EncoderMapBaseCallback method) on_train_batch_end() (encodermap.callbacks.callbacks.EarlyStop method) (encodermap.callbacks.callbacks.IncreaseCartesianCost method) (encodermap.callbacks.callbacks.ProgressBar method) (encodermap.callbacks.callbacks.TensorboardWriteBool method) (encodermap.EncoderMapBaseCallback method) on_train_begin() (encodermap.callbacks.callbacks.EarlyStop method) (encodermap.callbacks.callbacks.ProgressBar method) on_train_end() (encodermap.callbacks.callbacks.EarlyStop method) (encodermap.callbacks.callbacks.ProgressBar method) onselect() (encodermap.plot.utils.SelectFromCollection method) optimizer (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] options (encodermap.loading.features.SideChainDihedrals attribute), [1], [2], [3]

P

p (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] pairwise_dist() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.distances) pairwise_dist_periodic() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.distances) PairwiseDistances (class in encodermap.models.layers) Parameters (class in encodermap) (class in encodermap.encodermap_tf1.parameters) (class in encodermap.parameters.parameters), [1] ParametersFramework (class in encodermap.encodermap_tf1.parameters) path() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) PathGenerateCartesians (class in encodermap.encodermap_tf1.plot) PathGenerateDihedrals (class in encodermap.encodermap_tf1.plot) PathSelect (class in encodermap.encodermap_tf1.plot) periodic_distance() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.distances) periodic_distance_np() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.distances) PeriodicInput (class in encodermap.models.layers), [1] periodicity (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] PeriodicOutput (class in encodermap.models.layers), [1]

plot_model() (in module encodermap.misc.misc) plot_network() (encodermap.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1], [2], [3] polygon() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) Positions (class in encodermap.encodermap_tf1.moldata) potential_energy() (in module encodermap.encodermap_tf1.misc) prefix_label (encodermap.loading.features.AllBondDistances attribute), [1], [2], [3] (encodermap.loading.features.AllCartesians attribute), [1], [2], [3] (encodermap.loading.features.CentralAngles attribute), [1], [2], [3] (encodermap.loading.features.CentralBondDistances attribute), [1], [2], [3] (encodermap.loading.features.CentralCartesians attribute), [1], [2], [3] (encodermap.loading.features.SideChainAngles attribute), [1], [2], [3] (encodermap.loading.features.SideChainBondDistances attribute), [1], [2], [3] (encodermap.loading.features.SideChainCartesians attribute), [1], [2], [3] print_catalogue() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) profile() (encodermap.encodermap_tf1.autoencoder.Autoencoder method) ProgressBar (class in encodermap.callbacks.callbacks) projects (encodermap.Repository property) (encodermap.trajinfo.repository.Repository property) Props (class in encodermap.plot.utils) pts (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) put_nan_back_in() (in module encodermap.loading.utils)

R

random_on_cube_edges() (in module encodermap.encodermap_tf1.misc) read_from_log() (in module encodermap.encodermap_tf1.misc) read_only (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] reconstruction_loss() (in module encodermap.loss_functions.loss_functions), [1] rectangle() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) regularization_loss() (in module encodermap.loss_functions.loss_functions), [1] render_move() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method)

Repository (class in encodermap) (class in encodermap.trajinfo.repository) reset() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) residues (encodermap.trajinfo.info_single.SingleTraj attribute), [1] rotation_matrix() (in module encodermap.encodermap_tf1.misc) run_path() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.misc)

S

save() (encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.Autoencoder method) (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1] (encodermap.encodermap_tf1.parameters.ParametersFramework method) (encodermap.trajinfo.info_all.TrajEnsemble method), [1] (encodermap.trajinfo.info_single.SingleTraj method), [1] save_CV_as_numpy() (encodermap.trajinfo.info_single.SingleTraj method), [1] save_CVs() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] save_model() (in module encodermap.misc.saving_loading_models) save_netcdf_alongside_mdtraj() (in module encodermap.misc.xarray_save_wrong_hdf5) search() (encodermap.Repository method) (encodermap.trajinfo.repository.Repository method) search_and_replace() (in module encodermap.encodermap_tf1.misc) seed (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] select() (encodermap.trajinfo.info_single.SingleTraj method), [1] SelectFromCollection (class in encodermap.plot.utils) SequentialModel (class in encodermap.models.models) set() (encodermap.plot.utils.MenuItem method) (encodermap.plot.utils.ModeButton method) set_axes() (encodermap.plot.utils.MenuItem method) set_data() (encodermap.plot.utils.MenuItem method) set_figure() (encodermap.plot.utils.MenuItem method) set_hover() (encodermap.plot.utils.MenuItem method) (encodermap.plot.utils.ModeButton method) set_hover_props() (encodermap.plot.utils.MenuItem method) set_idle() (encodermap.plot.utils.StatusMenu method) set_points() (encodermap.InteractivePlotting method) (encodermap.plot.interactive_plotting.InteractivePlotting method) set_transform() (encodermap.plot.utils.MenuItem method) show_traj() (encodermap.trajinfo.info_single.SingleTraj method), [1] side_dihedral_cost_reference (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1]

side_dihedral_cost_scale (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] side_dihedral_cost_variant (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1] side_dihedral_loss() (in module encodermap.loss_functions.loss_functions) SideChainAngles (class in encodermap.loading.features), [1] SideChainBondDistances (class in encodermap.loading.features), [1] SideChainCartesians (class in encodermap.loading.features), [1] SideChainDihedrals (class in encodermap.loading.features), [1] sigmoid() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.distances) sigmoid_loss() (in module encodermap.loss_functions.loss_functions) SingleTraj (class in encodermap.trajinfo.info_single), [1] sort_key() (encodermap.encodermap_tf1.moldata.MolData static method) (encodermap.MolData static method) Sparse (class in encodermap.models.layers), [1] (class in encodermap.models.models) SparseFunctionalModel (class in encodermap.models.models) SparseModel (class in encodermap.models.models) SparseReshape (class in encodermap.models.layers) split_into_frames() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] stack() (encodermap.Repository method) (encodermap.trajinfo.info_single.SingleTraj method), [1] (encodermap.trajinfo.repository.Repository method) status_menu_ax (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) StatusMenu (class in encodermap.plot.utils) statusmenu (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) steps_counter (encodermap.EncoderMapBaseCallback attribute) straight_tetrahedral_chain() (in module encodermap.encodermap_tf1.backmapping) subsample() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] summary_step (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] superpose() (encodermap.trajinfo.info_single.SingleTraj method), [1]

T

tensorboard (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] TensorboardWriteBool (class in encodermap.callbacks.callbacks) tool (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute) top (encodermap.loading.features.AllBondDistances attribute), [1] (encodermap.loading.features.AllCartesians attribute), [1] (encodermap.loading.features.CentralAngles attribute), [1] (encodermap.loading.features.CentralBondDistances attribute), [1] (encodermap.loading.features.CentralCartesians attribute), [1] (encodermap.loading.features.CentralDihedrals attribute), [1] (encodermap.loading.features.SideChainAngles attribute), [1] (encodermap.loading.features.SideChainBondDistances attribute), [1] (encodermap.loading.features.SideChainCartesians attribute), [1] (encodermap.loading.features.SideChainDihedrals attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble attribute), [1] (encodermap.trajinfo.info_all.TrajEnsemble property), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] top_file (encodermap.trajinfo.info_single.SingleTraj attribute), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] top_files (encodermap.trajinfo.info_all.TrajEnsemble property), [1]

train() (encodermap.AngleDihedralCartesianEncoderMap method) (encodermap.Autoencoder method), [1] (encodermap.autoencoder.autoencoder.AngleDihedralCartesianEncoderMap method), [1] (encodermap.autoencoder.autoencoder.Autoencoder method), [1], [2], [3] (encodermap.encodermap_tf1.autoencoder.Autoencoder method) train_data (encodermap.Autoencoder attribute) (encodermap.autoencoder.autoencoder.Autoencoder attribute), [1] train_step() (encodermap.models.models.ADCSequentialModel method) (encodermap.models.models.FunctionalModel method) (encodermap.models.models.SequentialModel method) training (encodermap.Parameters attribute) (encodermap.parameters.parameters.Parameters attribute), [1] traj (encodermap.trajinfo.info_single.SingleTraj property), [1] traj_file (encodermap.trajinfo.info_single.SingleTraj attribute), [1] (encodermap.trajinfo.info_single.SingleTraj property), [1] traj_files (encodermap.trajinfo.info_all.TrajEnsemble property), [1] traj_joined (encodermap.trajinfo.info_all.TrajEnsemble property), [1] traj_num (encodermap.trajinfo.info_single.SingleTraj attribute), [1] traj_nums (encodermap.trajinfo.info_all.TrajEnsemble property), [1] TrajEnsemble (class in encodermap.trajinfo.info_all), [1] trajs (encodermap.InteractivePlotting attribute) (encodermap.plot.interactive_plotting.InteractivePlotting attribute)

U

unload() (encodermap.trajinfo.info_all.TrajEnsemble method), [1] (encodermap.trajinfo.info_single.SingleTraj method), [1] unpack_data_and_feature() (in module encodermap.misc.xarray) url (encodermap.Repository attribute) (encodermap.trajinfo.repository.Repository attribute) use_backbone_angles (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1]

use_points() (encodermap.encodermap_tf1.plot.ManualPath method) (encodermap.encodermap_tf1.plot.PathGenerateCartesians method) (encodermap.encodermap_tf1.plot.PathGenerateDihedrals method) (encodermap.encodermap_tf1.plot.PathSelect method) use_sidechains (encodermap.ADCParameters attribute) (encodermap.parameters.parameters.ADCParameters attribute), [1]

V

variable_summaries() (in module encodermap.encodermap_tf1.misc)

W

write() (encodermap.encodermap_tf1.moldata.MolData method) (encodermap.InteractivePlotting method) (encodermap.MolData method) (encodermap.plot.interactive_plotting.InteractivePlotting method)

write_tfrecords() (encodermap.moldata.moldata.NewMolData method)

X

xyz (encodermap.trajinfo.info_all.TrajEnsemble property), [1]