Index Symbols | _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X Symbols --del-robots run_docbuild_test_and_cover command line option --doc-only run_docbuild_test_and_cover command line option --exclude run_doctests command line option --force run_docbuild_test_and_cover command line option --force-notebook run_docbuild_test_and_cover command line option --log run_docbuild_test_and_cover command line option --module run_doctests command line option --only run_doctests command line option --remote run_docbuild_test_and_cover command line option --run-expensive-tests run_docbuild_test_and_cover command line option --test-only run_docbuild_test_and_cover command line option -d run_docbuild_test_and_cover command line option -f run_docbuild_test_and_cover command line option -fb run_docbuild_test_and_cover command line option -t run_docbuild_test_and_cover command line option _ _args (CustomFeature attribute), [1] _batch_fro() (in module encodermap.models.layers) _check_aas() (in module encodermap.loading.features) _check_all_templates_defined() (in module encodermap.plot.utils) _cluster_col (InteractivePlotting attribute), [1], [2] _cluster_method (InteractivePlotting attribute), [1], [2] _concatenate_inputs() (in module encodermap.models.models) _concatenate_inputs_reconstruct_sidechains() (in module encodermap.models.models) _create_inputs_non_periodic_maybe_sparse() (in module encodermap.models.models) _create_inputs_periodic_maybe_sparse() (in module encodermap.models.models) _create_readme() (in module encodermap.plot.utils) _CVs (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] _defaults (ADCParameters attribute), [1], [2] (Parameters attribute), [1], [2] _describe_atom() (in module encodermap.loading.features) _do_nothing() (in module encodermap.loss_functions.loss_functions) _encodermap_logo (Dashboard attribute) _expand_universe() (in module encodermap.encodermap_tf1.backmapping) _frames (SingleTraj property), [1] _fun (CustomFeature attribute), [1] _get_adc_decoder() (in module encodermap.models.models) _get_decoder_model() (in module encodermap.models.models) _get_deterministic_random_normal() (in module encodermap.models.models) _get_deterministic_variance_scaling() (in module encodermap.models.models) _get_encoder_model() (in module encodermap.models.models) _get_system_info() (in module encodermap.plot.utils) _help_url (InteractivePlotting attribute), [1], [2] _is_custom (CustomFeature attribute), [1] _kwargs (CustomFeature attribute), [1] _max_filepath_len (InteractivePlotting attribute), [1], [2] _max_slider_len (InteractivePlotting attribute), [1], [2] _mdtraj_attr (SingleTraj attribute) _n_frames_base_h5_file (SingleTraj property), [1] _nbins (InteractivePlotting attribute), [1], [2] _nonstandard_transform_args (ContactFeature attribute), [1] (CustomFeature attribute), [1] (GroupCOMFeature attribute), [1] (MinRmsdFeature attribute), [1] (ResidueMinDistanceFeature attribute), [1] _original_frame_indices (SingleTraj property), [1] _placeholder (LocalUploadTraj attribute) _raise_on_unitcell (AlignFeature attribute), [1] (AllBondDistances attribute), [1] (AllCartesians attribute), [1] (AngleFeature attribute), [1] (BackboneTorsionFeature attribute), [1] (CentralAngles attribute), [1] (CentralBondDistances attribute), [1] (CentralCartesians attribute), [1] (CentralDihedrals attribute), [1] (ContactFeature attribute), [1] (CustomFeature attribute), [1] (DihedralFeature attribute), [1] (DistanceFeature attribute), [1] (Feature attribute) (GroupCOMFeature attribute), [1] (InverseDistanceFeature attribute), [1] (MinRmsdFeature attribute), [1] (ResidueCOMFeature attribute), [1] (ResidueMinDistanceFeature attribute), [1] (SelectionFeature attribute), [1] (SideChainAngles attribute), [1] (SideChainBondDistances attribute), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SideChainTorsions attribute), [1] _redefine_open() (in module encodermap.plot.dashboard) _redefine_os_path_exists() (in module encodermap.plot.dashboard) _rotation_matrices() (in module encodermap.models.layers) _set_dihedral() (in module encodermap.encodermap_tf1.backmapping) _summary_cost() (in module encodermap.loss_functions.loss_functions) _traj (SingleTraj property), [1] _unit_vector() (in module encodermap.models.layers) _unpack_and_assert_input_shapes() (in module encodermap.models.models) _unpack_and_assert_input_shapes_multimers() (in module encodermap.models.models) _unpack_and_assert_input_shapes_w_sidechains() (in module encodermap.models.models) _unpack_cluster_info() (in module encodermap.plot.utils) _use_angle (AlignFeature attribute), [1] (AllBondDistances attribute), [1] (AllCartesians attribute), [1] (AngleFeature attribute), [1] (BackboneTorsionFeature attribute), [1] (CentralAngles attribute), [1] (CentralBondDistances attribute), [1] (CentralCartesians attribute), [1] (CentralDihedrals attribute), [1] (ContactFeature attribute), [1] (CustomFeature attribute), [1] (DihedralFeature attribute), [1] (DistanceFeature attribute), [1] (Feature attribute) (GroupCOMFeature attribute), [1] (InverseDistanceFeature attribute), [1] (MinRmsdFeature attribute), [1] (ResidueCOMFeature attribute), [1] (ResidueMinDistanceFeature attribute), [1] (SelectionFeature attribute), [1] (SideChainAngles attribute), [1] (SideChainBondDistances attribute), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SideChainTorsions attribute), [1] _use_omega (AlignFeature attribute), [1] (AllBondDistances attribute), [1] (AllCartesians attribute), [1] (AngleFeature attribute), [1] (BackboneTorsionFeature attribute), [1] (CentralAngles attribute), [1] (CentralBondDistances attribute), [1] (CentralCartesians attribute), [1] (CentralDihedrals attribute), [1] (ContactFeature attribute), [1] (CustomFeature attribute), [1] (DihedralFeature attribute), [1] (DistanceFeature attribute), [1] (Feature attribute) (GroupCOMFeature attribute), [1] (InverseDistanceFeature attribute), [1] (MinRmsdFeature attribute), [1] (ResidueCOMFeature attribute), [1] (ResidueMinDistanceFeature attribute), [1] (SelectionFeature attribute), [1] (SideChainAngles attribute), [1] (SideChainBondDistances attribute), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SideChainTorsions attribute), [1] _use_periodic (AlignFeature attribute), [1] (AllBondDistances attribute), [1] (AllCartesians attribute), [1] (AngleFeature attribute), [1] (BackboneTorsionFeature attribute), [1] (CentralAngles attribute), [1] (CentralBondDistances attribute), [1] (CentralCartesians attribute), [1] (CentralDihedrals attribute), [1] (ContactFeature attribute), [1] (CustomFeature attribute), [1] (DihedralFeature attribute), [1] (DistanceFeature attribute), [1] (Feature attribute) (GroupCOMFeature attribute), [1] (InverseDistanceFeature attribute), [1] (MinRmsdFeature attribute), [1] (ResidueCOMFeature attribute), [1] (ResidueMinDistanceFeature attribute), [1] (SelectionFeature attribute), [1] (SideChainAngles attribute), [1] (SideChainBondDistances attribute), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SideChainTorsions attribute), [1] A abc_to_rgb() (in module encodermap.plot.utils) activation_functions (Parameters attribute), [1], [2], [3] active_features (DaskFeaturizer property) ADCClashMetric (class in encodermap.callbacks.metrics) ADCFunctionalModel (class in encodermap.models.models) ADCFunctionalModelSidechainReconstruction (class in encodermap.models.models) ADCParameters (class in encodermap), [1] (class in encodermap.encodermap_tf1.parameters) (class in encodermap.parameters.parameters), [1] ADCRMSDMetric (class in encodermap.callbacks.metrics) ADCSparseFunctionalModel (class in encodermap.models.models) add_amino_acid_codes() (CustomTopology method), [1] add_bond() (NewResidue method) add_bonds() (CustomTopology method), [1] add_callback() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3] add_custom_feature() (DaskFeaturizer method) add_dihedral() (NewResidue method) add_images_to_tensorboard() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3], [4], [5], [6], [7] add_items() (Menu method) (StatusMenu method) add_layer_summaries() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.summaries) add_loss() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3] add_metric() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3] add_new_residue() (CustomTopology method), [1] advance_path() (InteractivePlotting method), [1], [2] AlignFeature (class in encodermap.loading.features), [1] AllBondDistances (class in encodermap.loading.features), [1] AllCartesians (class in encodermap.loading.features), [1] alpha (Props attribute) analysis_path (Parameters attribute), [1], [2], [3] angle_cost_reference (ADCParameters attribute), [1], [2], [3] angle_cost_scale (ADCParameters attribute), [1], [2], [3] angle_cost_variant (ADCParameters attribute), [1], [2], [3] angle_loss() (in module encodermap.loss_functions.loss_functions), [1] AngleDihedralCartesianEncoderMap (class in encodermap), [1] (class in encodermap.autoencoder.autoencoder), [1] (class in encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap) AngleDihedralCartesianEncoderMapBaseMetric (class in encodermap.callbacks.metrics) AngleDihedralCartesianEncoderMapDummy (class in encodermap.encodermap_tf1.angle_dihedral_cartesian_encodermap) AngleFeature (class in encodermap.loading.features), [1] Angles (class in encodermap.encodermap_tf1.moldata) animate_lowd_trajectory() (in module encodermap.plot.plotting) app_layout (Dashboard property) as_amino_acid_dict_entry() (NewResidue method) atom1 (Bond attribute), [1] (Dihedral attribute), [1] atom2 (Bond attribute), [1] (Dihedral attribute), [1] atom3 (Dihedral attribute), [1] atom4 (Dihedral attribute), [1] atom_feature (AlignFeature attribute), [1] (AllBondDistances attribute), [1] (AllCartesians attribute), [1] (AngleFeature attribute), [1] (BackboneTorsionFeature attribute), [1] (CentralAngles attribute), [1] (CentralBondDistances attribute), [1] (CentralCartesians attribute), [1] (CentralDihedrals attribute), [1] (ContactFeature attribute), [1] (CustomFeature attribute), [1] (DihedralFeature attribute), [1] (DistanceFeature attribute), [1] (Feature attribute) (GroupCOMFeature attribute), [1] (InverseDistanceFeature attribute), [1] (MinRmsdFeature attribute), [1] (ResidueCOMFeature attribute), [1] (ResidueMinDistanceFeature attribute), [1] (SelectionFeature attribute), [1] (SideChainAngles attribute), [1] (SideChainBondDistances attribute), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SideChainTorsions attribute), [1] atom_sequence() (CustomTopology method), [1] atom_slice() (SingleTraj method), [1] atoms (SingleTraj attribute), [1] auto_cost_scale (Parameters attribute), [1], [2], [3] auto_cost_variant (Parameters attribute), [1], [2], [3] auto_loss() (in module encodermap.loss_functions.loss_functions), [1] Autoencoder (class in encodermap), [1] (class in encodermap.autoencoder.autoencoder), [1] (class in encodermap.encodermap_tf1.autoencoder) B backbone_hydrogen_oxygen_crossproduct() (in module encodermap.misc.backmapping) backbone_sequence() (CustomTopology method), [1] BackboneTorsionFeature (class in encodermap.loading.features), [1] backend (SingleTraj attribute), [1] BackMapLayer (class in encodermap.models.layers), [1] BackMapLayerTransformations (class in encodermap.models.layers) BackMapLayerWithSidechains (class in encodermap.models.layers) basename (SingleTraj property), [1] basenames (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] basic_loss_combinator() (in module encodermap.loss_functions.loss_functions) batch_iterator() (TrajEnsemble method), [1] batch_size (Parameters attribute), [1], [2], [3] batched (Parameters attribute), [1], [2], [3] Bernstein() (in module encodermap.plot.utils) Bezier() (in module encodermap.plot.utils) BezierBuilder (class in encodermap.plot.utils) bgcolor (Props attribute) bgcolor_rgb (Props attribute) (Props property) Bond (class in encodermap.trajinfo.trajinfo_utils) bonds (NewResidue attribute), [1] (SingleTraj attribute), [1] build() (SequentialModel method) build_dask_xarray() (in module encodermap.loading.delayed) build_graph() (DaskFeaturizer method) C calc_bravais_box() (in module encodermap.loading.delayed) calc_current_cartesian_cost_scale() (IncreaseCartesianCost method) call() (BackMapLayer method), [1] (BackMapLayerTransformations method) (BackMapLayerWithSidechains method) (MeanAngles method), [1] (PairwiseDistances method) (PeriodicInput method), [1] (PeriodicOutput method), [1] (SequentialModel method) callbacks (Autoencoder attribute), [1], [2], [3] Capturing (class in encodermap.trajinfo.info_single) cartesian_cost_reference (ADCParameters attribute), [1], [2], [3] cartesian_cost_scale (ADCParameters attribute), [1], [2], [3] cartesian_cost_scale_soft_start (ADCParameters attribute), [1], [2], [3] cartesian_cost_variant (ADCParameters attribute), [1], [2], [3] cartesian_dist_sig_parameters (ADCParameters attribute), [1], [2], [3] cartesian_distance_cost_scale (ADCParameters attribute), [1], [2], [3] cartesian_distance_loss() (in module encodermap.loss_functions.loss_functions), [1] cartesian_loss() (in module encodermap.loss_functions.loss_functions), [1] cartesian_pwd_start (ADCParameters attribute), [1], [2], [3] cartesian_pwd_step (ADCParameters attribute), [1], [2], [3] cartesian_pwd_stop (ADCParameters attribute), [1], [2], [3] center_cost_scale (Parameters attribute), [1], [2], [3] 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 (SingleTraj attribute), [1] check_select() (MenuItem method) (ModeButton method) checkpoint_step (Parameters attribute), [1], [2], [3] CheckpointSaver (class in encodermap.callbacks.callbacks) CitePYEMMAWarning close() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3], [4] (ReplaceOpenWithStringIO method) cluster() (InteractivePlotting method), [1], [2] (TrajEnsemble method), [1] combine_chains() (CustomTopology method), [1] common_str (NewResidue attribute), [1] (SingleTraj attribute), [1] compile() (ADCFunctionalModel method) (SequentialModel method) construct_xarray_from_numpy() (in module encodermap.misc.xarray) ContactFeature (class in encodermap.loading.features), [1] copy() (SingleTraj method), [1] (TrajEnsemble method) 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_training_step (Parameters attribute), [1], [2], [3] custom_update_state (ADCClashMetric attribute) (ADCRMSDMetric attribute) (AngleDihedralCartesianEncoderMapBaseMetric attribute) (EncoderMapBaseMetric attribute) (OmegaAngleBaseMetric attribute) (SidechainVsBackboneFrequencyBaseMetric attribute) CustomFeature (class in encodermap.loading.features), [1] CustomTopology (class in encodermap.trajinfo.trajinfo_utils), [1] CVs (SingleTraj property), [1] (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] CVs_in_file (SingleTraj property), [1] (TrajEnsemble property), [1] D dash_summary() (SingleTraj method), [1] (TrajEnsemble method), [1] Dashboard (class in encodermap.plot.dashboard) dask_indices (AngleFeature property), [1] (ContactFeature property), [1] (CustomFeature property), [1] (DistanceFeature property), [1] (GroupCOMFeature property), [1] (InverseDistanceFeature property), [1] (MinRmsdFeature property), [1] (ResidueMinDistanceFeature property), [1] (SelectionFeature property), [1] dask_transform() (AngleFeature static method), [1] (ContactFeature static method), [1] (CustomFeature static method), [1] (DihedralFeature static method), [1] (DistanceFeature static method), [1] (GroupCOMFeature static method), [1] (InverseDistanceFeature static method), [1] (MinRmsdFeature static method), [1] (ResidueMinDistanceFeature static method), [1] (SelectionFeature static method), [1] DaskFeaturizer (class in encodermap.loading.featurizer) dataset (Autoencoder attribute), [1], [2], [3] debug (Dashboard property) DebugPage (class in encodermap.plot.dashboard) decode() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3], [4], [5], [6], [7] decoder (ADCFunctionalModel property) (AngleDihedralCartesianEncoderMap property), [1], [2], [3] (Autoencoder attribute), [1], [2], [3] (Autoencoder property), [1], [2], [3] decoder() (SequentialModel method) defaults (Parameters attribute), [1], [2], [3] (Props attribute), [1] defaults_description() (ADCParameters class method), [1], [2], [3] (Parameters class method), [1], [2], [3] del_CVs() (SingleTraj method), [1] (TrajEnsemble method), [1] del_featurizer() (TrajEnsemble method), [1] delayed (CustomFeature attribute), [1] delete (Dihedral attribute), [1] density (InteractivePlotting property), [1], [2] describe() (AllBondDistances method), [1] (AllCartesians method), [1] (AngleFeature method), [1] (BackboneTorsionFeature method), [1] (CentralAngles method), [1] (CentralCartesians method), [1] (CentralDihedrals method), [1] (CustomFeature method), [1] (DaskFeaturizer method) (DihedralFeature method), [1] (DistanceFeature method), [1] (GroupCOMFeature method), [1] (MinRmsdFeature method), [1] (ResidueMinDistanceFeature method), [1] (SelectionFeature method), [1] (SideChainAngles method), [1] (SideChainCartesians method), [1] (SideChainDihedrals method), [1] (SideChainTorsions method), [1] describe_last_feats() (in module encodermap.loading.features) digitize_dssp() (in module encodermap.plot.utils) Dihedral (class in encodermap.trajinfo.trajinfo_utils) dihedral_backmapping() (in module encodermap.encodermap_tf1.backmapping) dihedral_cost_reference (ADCParameters attribute), [1], [2], [3] dihedral_cost_scale (ADCParameters attribute), [1], [2], [3] dihedral_cost_variant (ADCParameters attribute), [1], [2], [3] 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) DihedralFeature (class in encodermap.loading.features), [1] dihedrals (NewResidue attribute), [1] dihedrals_to_cartesian_tf() (in module encodermap.encodermap_tf1.backmapping) dihedrals_to_cartesian_tf_old() (in module encodermap.encodermap_tf1.backmapping) dimension (Feature property) dimension() (DaskFeaturizer method) disconnect() (BezierBuilder method) (DummyTool method) (SelectFromCollection method) display_custom_aas() (TopPage method) display_plot() (TopPage method) display_top() (TopPage method) display_traj() (TrajPage method) display_trajs() (TrajPage method) dist_sig_parameters (Parameters attribute), [1], [2], [3] distance_cost() (in module encodermap.encodermap_tf1.misc) distance_cost_scale (Parameters attribute), [1], [2], [3] distance_histogram() (in module encodermap.encodermap_tf1.plot) (in module encodermap.plot.plotting) distance_histogram_interactive() (in module encodermap.plot.plotting) distance_loss() (in module encodermap.loss_functions.loss_functions), [1] DistanceFeature (class in encodermap.loading.features), [1] draw() (MenuItem method) DummyTool (class in encodermap.plot.utils) E EarlyStop (class in encodermap.callbacks.callbacks) encode() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3], [4], [5], [6], [7], [8] encoder (ADCFunctionalModel property) (AngleDihedralCartesianEncoderMap property), [1], [2], [3] (Autoencoder attribute), [1], [2], [3] (Autoencoder property), [1], [2], [3] encoder() (SequentialModel method) encodermap module, [1] EncoderMap (class in encodermap), [1] (class in encodermap.autoencoder.autoencoder), [1] (class in encodermap.encodermap_tf1.encodermap) encodermap._typing module, [1] encodermap._version module, [1] 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.kondata module, [1] encodermap.loading module encodermap.loading.delayed module encodermap.loading.features module, [1] encodermap.loading.featurizer module encodermap.loss_functions module encodermap.loss_functions.loss_classes 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.function_def module encodermap.misc.misc module encodermap.misc.rotate module encodermap.misc.saving_loading_models module encodermap.misc.summaries 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.dashboard module encodermap.plot.interactive_plotting module encodermap.plot.jinja_template module encodermap.plot.plotting module encodermap.plot.utils module encodermap.trajinfo module encodermap.trajinfo.info_all module encodermap.trajinfo.info_single module, [1] encodermap.trajinfo.load_traj module encodermap.trajinfo.trajinfo_utils module, [1] EncoderMapBaseCallback (class in encodermap), [1] (class in encodermap.callbacks.callbacks) EncoderMapBaseLayer (class in encodermap.models.layers) EncoderMapBaseMetric (class in encodermap.callbacks.metrics) extension (SingleTraj property), [1] F Feature (class in encodermap.loading.features) feature_containers (DaskFeaturizer property) FeatureMeta (class in encodermap.loading.features) Featurizer (class in encodermap), [1] (class in encodermap.loading.featurizer), [1] featurizer (SingleTraj property) (TrajEnsemble property) fill_dropdown() (TopPage method) flatten() (in module encodermap.trajinfo.trajinfo_utils) fontsize (Props attribute) frames (TrajEnsemble property), [1] from_checkpoint() (AngleDihedralCartesianEncoderMap class method), [1], [2], [3] (Autoencoder class method), [1], [2], [3] (Autoencoder method), [1], [2], [3] (EncoderMap class method), [1], [2], [3] from_config() (ADCClashMetric class method) (ADCFunctionalModel class method) (ADCFunctionalModelSidechainReconstruction class method) (ADCSparseFunctionalModel class method) (AngleDihedralCartesianEncoderMapBaseMetric class method) (BackMapLayer class method), [1] (BackMapLayerTransformations class method) (BackMapLayerWithSidechains class method) (EncoderMapBaseLayer class method) (EncoderMapBaseMetric class method) (PairwiseDistances class method) (SequentialModel class method) from_dataset() (TrajEnsemble class method) from_dict() (CustomTopology class method), [1] from_hdf5_file() (CustomTopology class method), [1] from_json() (CustomTopology class method), [1] from_pdb_id() (SingleTraj class method), [1] from_project() (InteractivePlotting class method), [1], [2] from_textfile() (TrajEnsemble class method), [1] from_yaml() (CustomTopology class method), [1] fsel (SingleTraj property) function() (in module encodermap), [1] (in module encodermap.misc.function_def) G gen_functional_model() (in module encodermap.models.models), [1] gen_sequential_model() (in module encodermap.models.models), [1] generate() (AngleDihedralCartesianEncoderMap method), [1], [2], [3], [4] (Autoencoder method), [1], [2], [3], [4], [5], [6], [7], [8] (DihedralEncoderMap method) (InteractivePlotting method), [1], [2] generic_describe() (AllBondDistances method), [1] (AllCartesians method), [1] (CentralAngles method), [1] (CentralBondDistances method), [1] (CentralCartesians method), [1] (CentralDihedrals method), [1] (SideChainAngles method), [1] (SideChainBondDistances method), [1] (SideChainCartesians method), [1] (SideChainDihedrals method), [1] get_config() (ADCClashMetric method) (ADCFunctionalModel method) (ADCFunctionalModelSidechainReconstruction method) (ADCSparseFunctionalModel method) (AngleDihedralCartesianEncoderMapBaseMetric method) (BackMapLayer method), [1] (BackMapLayerTransformations method) (BackMapLayerWithSidechains method) (EncoderMapBaseLayer method) (EncoderMapBaseMetric method) (in module encodermap._version), [1] (PairwiseDistances method) (SequentialModel method) get_coords() (Menu method) get_dihedral_by_type() (NewResidue method) get_from_kondata() (in module encodermap.kondata), [1] get_full_common_str_and_ref() (in module encodermap.misc.misc) get_keywords() (in module encodermap._version), [1] get_loss() (ADCFunctionalModel method) (ADCFunctionalModelSidechainReconstruction method) (ADCSparseFunctionalModel method) get_lowd() (ImageCallback method) get_options() (TopPage method) get_output() (DaskFeaturizer method) get_single_frame() (SingleTraj method), [1] (TrajEnsemble method), [1] get_single_residue_atom_ids() (CustomTopology method), [1] get_train_data_from_trajs() (AngleDihedralCartesianEncoderMap static method), [1], [2], [3] get_versions() (in module encodermap._version), [1] git_get_keywords() (in module encodermap._version), [1] git_pieces_from_vcs() (in module encodermap._version), [1] git_versions_from_keywords() (in module encodermap._version), [1] gpu_memory_fraction (Parameters attribute), [1], [2], [3] GroupCOMFeature (class in encodermap.loading.features), [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 help() (InteractivePlotting method), [1], [2] I id (Parameters attribute), [1], [2], [3] (SingleTraj property), [1] (TrajEnsemble property), [1] idx (NewResidue attribute), [1] ignore (NewResidue attribute), [1] image_summary() (in module encodermap.misc.summaries) ImageCallback (class in encodermap.callbacks.callbacks) IncreaseCartesianCost (class in encodermap.callbacks.callbacks) ind (BezierBuilder property) index (SingleTraj attribute), [1] index_arr (TrajEnsemble property), [1] indexes (AllBondDistances attribute), [1] (AllBondDistances property), [1] (AllCartesians attribute), [1] (CentralAngles attribute), [1] (CentralAngles property), [1] (CentralBondDistances attribute), [1] (CentralBondDistances property), [1] (CentralDihedrals attribute), [1] (CentralDihedrals property), [1] (CustomFeature attribute), [1] (SideChainAngles attribute), [1] (SideChainAngles property), [1] (SideChainBondDistances attribute), [1] (SideChainBondDistances property), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SideChainDihedrals property), [1] indices_chi1 (SingleTraj property), [1] indices_chi1() (CustomTopology method), [1] indices_chi2 (SingleTraj property), [1] indices_chi2() (CustomTopology method), [1] indices_chi3 (SingleTraj property), [1] indices_chi3() (CustomTopology method), [1] indices_chi4 (SingleTraj property), [1] indices_chi4() (CustomTopology method), [1] indices_chi5 (SingleTraj property), [1] indices_chi5() (CustomTopology method), [1] indices_omega (SingleTraj property), [1] indices_omega() (CustomTopology method), [1] indices_phi (SingleTraj property), [1] indices_phi() (CustomTopology method), [1] indices_psi (SingleTraj property), [1] indices_psi() (CustomTopology method), [1] interact() (ProjectionPage method) interactive_path_visualization() (in module encodermap.plot.plotting) InteractivePlotting (class in encodermap), [1] (class in encodermap.plot.interactive_plotting) InverseDistanceFeature (class in encodermap.loading.features), [1] iterframes() (SingleTraj method), [1] (TrajEnsemble method), [1] itertrajs() (TrajEnsemble method), [1] J join() (SingleTraj method), [1] (TrajEnsemble method) K kabsch_tf() (in module encodermap.callbacks.metrics) kabsch_weighted() (in module encodermap.callbacks.metrics) L l2_reg_constant (Parameters attribute), [1], [2], [3] labelcolor (Props attribute) labelcolor_rgb (Props attribute) (Props property) layout (Dashboard property) (DebugPage property) learning_rate (Parameters attribute), [1], [2], [3] load() (in module encodermap), [1] (ParametersFramework class method) load_custom_topology() (SingleTraj method), [1] (TrajEnsemble method), [1] load_CV() (SingleTraj method), [1] load_CV_from_string_or_path() (in module encodermap.trajinfo.trajinfo_utils) load_CVs() (TrajEnsemble method), [1] load_CVs_ensemble() (in module encodermap.trajinfo.trajinfo_utils) load_CVs_ensembletraj() (in module encodermap.trajinfo.trajinfo_utils), [1] load_CVs_from_dir() (in module encodermap.trajinfo.trajinfo_utils) load_CVs_singletraj() (in module encodermap.trajinfo.trajinfo_utils), [1] load_model() (in module encodermap.misc.saving_loading_models) load_traj() (SingleTraj method), [1] load_trajs() (LocalUploadTraj method) (TrajEnsemble method), [1] load_xyz() (in module encodermap.loading.delayed) load_xyz_from_h5() (in module encodermap.loading.delayed) local (Dashboard property) LocalUploadTraj (class in encodermap.plot.dashboard) locations (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] loss (Autoencoder attribute), [1], [2], [3] (Parameters attribute), [1], [2], [3] loss_combinator() (in module encodermap.loss_functions.loss_functions), [1] lower() (ReplaceOpenWithStringIO method) M main_path (Parameters attribute), [1], [2], [3] ManualPath (class in encodermap.encodermap_tf1.plot) mdtraj_backmapping() (in module encodermap.misc.backmapping) mdtraj_rotate() (in module encodermap.misc.rotate) MeanAngles (class in encodermap.models.layers), [1] Menu (class in encodermap.plot.utils) MenuItem (class in encodermap.plot.utils) merge_cartesians() (in module encodermap.encodermap_tf1.backmapping) metrics (Autoencoder attribute), [1], [2], [3] MinRmsdFeature (class in encodermap.loading.features), [1] MixedUpInputs ModeButton (class in encodermap.plot.utils) model_api (Parameters attribute), [1], [2], [3] module encodermap, [1] encodermap._typing, [1] encodermap._version, [1] 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.kondata, [1] encodermap.loading encodermap.loading.delayed encodermap.loading.features, [1] encodermap.loading.featurizer encodermap.loss_functions encodermap.loss_functions.loss_classes encodermap.loss_functions.loss_functions, [1] encodermap.misc encodermap.misc.backmapping encodermap.misc.clustering encodermap.misc.distances encodermap.misc.function_def encodermap.misc.misc encodermap.misc.rotate encodermap.misc.saving_loading_models encodermap.misc.summaries 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.dashboard encodermap.plot.interactive_plotting encodermap.plot.jinja_template encodermap.plot.plotting encodermap.plot.utils encodermap.trajinfo encodermap.trajinfo.info_all encodermap.trajinfo.info_single, [1] encodermap.trajinfo.load_traj encodermap.trajinfo.trajinfo_utils, [1] MolData (class in encodermap.encodermap_tf1.moldata) (in module encodermap), [1] molStyles (ProjectionPage property) multimer_connection_bridges (ADCParameters attribute), [1], [2], [3] multimer_lengths (ADCParameters attribute), [1], [2], [3] multimer_topology_classes (ADCParameters attribute), [1], [2], [3] multimer_training (ADCParameters attribute), [1], [2], [3] MyBiasInitializer (class in encodermap.models.models) MyKernelInitializer (class in encodermap.models.models) N n_atoms (SingleTraj property), [1] n_chains (SingleTraj property), [1] n_frames (SingleTraj property), [1] (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] n_neurons (Parameters attribute), [1], [2], [3] n_residues (SingleTraj property), [1] (TrajEnsemble property), [1] n_steps (Parameters attribute), [1], [2], [3] n_trajs (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] name (AllBondDistances property), [1] (AllCartesians property), [1] (CentralAngles property), [1] (CentralBondDistances property), [1] (CentralCartesians property), [1] (CentralDihedrals property), [1] (NewResidue attribute), [1] (SideChainAngles property), [1] (SideChainBondDistances property), [1] (SideChainCartesians property), [1] (SideChainDihedrals property), [1] name_arr (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] navbar (Dashboard property) new_atoms_def (Dihedral property) new_residues (CustomTopology property), [1] NewMolData (class in encodermap.moldata.moldata) NewResidue (class in encodermap.trajinfo.trajinfo_utils) NoneInterruptCallback (class in encodermap.callbacks.callbacks) np_to_xr() (in module encodermap.trajinfo.trajinfo_utils) O old_distance_loss() (in module encodermap.loss_functions.loss_functions) OmegaAngleBaseMetric (class in encodermap.callbacks.metrics) on_canvas_mouse_down() (InteractivePlotting method), [1], [2] on_canvas_mouse_move() (InteractivePlotting method), [1], [2] on_canvas_mouse_up() (InteractivePlotting method), [1], [2] on_checkpoint_step() (CheckpointSaver method) (EncoderMapBaseCallback method), [1], [2] on_click() (StatusMenu method) on_epoch_end() (ImageCallback method) on_move() (Menu method) on_select() (InteractivePlotting method), [1], [2] on_summary_step() (EncoderMapBaseCallback method), [1], [2] (ProgressBar method) on_train_batch_end() (EarlyStop method) (EncoderMapBaseCallback method), [1], [2] (ImageCallback method) (IncreaseCartesianCost method) (NoneInterruptCallback method) (ProgressBar method) (TensorboardWriteBool method) on_train_begin() (EarlyStop method) (ProgressBar method) on_train_end() (EarlyStop method) (ProgressBar method) one_letter_code (NewResidue attribute), [1] onselect() (SelectFromCollection method) options (SideChainDihedrals attribute), [1], [2], [3] (SideChainTorsions attribute), [1] P p (Autoencoder attribute), [1], [2], [3] pair() (in module encodermap.loading.features) 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), [1] (class in encodermap.encodermap_tf1.parameters) (class in encodermap.parameters.parameters), [1] ParametersFramework (class in encodermap.encodermap_tf1.parameters) parse_bonds_and_dihedrals() (NewResidue method) parse_clustal_w_alignment() (TrajEnsemble method), [1] parse_trajs() (TrajPage method) PathGenerateCartesians (class in encodermap.encodermap_tf1.plot) PathGenerateDihedrals (class in encodermap.encodermap_tf1.plot) PathSelect (class in encodermap.encodermap_tf1.plot) pep440_split_post() (in module encodermap._version), [1] 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 (Parameters attribute), [1], [2], [3] PeriodicOutput (class in encodermap.models.layers), [1] placeholder (Dashboard property) plot_ball_and_stick() (in module encodermap.plot.plotting) plot_dssp() (in module encodermap.plot.plotting) plot_end2end() (in module encodermap.plot.plotting) plot_free_energy() (in module encodermap.plot.plotting) plot_model() (in module encodermap.misc.misc) plot_network() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3], [4], [5], [6], [7] plot_ramachandran() (in module encodermap.plot.plotting) plot_raw_data() (in module encodermap.plot.plotting) plot_trajs_by_parameter() (in module encodermap.plot.plotting) plus_or_dot() (in module encodermap._version), [1] Positions (class in encodermap.encodermap_tf1.moldata) potential_energy() (in module encodermap.encodermap_tf1.misc) prefix_label (AlignFeature attribute), [1] (AllBondDistances attribute), [1], [2], [3] (AllCartesians attribute), [1], [2], [3] (CentralAngles attribute), [1], [2], [3] (CentralBondDistances attribute), [1], [2], [3] (CentralCartesians attribute), [1] (ContactFeature attribute), [1] (DistanceFeature attribute), [1] (InverseDistanceFeature attribute), [1] (SelectionFeature attribute), [1] (SideChainAngles attribute), [1], [2], [3] (SideChainBondDistances attribute), [1], [2], [3] (SideChainCartesians attribute), [1], [2], [3] profile() (Autoencoder method) ProgressBar (class in encodermap.callbacks.callbacks) ProjectionPage (class in encodermap.plot.dashboard) Props (class in encodermap.plot.utils) R random_on_cube_edges() (in module encodermap.encodermap_tf1.misc) read() (ReplaceOpenWithStringIO method) read_from_log() (in module encodermap.encodermap_tf1.misc) read_only (Autoencoder attribute), [1], [2], [3] reconstruct_sidechains (ADCParameters attribute), [1], [2], [3] reconstruction_loss() (in module encodermap.loss_functions.loss_functions), [1] register_vcs_handler() (in module encodermap._version), [1] regularization_loss() (in module encodermap.loss_functions.loss_functions), [1] render() (in module encodermap._version), [1] render_git_describe() (in module encodermap._version), [1] render_git_describe_long() (in module encodermap._version), [1] render_pep440() (in module encodermap._version), [1] render_pep440_branch() (in module encodermap._version), [1] render_pep440_old() (in module encodermap._version), [1] render_pep440_post() (in module encodermap._version), [1] render_pep440_post_branch() (in module encodermap._version), [1] render_pep440_pre() (in module encodermap._version), [1] ReplaceOpenWithStringIO (class in encodermap.plot.dashboard) ResidueCOMFeature (class in encodermap.loading.features), [1] ResidueMinDistanceFeature (class in encodermap.loading.features), [1] residues (SingleTraj attribute), [1] resname (Bond attribute), [1] (Dihedral attribute), [1] resSeq (NewResidue attribute), [1] result() (ADCClashMetric method) (ADCRMSDMetric method) (EncoderMapBaseMetric method) rmsd() (in module encodermap.callbacks.metrics) rmsd_numpy() (in module encodermap.callbacks.metrics) rmsd_tf() (in module encodermap.callbacks.metrics) rotation_matrix() (in module encodermap.encodermap_tf1.misc) run() (Dashboard method) run_code() (DebugPage static method) run_command() (in module encodermap._version), [1] run_docbuild_test_and_cover command line option --del-robots --doc-only --force --force-notebook --log --remote --run-expensive-tests --test-only -d -f -fb -t run_doctests command line option --exclude --module --only run_path() (in module encodermap.encodermap_tf1.misc) (in module encodermap.misc.misc) S save() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3] (InteractivePlotting method), [1], [2] (ParametersFramework method) (SingleTraj method), [1] (TrajEnsemble method), [1] save_CV_as_numpy() (SingleTraj method), [1] save_CVs() (TrajEnsemble method), [1] save_image_to_dir() (ImageCallback method) save_model() (in module encodermap.misc.saving_loading_models) save_netcdf_alongside_mdtraj() (in module encodermap.misc.xarray_save_wrong_hdf5) scatter (InteractivePlotting property), [1], [2] scatter_on_click() (InteractivePlotting method), [1], [2] search_and_replace() (in module encodermap.encodermap_tf1.misc) seed (Parameters attribute), [1], [2], [3] select() (SingleTraj method), [1] SelectFromCollection (class in encodermap.plot.utils) SelectionFeature (class in encodermap.loading.features), [1] SequentialModel (class in encodermap.models.models) set() (MenuItem method) (ModeButton method) set_axes() (MenuItem method) set_data() (MenuItem method) set_figure() (MenuItem method) set_hover() (MenuItem method) (ModeButton method) set_hover_props() (MenuItem method) set_idle() (StatusMenu method) set_train_data() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3] set_transform() (MenuItem method) show_traj() (SingleTraj method), [1] side_dihedral_cost_reference (ADCParameters attribute), [1], [2], [3] side_dihedral_cost_scale (ADCParameters attribute), [1], [2], [3] side_dihedral_cost_variant (ADCParameters attribute), [1], [2], [3] side_dihedral_loss() (in module encodermap.loss_functions.loss_functions) sidechain_indices_by_residue() (CustomTopology method), [1] sidechain_info() (SingleTraj method), [1] (TrajEnsemble method), [1] sidechain_sequence() (CustomTopology method), [1] 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] SideChainTorsions (class in encodermap.loading.features), [1] SidechainVsBackboneFrequencyBaseMetric (class in encodermap.callbacks.metrics) 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] SingleTrajFsel (class in encodermap.trajinfo.info_single) sort_key() (MolData static method) split_into_frames() (TrajEnsemble method), [1] stack() (SingleTraj method), [1] (TrajEnsemble method) StatusMenu (class in encodermap.plot.utils) steps_counter (EncoderMapBaseCallback attribute), [1], [2] straight_tetrahedral_chain() (in module encodermap.encodermap_tf1.backmapping) stride (InteractivePlotting attribute), [1], [2] subsample() (TrajEnsemble method), [1] summary_step (Parameters attribute), [1], [2], [3] superpose() (SingleTraj method), [1] switch_between_density_and_scatter() (InteractivePlotting method), [1], [2] T tensorboard (Parameters attribute), [1], [2], [3] TensorboardWriteBool (class in encodermap.callbacks.callbacks) text_area (DebugPage property) tf_dataset() (TrajEnsemble method) to_alignment_query() (TrajEnsemble method), [1] to_dataframe() (TrajEnsemble method) to_dict() (CustomTopology method), [1] to_hdf_file() (CustomTopology method), [1] to_json() (CustomTopology method), [1] to_netcdf() (DaskFeaturizer method) to_yaml() (CustomTopology method), [1] top (AllBondDistances attribute), [1] (AllCartesians attribute), [1] (CentralAngles attribute), [1] (CentralBondDistances attribute), [1] (CentralDihedrals attribute), [1] (CustomFeature attribute), [1] (CustomTopology property), [1] (SideChainAngles attribute), [1] (SideChainBondDistances attribute), [1] (SideChainCartesians attribute), [1] (SideChainDihedrals attribute), [1] (SingleTraj property), [1] (TrajEnsemble attribute), [1] (TrajEnsemble property), [1] top_file (SingleTraj attribute), [1] (SingleTraj property), [1] top_files (TrajEnsemble property), [1] topology (NewResidue attribute) TopPage (class in encodermap.plot.dashboard) track_clashes (ADCParameters attribute), [1], [2], [3] track_RMSD (ADCParameters attribute), [1], [2], [3] train() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] (Autoencoder method), [1], [2], [3], [4], [5], [6], [7], [8] train_data (Autoencoder attribute), [1], [2], [3] train_for_references() (AngleDihedralCartesianEncoderMap method), [1], [2], [3] train_step() (ADCFunctionalModel method) (SequentialModel method) trainable_dense_to_sparse (Parameters attribute), [1], [2], [3] training (Parameters attribute), [1], [2], [3] traj (CustomFeature attribute), [1] (SingleTraj property), [1] traj_file (SingleTraj attribute), [1] (SingleTraj property), [1] traj_files (TrajEnsemble property), [1] traj_joined (TrajEnsemble property), [1] traj_loaded_layout() (TrajPage method) traj_num (SingleTraj attribute), [1] traj_nums (TrajEnsemble property), [1] traj_to_pdb() (in module encodermap.plot.dashboard) TrajEnsemble (class in encodermap.trajinfo.info_all), [1] TrajPage (class in encodermap.plot.dashboard) trajs_by_common_str (TrajEnsemble property), [1] trajs_by_top (TrajEnsemble property), [1] trajs_by_traj_num (TrajEnsemble property) trajs_combine_attrs() (in module encodermap.trajinfo.trajinfo_utils) transform() (AlignFeature method), [1] (AngleFeature method), [1] (ContactFeature method), [1] (CustomFeature method), [1] (DaskFeaturizer method) (DihedralFeature method), [1] (DistanceFeature method), [1] (Feature method) (GroupCOMFeature method), [1] (InverseDistanceFeature method), [1] (MinRmsdFeature method), [1] (ResidueMinDistanceFeature method), [1] (SelectionFeature method), [1] tsel (TrajEnsemble property) type (Bond attribute), [1] (Dihedral attribute), [1] U unload() (SingleTraj method), [1] (TrajEnsemble method), [1] unpack_data_and_feature() (in module encodermap.misc.xarray) unpair() (in module encodermap.loading.features) update_state() (ADCClashMetric method) (ADCRMSDMetric method) (EncoderMapBaseMetric method) update_theme() (Dashboard method) use_backbone_angles (ADCParameters attribute), [1], [2], [3] use_points() (ManualPath method) (PathGenerateCartesians method) (PathGenerateDihedrals method) (PathSelect method) use_sidechains (ADCParameters attribute), [1], [2], [3] using_hypercube (Parameters attribute), [1], [2], [3] V variable_summaries() (in module encodermap.encodermap_tf1.misc) versions_from_parentdir() (in module encodermap._version), [1] visualize() (DaskFeaturizer method) W with_overwrite_trajnums() (TrajEnsemble class method), [1] write() (MolData method) (ReplaceOpenWithStringIO method) write_summary (Parameters attribute), [1], [2], [3] write_tfrecords() (NewMolData method) X xyz (TrajEnsemble property), [1]
