Index

_

__add__() (StateSelection method), [1] (StructureSelection method), [1] __and__() (StateSelection method), [1] (StructureSelection method), [1] __atnum2symbol__ (in module shnitsel.data.atom_helpers) __build_conjugated_smarts() (StructureSelection static method), [1] __call__() (Converter method) (StructureMapping method) __class_getitem__() (TreeNode class method), [1] __codata_version__ (in module shnitsel.units.definitions) __contains__() (ShnitselDataset method), [1] (TreeNode method), [1] __delattr__() (Proxy method) __dir__() (ShnitselDataset method), [1] __get_active_atoms() (StructureSelection method), [1] __get_active_bonds() (StructureSelection method), [1] __get_smiles_order() (StructureSelection static method), [1] __getattr__() (ShnitselDataset method), [1] __getattribute__() (Proxy method) __getitem__() (ShnitselDataset method), [1] (TreeNode method), [1] __hash__() (Proxy method) __invert__() (StateSelection method), [1] (StructureSelection method), [1] __len__() (TreeNode method), [1] __match_pattern() (StructureSelection static method), [1] __name__ (Converter attribute) __nonzero__() (Proxy method) __or__ (StateSelection attribute), [1] (StructureSelection attribute), [1] __repr__() (Proxy method) (TreeNode method), [1] __setattr__() (Proxy method) __setitem__() (TreeNode method), [1] __slots__ (Proxy attribute) __str__() (Proxy method) (TreeNode method), [1] __sub__() (StateSelection method), [1] (StructureSelection method), [1] __symbol2atnum__ (in module shnitsel.data.atom_helpers) _absolute_statistics (PopulationStatistics attribute) _abstract_state_comb_spec() (StateSelection static method), [1] _amount_unit_scales (in module shnitsel.units.definitions) _apply_indexes() (in module shnitsel.data.tree.selection) _apply_indexes_fast() (in module shnitsel.data.tree.selection) _ase_default_pattern_glob (in module shnitsel.io.ase.format_reader) _ase_default_pattern_regex (in module shnitsel.io.ase.format_reader) _attr_sources (ShnitselDataset property), [1] _attrs (TreeNode attribute), [1] _base_dataset (ShnitselDerivedDataset attribute) _basis_data (MultiSeriesDataset attribute), [1] _binning_with_min_entries() (in module shnitsel.vis.plot.pca_biplot) _bokeh_package_available (in module shnitsel.vis.plot.select) _calc_classical_populations() (PopulationStatistics static method) _calculate_fosc() (in module shnitsel.analyze.spectra) _charge_unit_scales (in module shnitsel.units.definitions) _check_matching_dimensions() (in module shnitsel.data.traj_combiner_methods) _check_matching_var_meta() (in module shnitsel.data.traj_combiner_methods) _children (TreeNode attribute), [1] _class_cache (in module shnitsel.data.tree.node) _collect_metadata() (in module shnitsel.io.ase.write) _colon_whitespace_pattern (in module shnitsel.io.pyrai2md.parse) _compare_dicts_of_values() (in module shnitsel.data.traj_combiner_methods) _compound_info (CompoundGroup attribute), [1] _CONVERTERS (in module shnitsel.units.conversion) _coordinate_meta_keys (in module shnitsel.data.traj_combiner_methods) _copy_data() (Datasheet method), [1] (DatasheetPage method) _create_class_proxy() (Proxy class method) _create_extended_node_class() (TreeNode class method), [1] _data (TreeNode attribute), [1] _data_is_set (DelayedDataLeaf attribute) _data_provider (DelayedDataLeaf attribute) _dataset_to_encoding() (in module shnitsel.io.shnitsel.write) _Datasheet_default_page_key (in module shnitsel.vis.datasheet.datasheet) _datatree_level_attribute_key (in module shnitsel.data.tree.datatree_level) _decode_shnitsel_v1_1_dataset() (in module shnitsel.io.shnitsel.parse) _decode_shnitsel_v1_1_datatree() (in module shnitsel.io.shnitsel.parse) _decode_shnitsel_v1_2_datatree() (in module shnitsel.io.shnitsel.parse) _default_trajid_pattern_regex (in module shnitsel.io.format_reader_base) _dihedral_deg() (in module dihedrals) _dihedral_trig_() (in module dihedrals) _dipole_unit_scales (in module shnitsel.units.definitions) _distance_unit_scales (in module shnitsel.units.definitions) _double_whitespace_pattern (in module shnitsel.io.pyrai2md.parse) _dtype (TreeNode attribute), [1] _dtype_guess_from_children() (TreeNode static method), [1] _energy_unit_scales (in module shnitsel.units.definitions) _eval_kdes() (in module shnitsel.vis.plot.kde) _fields (in module shnitsel._contracts) _filter_cluster_coords() (in module shnitsel.vis.plot.pca_biplot) _filter_mask_from_criterion_mask() (in module shnitsel.clean.common) _filter_mask_from_dataset() (in module shnitsel.clean.common) _filter_mask_from_filtranda() (in module shnitsel.clean.common) _find_atom_pairs() (in module shnitsel.geo.analogs) _fit_and_eval_kdes() (in module shnitsel.vis.plot.kde) _fit_kdes() (in module shnitsel.vis.plot.kde) _flatten() (StructureSelection static method), [1] _float_pattern (in module shnitsel.io.pyrai2md.parse) _force_unit_scales (in module shnitsel.units.definitions) _full_mapping (StructureMapping attribute) _get_axs() (in module shnitsel.vis.plot.pca_biplot) _get_clusters_coords() (in module shnitsel.vis.plot.pca_biplot) _get_default_state_selection() (in module shnitsel.filtering.helpers) _get_default_structure_selection() (in module shnitsel.filtering.helpers) _get_extended_class_name() (TreeNode class method), [1] _get_indexes_dict() (in module shnitsel.data.dataset_containers.dataset_vis) _get_xx_yy() (in module shnitsel.vis.plot.kde) _group_info (DataGroup attribute), [1] _icon() (in module shnitsel.data.tree.tree_vis) _ignore_none (ConsistentValue attribute) _individual_plots (MultiPlot attribute) _inlabel() (in module shnitsel.vis.plot.spectra3d)

_int_pattern (in module shnitsel.io.pyrai2md.parse) _ipython_key_completions_() (ShnitselAccessor method) (ShnitselDataset method), [1] _is_multi_trajectory (DataSeries attribute), [1] (Frames attribute), [1] (Trajectory attribute), [1] _isel_fancy() (in module shnitsel.data.tree.selection) _item_sources (ShnitselDataset property), [1] (ShnitselDerivedDataset property) _layered_repr_cached (MultiSeriesStacked attribute), [1] _length_unit_scales (in module shnitsel.units.definitions) _level_name (TreeNode attribute), [1] _list_analogs() (in module shnitsel.geo.analogs) _load_static_files() (in module shnitsel.data.tree.tree_vis) _log_omit() (in module shnitsel.clean.common) _mapping_section() (in module shnitsel.data.tree.tree_vis) _merge_traj_metadata() (in module shnitsel.data.traj_combiner_methods) _method_needs (ShnitselAccessor attribute) _methods (DataArrayAccessor attribute) (DatasetAccessor attribute) (ShnitselAccessor attribute) _most_stable_frame() (in module shnitsel.bridges) _mult_label_transl() (StateSelection static method), [1] _nacs_unit_scales (in module shnitsel.units.definitions) _name (TreeNode attribute), [1] _ndarray_to_json_ser() (in module shnitsel.io.ase.write) _new_angle_selection_from_atoms() (StructureSelection method), [1] _new_bond_selection_from_atoms() (StructureSelection method), [1] _new_dihedral_selection_from_atoms() (StructureSelection method), [1] _new_pyramid_selection_from_atoms() (StructureSelection method), [1] _newton_reader (in module shnitsel.io.format_registry) _newtonx_default_pattern_glob (in module shnitsel.io.newtonx.format_reader) _newtonx_default_pattern_regex (in module shnitsel.io.newtonx.format_reader) _obj (ShnitselAccessor attribute) _obj_repr() (in module shnitsel.data.tree.tree_vis) _omit (in module shnitsel.clean.common) _optional_shnitsel_attributes (in module trajectory_verification) _optional_shnitsel_variables (in module trajectory_verification) _orig_mol (StructureMapping attribute) _original_frames (InterState attribute), [1] (PerState attribute), [1] _param_from_vars_or_attrs() (DataSeries method), [1] _parent (TreeNode attribute), [1] _parse_shnitsel_file_v1_0() (in module shnitsel.io.shnitsel.parse) _parse_shnitsel_file_v1_1() (in module shnitsel.io.shnitsel.parse) _parse_shnitsel_file_v1_2() (in module shnitsel.io.shnitsel.parse) _pca_components (PCAResult attribute) _pca_dimension (PCAResult attribute) _pca_inputs (PCAResult attribute) _pca_inputs_projected (PCAResult attribute) _pca_object (PCAResult attribute) _pca_pipeline (PCAResult attribute) _per_traj() (in module shnitsel.io.read) _plot_kdes() (in module shnitsel.vis.plot.kde) _prepare_dataset() (in module shnitsel.io.shnitsel.write) _prepare_datatree() (in module shnitsel.io.shnitsel.write) _prepare_for_write_schnetpack() (in module shnitsel.io.ase.write) _raw_dataset (ShnitselDataset attribute), [1] _re_grads (in module shnitsel.io.sharc.parse_initial_conditions) _re_nac_header_line (in module shnitsel.io.pyrai2md.parse) _re_nacs (in module shnitsel.io.sharc.parse_initial_conditions) _re_soc_line (in module shnitsel.io.pyrai2md.parse) _re_state_map_entry (in module shnitsel.io.sharc.parse_initial_conditions) _read_dim_or_transition_identification_line() (in module shnitsel.io.sharc.parse_initial_conditions) _reasons_unavailable() (ShnitselAccessor method) _repr_html_() (ShnitselAccessor method) (ShnitselDataset method), [1] (TreeNode method), [1] _required_shnitsel_attributes (in module trajectory_verification) _required_shnitsel_variables (in module trajectory_verification) _sel_trajids() (in module shnitsel.data.multi_indices) _sel_trajs_unstacked() (in module shnitsel.data.multi_indices) _selected_on_change() (FrameSelector method) (TrajSelector method) _separate_angles() (in module shnitsel.vis.plot.pca_biplot) _set_axes() (in module shnitsel.vis.plot.time) _setting_name_pattern (in module shnitsel.io.pyrai2md.parse) _sharc_default_pattern_glob_icond (in module shnitsel.io.sharc.format_reader) _sharc_default_pattern_glob_traj (in module shnitsel.io.sharc.format_reader) _sharc_default_pattern_regex (in module shnitsel.io.sharc.format_reader) _shnitsel_default_pattern_glob (in module shnitsel.io.shnitsel.format_reader) _shnitsel_default_pattern_regex (in module shnitsel.io.shnitsel.format_reader) _SHNITSEL_READERS (in module shnitsel.io.shnitsel.parse) _socs_unit_scale (in module shnitsel.units.definitions) _special_names (Proxy attribute) _stacked_repr_cached (MultiSeriesLayered attribute), [1] _standard_state_comb_spec() (StateSelection static method), [1] _state_comb_canonicalized() (StateSelection static method), [1] _state_combs_match_pattern() (StateSelection method), [1] _state_combs_matches_pattern() (StateSelection method), [1] _state_combs_pattern (in module shnitsel.filtering.state_selection) _state_id_matches_pattern() (StateSelection method), [1] _state_id_pattern (in module shnitsel.filtering.state_selection) _state_ids_match_pattern() (StateSelection method), [1] _state_mult_pattern (in module shnitsel.filtering.state_selection) _state_name_pattern (in module shnitsel.filtering.state_selection) _submol (StructureMapping attribute) _substruct_match_to_mapping() (in module shnitsel.geo.analogs) _substruct_match_to_submol() (in module shnitsel.geo.analogs) _tcl_script_path (in module shnitsel.vis.vmd) _test_subfigures() (Datasheet method), [1] (DatasheetPage method) _time_unit_scales (in module shnitsel.units.definitions) _to_feature_level_str() (StructureSelection static method), [1] _trajectories (TrajectoryCollection attribute) _trajectory_key_func() (in module shnitsel.data.tree.node) _transect (in module shnitsel.clean.common) _transition_identification_re (in module shnitsel.io.sharc.parse_initial_conditions) _true_upto (in module shnitsel.clean.common) _truncate (in module shnitsel.clean.common) _val (ConsistentValue attribute) _velocity_unit_scales (in module shnitsel.units.definitions) _weak (ConsistentValue attribute) _write_trajectory_to_db() (in module shnitsel.io.ase.write)

A

absolute (PopulationStatistics property) active_state (ShnitselDataset property), [1] active_trajectory (Frames property), [1] ActiveFlag (in module shnitsel.filtering.structure_selection) ActualDataType (in module shnitsel.data.helpers) add_child() (TreeNode method), [1] add_compound() (ShnitselDBRoot method), [1] add_data_group() (CompoundGroup method), [1] (ShnitselDBRoot method), [1] aggregate_xr_over_levels() (in module shnitsel.data.shnitsel_db_helpers) AggType (in module shnitsel.data.shnitsel_db_helpers) algebra module all_bonds_smarts (GeometryFiltrationThresholds attribute) all_bonds_threshold (GeometryFiltrationThresholds attribute) all_h_to_C_or_N_bonds_SMARTS (GeometryFiltrationThresholds attribute) all_h_to_C_or_N_bonds_threshold (GeometryFiltrationThresholds attribute) amount_units (class in shnitsel.units.definitions) angle() (DataArray.st method) (DataArrayAccessor method) (in module angles) angle_() (in module algebra) angle_cos_sin() (in module angles) angle_cos_sin_() (in module algebra) AngleDescriptor (in module shnitsel.filtering.structure_selection) angles module angles (StructureSelection attribute), [1] angles_selected (StructureSelection attribute), [1] angles_types (StructureSelection attribute), [1] Angstrom (distance attribute) API() (in module shnitsel.core._api_info) apply() (StructureMapping method) apply_data_attributes() (TreeNode method), [1] apply_dataset_meta_from_db_metadata() (in module shnitsel.io.ase.parse) apply_gauss_broadening() (in module shnitsel.analyze.spectra) as_directed_selection() (StateSelection method), [1] as_frames (Frames property), [1] (Trajectory property), [1] as_layered (MultiSeriesDataset property), [1] (MultiSeriesLayered property), [1] (MultiSeriesStacked property), [1] (TreeNode property), [1] as_stacked (MultiSeriesDataset property), [1] (MultiSeriesLayered property), [1] (MultiSeriesStacked property), [1] (TreeNode property), [1]

as_trajectory (Frames property), [1] (Trajectory property), [1] as_undirected_selection() (StateSelection method), [1] as_xr_dataset() (InterState method), [1] (PerState method), [1] (ShnitselDataset method), [1] (ShnitselDerivedDataset method) (SupportsToXrConversion method) ase_time_units (time attribute), [1] ASEFormatInformation (class in shnitsel.io.ase.format_reader) ASEFormatReader (class in shnitsel.io.ase.format_reader) assign_children() (TreeNode method), [1] assign_hop_time() (DataArrayAccessor method) (DatasetAccessor method) (in module shnitsel.analyze.hops) assign_levels() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) assign_optional_settings() (in module trajectory_setup) assign_required_settings() (in module trajectory_setup) atom_names (ShnitselDataset property), [1] atom_numbers (ShnitselDataset property), [1] AtomDescriptor (in module shnitsel.filtering.structure_selection) atoms (StructureSelection attribute), [1] atoms_selected (StructureSelection attribute), [1] atoms_types (StructureSelection attribute), [1] atrajectory (Frames property), [1] attr_section (in module shnitsel.data.tree.tree_vis) attrs (DataSeries property), [1] (TreeNode property), [1] atXYZ (DataSeries property), [1] AtXYZ (in module shnitsel.core.typedefs) au (dipole attribute), [1] (distance attribute) (energy attribute), [1] (force attribute), [1] (nacs attribute) (socs attribute) (time attribute), [1] (velocity attribute) auto_assign_colors() (StateSelection method), [1]

B

base (ShnitselDerivedDataset property) biplot_kde() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.kde) bkapp() (FrameSelector method) (TrajSelector method) bla_chromophor module Bohr (distance attribute)

Bohr_per_atu (velocity attribute) Bohr_per_fs (velocity attribute) bond_descriptor_to_mol_index() (StructureSelection method), [1] BondDescriptor (in module shnitsel.filtering.structure_selection) bonds (StructureSelection attribute), [1] bonds_selected (StructureSelection attribute), [1] bonds_types (StructureSelection attribute), [1] build_shnitsel_db() (in module shnitsel.data.tree.tree_completion)

C

calc_all() (Datasheet method), [1] (DatasheetPage method) calc_classical_populations() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.populations) calc_confidence_interval() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.stats) calc_confidence_interval_in_array_dimensions() (in module shnitsel.analyze.stats) calc_pops (in module shnitsel.analyze.populations) calc_truncation_maximum() (in module shnitsel.vis.datasheet.figures.hist) calculate_bond_length_filtranda() (DatasetAccessor method) (in module shnitsel.clean.filter_geo) calculate_energy_filtranda() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.clean.filter_energy) calculate_fosc() (in module shnitsel.analyze.spectra) can (DatasheetPage attribute) canonicalize_angle() (StructureSelection static method), [1] canonicalize_bond() (StructureSelection static method), [1] canonicalize_dihedral() (StructureSelection static method), [1] canonicalize_pyramid() (StructureSelection static method), [1] case_sensitive_mapping (Converter attribute) center() (in module shnitsel.analyze.generic) centertext() (in module shnitsel.vis.datasheet.figures.common) charge (class in shnitsel.units.definitions) (DatasheetPage attribute) (ShnitselDataset property), [1] (StateInfo attribute) (unit_dimensions attribute) charge_in_e (TrajectoryGroupingMetadata attribute) check_dims() (in module shnitsel.io.sharc.parse_initial_conditions) check_path_for_format_info() (ASEFormatReader method) (FormatReader method) (NewtonXFormatReader method) (PyrAI2mdFormatReader method) (SHARCFormatReader method) (ShnitselFormatReader method) check_shnitsel_trajectory_data() (in module trajectory_verification) check_thresholds() (in module shnitsel.vis.plot.filtration) children (TreeNode property), [1] ChildType (in module shnitsel.data.tree.node) (in module shnitsel.data.tree.support_functions) circbins() (in module shnitsel.vis.plot.pca_biplot) clean_unassigned_variables() (in module variable_flagging) cluster_general() (in module shnitsel.vis.plot.pca_biplot) cluster_loadings() (in module shnitsel.vis.plot.pca_biplot) collapsible_section() (in module shnitsel.data.tree.tree_vis) collect_and_clean_queue_handler() (in module messages) collect_data() (TreeNode method), [1] collect_data_nodes() (DataGroup method), [1] combination_info() (StateSelection method), [1] complete_shapes_guesses_from_variables() (in module shnitsel.io.ase.parse) complete_shnitsel_tree (in module shnitsel.data.tree) (in module shnitsel.data.tree.tree_completion) completed (DataSeries property), [1] (NewtonXSettingsResult attribute) (RequiredTrajectorySettings attribute) compound_info (CompoundGroup property), [1] compound_name (CompoundInfo attribute), [1] compound_smiles (CompoundInfo attribute), [1]

CompoundGroup (class in shnitsel.data.tree) (class in shnitsel.data.tree.compound) CompoundInfo (class in shnitsel.data.tree) (class in shnitsel.data.tree.compound) compounds (ShnitselDBRoot property), [1] concat_subtree() (in module shnitsel.data.shnitsel_db_helpers) concat_trajs() (in module shnitsel.data.traj_combiner_methods) confidence_interval_aggregate_last_dim() (in module shnitsel.analyze.stats) ConsistentValue (class in helpers) construct_copy() (CompoundGroup method), [1] (DataGroup method), [1] (DataLeaf method), [1] (ShnitselDBRoot method), [1] (TreeNode method), [1] construct_default_mol() (in module shnitsel.bridges) conversions (Converter attribute) convert() (ShnitselDataset method), [1] convert_all_units_to_shnitsel_defaults() (in module shnitsel.units.conversion) convert_charge (in module shnitsel.units.conversion) convert_datarray_with_unitdim() (in module shnitsel.units.conversion) convert_datarray_with_unitdim_to_shnitsel_defaults() (in module shnitsel.units.conversion) convert_dipole (in module shnitsel.units) (in module shnitsel.units.conversion) convert_dipole() (DataArrayAccessor method) convert_energy (in module shnitsel.units) (in module shnitsel.units.conversion) convert_energy() (DataArrayAccessor method) convert_force (in module shnitsel.units) (in module shnitsel.units.conversion) convert_force() (DataArrayAccessor method) convert_length (in module shnitsel.units) (in module shnitsel.units.conversion) convert_length() (DataArrayAccessor method) convert_nacs (in module shnitsel.units) (in module shnitsel.units.conversion) convert_nacs() (DataArrayAccessor method) convert_socs (in module shnitsel.units) (in module shnitsel.units.conversion) convert_time (in module shnitsel.units) (in module shnitsel.units.conversion) convert_time() (DataArrayAccessor method) convert_to_shnitsel module convert_to_target_units() (in module shnitsel.units.conversion) convert_value() (Converter method) convert_velocity (in module shnitsel.units.conversion) Converter (class in shnitsel.units.conversion) coords (Needs attribute) (ShnitselDataset property), [1] coords_or_vars (Needs attribute) copy_or_update() (StateSelection method), [1] (StructureSelection method), [1] Coulomb (charge attribute) CoulombMeter (dipole attribute), [1] create_initial_dataset() (in module trajectory_setup) create_marginals() (in module shnitsel.vis.datasheet.figures.hist) create_marginals_dict() (in module shnitsel.vis.datasheet.figures.hist) cum_max_quantiles() (Filtration method) (in module shnitsel.clean.common) cumulative_mask (Filtration property) custom_ylgnr (in module shnitsel.vis.colormaps)

D

DAManualAccessor (class in shnitsel._accessors) data (DelayedDataLeaf property) (Trajres attribute) (TreeNode property), [1] data_ready() (ProvidesDelayedData method) data_source (Datasheet attribute), [1] data_to_xarray_dataset() (in module shnitsel.data.dataset_containers.xr_conversion) data_vars (Needs attribute) (ShnitselDataset property), [1] DATAARRAY_ACCESSOR_NAME (in module shnitsel._accessors) (in module shnitsel._state) DATAARRAY_ACCESSOR_REGISTERED (in module shnitsel._state) DataArrayAccessor (class in shnitsel._generated_accessors) DataArrayOrVar (in module shnitsel.core.typedefs) dataclass_from_dict() (in module shnitsel.data.helpers) DataGroup (class in shnitsel.data.tree) (class in shnitsel.data.tree.data_group) DataLeaf (class in shnitsel.data.tree) (class in shnitsel.data.tree.data_leaf) DataSeries (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.data_series) dataset (ShnitselDataset property), [1] DATASET_ACCESSOR_NAME (in module shnitsel._accessors) (in module shnitsel._state) DATASET_ACCESSOR_REGISTERED (in module shnitsel._state) DatasetAccessor (class in shnitsel._generated_accessors) DatasetOrArray (in module shnitsel._contracts) (in module shnitsel.core.typedefs) (in module shnitsel.data.multi_indices) (in module shnitsel.geo.analogs) Datasheet (class in shnitsel.vis.datasheet) (class in shnitsel.vis.datasheet.datasheet) datasheet_pages (Datasheet attribute), [1] DatasheetPage (class in shnitsel.vis.datasheet.datasheet_page) DATATREE_ACCESSOR_NAME (in module shnitsel._accessors) datatree_child_repr() (in module shnitsel.data.tree.tree_vis) DataTreeLevelMap (in module shnitsel.data.tree.datatree_level) DataType (in module shnitsel.analyze.pca) (in module shnitsel.data.helpers) (in module shnitsel.data.shnitsel_db_helpers) (in module shnitsel.data.traj_combiner_methods) (in module shnitsel.data.tree.compound) (in module shnitsel.data.tree.data_group) (in module shnitsel.data.tree.data_leaf) (in module shnitsel.data.tree.node) (in module shnitsel.data.tree.support_functions) (in module shnitsel.data.tree.tree) (in module shnitsel.data.tree.tree_completion) (in module shnitsel.data.tree.xr_conversion) (in module shnitsel.io.ase.format_reader) (in module shnitsel.io.format_reader_base) (in module shnitsel.io.newtonx.format_reader) (in module shnitsel.io.pyrai2md.format_reader) (in module shnitsel.io.read) (in module shnitsel.io.sharc.format_reader) (in module shnitsel.io.shnitsel.format_reader) (in module trajectory_finalization) DataType1 (in module shnitsel.data.tree.support_functions) DataType2 (in module shnitsel.data.tree.support_functions) DataType3 (in module shnitsel.data.tree.support_functions) DataType4 (in module shnitsel.data.tree.support_functions) db_from_data() (in module shnitsel.data.traj_combiner_methods) dcross() (in module algebra) ddot() (in module algebra) Debye (dipole attribute), [1]

decode_attrs() (in module shnitsel.io.shnitsel.parse) default() (NumpyDataEncoder method) default_mol (in module shnitsel._generated_accessors) (in module shnitsel.bridges) default_mol() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) default_state_name_assigner() (in module shnitsel.data.state_helpers) default_state_type_assigner() (in module shnitsel.data.state_helpers) defined (ConsistentValue attribute) degeneracy_group_states (StateSelection attribute), [1] DelayedDataLeaf (class in shnitsel.data.tree.data_leaf) delta_E (DatasheetPage property) delta_energy (InterState property), [1] delta_t (DataSeries property), [1] (NewtonXSettingsResult attribute) (RequiredTrajectorySettings attribute) delta_t_in_fs (TrajectoryGroupingMetadata attribute) derive_other_from_descriptor() (StructureSelection method), [1] df (FrameSelector attribute) df_selection (FrameSelector property) difference (StateSelection attribute), [1] (StructureSelection attribute), [1] different_multiplicity_transitions() (StateSelection method), [1] dihedral() (DataArray.st method) (DataArrayAccessor method) (in module dihedrals) DihedralDescriptor (in module shnitsel.filtering.structure_selection) dihedrals module dihedrals (StructureSelection attribute), [1] dihedrals_selected (StructureSelection attribute), [1] dihedrals_types (StructureSelection attribute), [1] dim (FrameSelector attribute) DimName (in module shnitsel.core.typedefs) dims (Needs attribute) (ShnitselDataset property), [1] dims_from_QM_log() (in module shnitsel.io.sharc.parse_initial_conditions) dims_from_QM_out() (in module shnitsel.io.sharc.parse_initial_conditions) dip_sep() (in module helpers) dipole (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) dipole_permanent (DataSeries property), [1] (PerState property), [1] dipole_permanent_norm (PerState property), [1] dipole_transition (DataSeries property), [1] (InterState property), [1] dipole_transition_norm (InterState property), [1] dispatch_filter() (in module shnitsel.clean.common) dispatch_plots() (in module shnitsel.clean.dispatch_plots) distance (class in shnitsel.units.definitions) distance() (DataArray.st method) (DataArrayAccessor method) (in module distances) distances module dnorm() (in module algebra) doublet_state_pattern_re (in module shnitsel.data.state_helpers) draw() (StructureSelection method), [1] DSManualAccessor (class in shnitsel._accessors) dtype (TreeNode property), [1] dtype_NA (class in shnitsel.data.multi_indices) dummy_leading_dim (in module shnitsel.io.ase.parse)

E

e (charge attribute) e_kin (DataSeries property), [1] Eh (energy attribute), [1] Eh_per_Angstrom (force attribute), [1] Eh_per_Bohr (force attribute), [1] ekin_step (EnergyFiltrationThresholds attribute) encode_attrs() (in module shnitsel.io.shnitsel.write) energy (class in shnitsel.units) (class in shnitsel.units.definitions) (DataSeries property), [1] (PerState property), [1] (unit_dimensions attribute) energy_file_path (PyrAI2mdFormatInformation attribute) energy_interstate (InterState property), [1] energy_unit (EnergyFiltrationThresholds attribute) EnergyFiltrationThresholds (class in shnitsel.clean.filter_energy) ensure_unstacked() (in module shnitsel.data.multi_indices) epot_active_step (EnergyFiltrationThresholds attribute) epot_hop_step (EnergyFiltrationThresholds attribute) error_reporting (LoadingParameters attribute)

ErrorOptions (in module shnitsel.core.typedefs) ErrorOptionsWithWarn (in module shnitsel.core.typedefs) est_level (DataSeries property), [1] (MetaInformation attribute), [1] (OptionalTrajectorySettings attribute) (TrajectoryGroupingMetadata attribute) etot_drift (EnergyFiltrationThresholds attribute) etot_step (EnergyFiltrationThresholds attribute) eV (energy attribute), [1] (socs attribute) eV_per_Angstrom (force attribute), [1] eV_per_Bohr (force attribute), [1] excited_state_transitions() (StateSelection method), [1] expand_midx() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) explain_loadings() (PCAResult method) extract_analogs() (in module shnitsel.geo.analogs) extrude() (in module shnitsel.vis.plot.common)

F

feature_level_colors (StructureSelection attribute), [1] FEATURE_LEVEL_DEFAULT_COLORS (in module shnitsel.filtering.structure_selection) FEATURE_LEVELS (in module shnitsel.filtering.structure_selection) FeatureDescriptor (in module shnitsel.filtering) (in module shnitsel.filtering.structure_selection) FeatureLevelOptions (in module shnitsel.filtering.structure_selection) FeatureLevelType (in module shnitsel.filtering.structure_selection) FeatureList (in module shnitsel.filtering.structure_selection) FeatureTypeLabel (in module shnitsel.filtering.structure_selection) femto_seconds (time attribute), [1] figax() (in module shnitsel.vis.plot.common) figaxs_defaults() (in module shnitsel.vis.datasheet.figures.common) fill_missing_dataset_variables() (in module trajectory_setup) filter_by_energy() (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.filter_energy) filter_by_length() (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.filter_geo) filter_data_at_hops() (DataArrayAccessor method) (DatasetAccessor method) (in module shnitsel.analyze.hops) filter_nodes() (TreeNode method), [1] filtranda (Filtration attribute) Filtration (class in shnitsel.clean.filtration_class) finalize_icond_dataset() (in module shnitsel.io.sharc.parse_initial_conditions) finalize_loaded_trajectory() (in module trajectory_finalization) find_candidates_in_directory() (ASEFormatReader method) (FormatReader method) (NewtonXFormatReader method) (PyrAI2mdFormatReader method) (SHARCFormatReader method) (ShnitselFormatReader method) find_child_key() (in module shnitsel.data.tree.child_support_functions) fitted_pca_object (PCAResult property) flatten_levels() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices)

flatten_midx() (in module shnitsel.data.multi_indices) focus_hops() (DataArrayAccessor method) (DatasetAccessor method) (in module shnitsel.analyze.hops) force (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) forces (DataSeries property), [1] (PerState property), [1] forces_format (DataSeries property), [1] (PerState property), [1] forces_norm (PerState property), [1] format_inchi() (in module shnitsel.vis.datasheet.figures.structure) format_name (FormatInformation attribute) FormatIdentifierType (in module shnitsel.io.format_registry) FormatInformation (class in shnitsel.io.format_reader_base) FormatReader (class in shnitsel.io.format_reader_base) fosc (InterState property), [1] fosc_time (DatasheetPage property) frame3D() (DataArrayAccessor method) (in module shnitsel.vis.plot.p3mhelpers) Frames (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.frames) (in module shnitsel.core.typedefs) frames3Dgrid() (DataArrayAccessor method) (in module shnitsel.vis.plot.p3mhelpers) FrameSelector (class in shnitsel.vis.plot.select) FrameSelector() (DataArrayAccessor method) (DatasetAccessor method) from_xr_dataset() (InterState class method), [1] (PerState class method), [1] (ShnitselDataset class method), [1] (ShnitselDerivedDataset class method) (SupportsFromXrConversion class method)

G

generate_datasheet module GeometryFiltrationThresholds (class in shnitsel.clean.filter_geo) get_angles() (DataArrayAccessor method) (in module angles) get_atom_number_from_symbol() (in module shnitsel.data.atom_helpers) get_available_io_handlers() (in module shnitsel.io.format_registry) get_bats() (DataArrayAccessor method) (in module shnitsel.geo.geocalc) get_bond_type() (StructureSelection method), [1] get_centered_geometry() (in module shnitsel.geo.alignment) (in module shnitsel.geo.geocalc) get_data() (ProvidesDelayedData method) get_data_name_candidate() (in module shnitsel.data.tree.child_support_functions) get_data_with_path() (in module shnitsel.data.shnitsel_db_helpers) get_default_input_attributes() (in module shnitsel.units.defaults) get_dihedrals() (DataArrayAccessor method) (in module dihedrals) get_dipoles_per_xyz() (in module shnitsel.io.xyz) (in module shnitsel.io.xyz.parse) get_distances() (DataArrayAccessor method) (in module distances) get_extra_coords_for_loadings() (PCAResult static method) get_fosc() (in module shnitsel.analyze.spectra) get_fosc_gauss_broadened() (in module shnitsel.analyze.spectra) get_full_match_dict() (GeometryFiltrationThresholds method) get_grouping_metadata() (DataSeries method), [1] (MultiSeriesDataset method), [1] get_independent_populations() (Filtration method) get_inter_state() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.stats) get_loading_parameters_with_defaults() (FormatReader method) get_loadings() (in module shnitsel.vis.plot.pca_biplot) get_max_chromophor_BLA() (DataArrayAccessor method) (in module bla_chromophor) get_MCS_smarts() (in module shnitsel.geo.analogs) get_most_significant_loadings() (PCAResult method) get_per_state() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.stats) get_positions() (in module positions) get_pyramidalization() (DataArrayAccessor method) (in module pyramids) get_registered_input_handler() (in module shnitsel.data.xr_io_registry) get_spectra() (DatasetAccessor method) (in module shnitsel.analyze.spectra) get_spectra_groups() (in module shnitsel.analyze.spectra) get_spectrum_at_time() (in module shnitsel.analyze.spectra) get_standardized_pairwise_dists (in module shnitsel.analyze.generic) get_state_color() (StateSelection method), [1] get_state_combination_color() (StateSelection method), [1] get_state_combination_degeneracy() (StateSelection method), [1]

get_state_combination_name_or_default() (StateSelection method), [1] get_state_combination_tex_label() (StateSelection method), [1] get_state_degeneracy() (StateSelection method), [1] get_state_name_or_default() (StateSelection method), [1] get_state_tex_label() (StateSelection method), [1] get_statecomb_coordinate() (in module trajectory_setup) get_subfigures_coupling_page() (DatasheetPage static method) get_subfigures_main_page() (DatasheetPage static method) get_subfigures_meta_page() (DatasheetPage static method) get_subfigures_pca_page() (DatasheetPage static method) get_symbol_from_atom_number() (in module shnitsel.data.atom_helpers) get_triangular() (in module helpers) get_type_marker() (DataSeries class method), [1] (Frames class method), [1] (InterState class method), [1] (MultiSeriesDataset class method), [1] (MultiSeriesLayered class method), [1] (MultiSeriesStacked class method), [1] (PerState class method), [1] (ShnitselDataset class method), [1] (ShnitselDerivedDataset class method) (SupportsFromXrConversion class method) (Trajectory class method), [1] get_units_with_defaults() (ASEFormatReader method) (FormatReader method) (NewtonXFormatReader method) (PyrAI2mdFormatReader method) (SHARCFormatReader method) (ShnitselFormatReader method) get_unstacked_cumulative_mask() (Filtration method) get_unstacked_cumulative_maxima() (Filtration method) get_unstacked_dataset() (Filtration method) get_unstacked_filtranda() (Filtration method) good_throughout (Filtration property) ground_state_id (StateSelection attribute), [1] ground_state_transitions() (StateSelection method), [1] group_attributes (GroupInfo attribute), [1] group_children_by() (DataGroup method), [1] (DataLeaf method), [1] (ShnitselDBRoot method), [1] (TreeNode method), [1] group_data_by_metadata() (TreeNode method), [1] group_indexers_by_index() (in module shnitsel.data.tree.selection) group_info (DataGroup property), [1] group_name (GroupInfo attribute), [1] groupable (Needs attribute) grouped_properties (GroupInfo attribute), [1] GroupInfo (class in shnitsel.data.tree) (class in shnitsel.data.tree.data_group) grouping_dimension (MultiSeriesDataset property), [1] (MultiSeriesLayered property), [1] (MultiSeriesStacked property), [1] groups_section (in module shnitsel.data.tree.tree_vis) guess_molecular_charge() (in module shnitsel.data.charge_helpers)

H

handle_records() (in module messages) Hartree (energy attribute), [1] (socs attribute) Hartree_per_Angstrom (force attribute), [1] Hartree_per_Bohr (force attribute), [1] has() (ShnitselDataset method), [1] has_coordinate() (ShnitselDataset method), [1] has_data (DelayedDataLeaf property) (TreeNode property), [1] has_data() (ShnitselDataset method), [1] has_dimension() (ShnitselDataset method), [1] has_forces (OptionalTrajectorySettings attribute) HAS_IPYTHON (in module shnitsel._state) has_required_properties() (in module trajectory_verification)

has_same_structure() (in module shnitsel.data.tree) (in module shnitsel.data.tree.support_functions) has_state() (StateSelection method), [1] has_state_combination() (StateSelection method), [1] has_variable() (ShnitselDataset method), [1] helpers module higher_order_state_pattern_re (in module shnitsel.data.state_helpers) highlight_pairs() (in module shnitsel.rd) hops (DatasheetPage property) hops() (in module shnitsel.analyze.hops) hops_mask_from_active_state() (DataArrayAccessor method) (DatasetAccessor method) (in module shnitsel.analyze.hops)

I

IcondPath (class in shnitsel.io.sharc.parse_initial_conditions) iconds_to_frames() (in module shnitsel.io.sharc) (in module shnitsel.io.sharc.parse_initial_conditions) id (StateInfo attribute) identify_analogs_mappings() (in module shnitsel.geo.analogs) identify_or_check_input_kind() (in module shnitsel.io.read) ids (StateCombInfo attribute) idx (IcondPath attribute) inchi (DatasheetPage property) InconsistentAttributeError IndividualPlotsources (in module shnitsel.vis.support.multi_plot) init_from_dataset() (StateSelection class method), [1] (StructureSelection class method), [1] init_from_descriptor() (StateSelection class method), [1] init_from_mol() (StructureSelection class method), [1] inlabel() (in module shnitsel.vis.plot.common) input_format (DataSeries property), [1] (MetaInformation attribute), [1] (RequiredTrajectorySettings attribute) input_format_name (TrajectoryGroupingMetadata attribute) input_format_version (DataSeries property), [1] (MetaInformation attribute), [1] (RequiredTrajectorySettings attribute) (TrajectoryGroupingMetadata attribute) input_type (DataSeries property), [1] (MetaInformation attribute), [1] (RequiredTrajectorySettings attribute) INPUT_TYPE_REGISTRY (in module shnitsel.data.xr_io_registry) input_units (LoadingParameters attribute) inputs (PCAResult property)

inter_state (DataSeries property), [1] (DatasheetPage property) INTERFACE_READERS (in module shnitsel.io.sharc.qm_helpers) internal() (in module shnitsel.core._api_info) intersect (StateSelection attribute), [1] (StructureSelection attribute), [1] InterState (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.inter_state) (in module shnitsel.core.typedefs) invert (StateSelection attribute), [1] (StructureSelection attribute), [1] IPythonVisualizable (class in shnitsel.vis.support.ipython_visualization) is_assignable_to() (in module shnitsel.data.helpers) is_directed (StateSelection attribute), [1] is_fancy_indexer() (in module shnitsel.data.tree.selection) is_flat_group (DataGroup property), [1] is_ipython_notebook() (in module shnitsel.core.feature_detection) is_leaf (TreeNode property), [1] is_level() (TreeNode method), [1] is_marked_for_cleanup() (in module variable_flagging) is_multi_trajectory (DataSeries property), [1] (OptionalTrajectorySettings attribute) (Trajectory property), [1] is_permitted_traj_result() (in module trajectory_verification) is_stacked() (in module shnitsel.data.multi_indices) is_variable_assigned() (in module variable_flagging) isel() (in module shnitsel.data.tree.selection) (ShnitselDataset method), [1] (TreeNode method), [1] isel_indexes() (in module shnitsel.data.tree.selection)

J

J (energy attribute), [1]

K

kabsch() (DataArrayAccessor method) (in module shnitsel.geo.alignment) (in module shnitsel.geo.geocalc) kcal (energy attribute), [1] keep_norming() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.generic)

keV (energy attribute), [1] KeyType (in module shnitsel.data.tree.data_group) (in module shnitsel.data.tree.node) (in module shnitsel.data.tree.tree) kJ (energy attribute), [1]

L

label_plot_grid() (in module shnitsel.vis.datasheet.figures.common) layer_subtree() (in module shnitsel.data.shnitsel_db_helpers) layer_trajs() (in module shnitsel.data.traj_combiner_methods) LDA (in module shnitsel.analyze.lda) lda() (DataArrayAccessor method) (in module shnitsel.analyze.lda) leading_dim (DataSeries property), [1] (Filtration attribute) (Frames property), [1] (Trajectory property), [1] leading_dimension (ShnitselDataset property), [1] leaves_section (in module shnitsel.data.tree.tree_vis) length (in module shnitsel.units) (in module shnitsel.units.definitions) (unit_dimensions attribute)

length_unit (GeometryFiltrationThresholds attribute) linear_discriminat_analysis (in module shnitsel.analyze.lda) list_iconds() (in module shnitsel.io.sharc.parse_initial_conditions) list_of_iconds (SHARCMultiInitialFormatInformation attribute) list_subtree() (in module shnitsel.data.shnitsel_db_helpers) LoadingParameters (class in helpers) loadings (PCAResult property) log_file_path (PyrAI2mdFormatInformation attribute) log_records (Trajres attribute) logger (LoadingParameters attribute) long_name (VariableInfoAttributes attribute)

M

magma_rw (in module shnitsel.vis.colormaps) main() (in module convert_to_shnitsel) (in module generate_datasheet) (in module merge_shnitsel_files) make_uniform_path() (in module helpers) map_data() (TreeNode method), [1] map_filtered_nodes() (TreeNode method), [1] map_flat_group_data() (TreeNode method), [1] map_index_queries() (in module shnitsel.data.tree.selection) map_subtree() (TreeNode method), [1] mark_dataset_for_cleanup() (in module variable_flagging) mark_variable_assigned() (in module variable_flagging) match_thresholds (GeometryFiltrationThresholds attribute) max_timestep (DataSeries property), [1] max_ts (DataSeries property), [1] (RequiredTrajectorySettings attribute) mdiff() (DataArrayAccessor method) (in module shnitsel.data.multi_indices) merge_shnitsel_files module messages module MetaData (in module shnitsel.data.xr_io_compatibility) MetaInformation (class in shnitsel.data.dataset_containers.data_series) (class in shnitsel.data.dataset_containers.trajectory) meter (distance attribute) meter_per_second (velocity attribute) mgroupby() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) midx_combs() (in module shnitsel.data.multi_indices) misc_error (Trajres attribute) misc_input_settings (DataSeries property), [1] (OptionalTrajectorySettings attribute) MissingValue (class in shnitsel.data.traj_combiner_methods) module algebra angles bla_chromophor convert_to_shnitsel dihedrals distances generate_datasheet helpers merge_shnitsel_files messages molcas_opt positions pyramids shnitsel, [1] shnitsel._accessors shnitsel._contracts shnitsel._generated_accessors shnitsel._state shnitsel.analyze shnitsel.analyze.generic shnitsel.analyze.hops shnitsel.analyze.lda shnitsel.analyze.pca shnitsel.analyze.pls shnitsel.analyze.populations shnitsel.analyze.spectra shnitsel.analyze.stats shnitsel.bridges shnitsel.clean shnitsel.clean.common shnitsel.clean.dispatch_plots shnitsel.clean.filter_energy shnitsel.clean.filter_geo shnitsel.clean.filtration_class shnitsel.core shnitsel.core._api_info shnitsel.core.feature_detection shnitsel.core.typedefs shnitsel.data shnitsel.data.atom_helpers shnitsel.data.charge_helpers shnitsel.data.dataset_containers shnitsel.data.dataset_containers.data_series shnitsel.data.dataset_containers.dataset_vis shnitsel.data.dataset_containers.frames shnitsel.data.dataset_containers.inter_state shnitsel.data.dataset_containers.multi_layered shnitsel.data.dataset_containers.multi_series shnitsel.data.dataset_containers.multi_stacked shnitsel.data.dataset_containers.per_state shnitsel.data.dataset_containers.shared shnitsel.data.dataset_containers.trajectory shnitsel.data.dataset_containers.trajectory_collection shnitsel.data.dataset_containers.xr_conversion shnitsel.data.helpers shnitsel.data.multi_indices shnitsel.data.proxy_class shnitsel.data.shnitsel_db shnitsel.data.shnitsel_db.db_function_decorator shnitsel.data.shnitsel_db_helpers shnitsel.data.state_helpers shnitsel.data.traj_combiner_methods shnitsel.data.trajectory_grouping_params shnitsel.data.trajectory_variable_description shnitsel.data.tree shnitsel.data.tree.child_support_functions shnitsel.data.tree.compound shnitsel.data.tree.data_group shnitsel.data.tree.data_leaf shnitsel.data.tree.datatree_level shnitsel.data.tree.node shnitsel.data.tree.selection shnitsel.data.tree.support_functions shnitsel.data.tree.tree shnitsel.data.tree.tree_completion shnitsel.data.tree.tree_vis shnitsel.data.tree.xr_conversion shnitsel.data.xr_io_compatibility shnitsel.data.xr_io_registry shnitsel.filtering shnitsel.filtering.helpers shnitsel.filtering.state_selection shnitsel.filtering.structure_selection shnitsel.geo shnitsel.geo.alignment shnitsel.geo.analogs shnitsel.geo.geocalc shnitsel.io shnitsel.io.ase shnitsel.io.ase.format_reader shnitsel.io.ase.parse shnitsel.io.ase.write shnitsel.io.format_reader_base shnitsel.io.format_registry shnitsel.io.newtonx shnitsel.io.newtonx.format_reader shnitsel.io.newtonx.parse shnitsel.io.pyrai2md shnitsel.io.pyrai2md.format_reader shnitsel.io.pyrai2md.parse shnitsel.io.read shnitsel.io.sharc shnitsel.io.sharc.format_reader shnitsel.io.sharc.parse_initial_conditions shnitsel.io.sharc.parse_trajectory shnitsel.io.sharc.qm_helpers shnitsel.io.shnitsel shnitsel.io.shnitsel.format_reader shnitsel.io.shnitsel.parse shnitsel.io.shnitsel.write shnitsel.io.xyz shnitsel.io.xyz.parse shnitsel.rd shnitsel.units shnitsel.units.conversion shnitsel.units.defaults shnitsel.units.definitions shnitsel.vis shnitsel.vis.colormaps shnitsel.vis.datasheet shnitsel.vis.datasheet.datasheet shnitsel.vis.datasheet.datasheet_page shnitsel.vis.datasheet.figures shnitsel.vis.datasheet.figures.common shnitsel.vis.datasheet.figures.dip_trans_hist shnitsel.vis.datasheet.figures.energy_bands shnitsel.vis.datasheet.figures.hist shnitsel.vis.datasheet.figures.nacs_hist shnitsel.vis.datasheet.figures.per_state_hist shnitsel.vis.datasheet.figures.soc_trans_hist shnitsel.vis.datasheet.figures.socs_hist shnitsel.vis.datasheet.figures.structure shnitsel.vis.datasheet.figures.time shnitsel.vis.plot shnitsel.vis.plot.common shnitsel.vis.plot.filtration shnitsel.vis.plot.kde shnitsel.vis.plot.p3mhelpers shnitsel.vis.plot.pca_biplot shnitsel.vis.plot.polychrom shnitsel.vis.plot.select shnitsel.vis.plot.spectra3d shnitsel.vis.plot.time shnitsel.vis.static shnitsel.vis.static.css shnitsel.vis.static.html shnitsel.vis.support shnitsel.vis.support.ipython_visualization shnitsel.vis.support.multi_plot shnitsel.vis.support.visualizeable shnitsel.vis.vmd shnitsel.xarray trajectory_finalization trajectory_setup trajectory_verification variable_flagging

mol (amount_units attribute) (DatasheetPage property) (ShnitselDataset property), [1] (StructureSelection attribute), [1] mol_skeletal (DatasheetPage property) mol_to_numbered_smiles() (in module shnitsel.rd) mol_to_png() (in module shnitsel.vis.datasheet.figures.structure) mol_to_svg() (in module shnitsel.vis.datasheet.figures.structure) molcas_opt module mpl_imshow_png() (in module shnitsel.vis.plot.common) mpl_svg_into_axes() (in module shnitsel.vis.plot.common) msel() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) multi_level_prefix (in module shnitsel.io.ase.parse) MultipleCompoundsError multiplicity (StateInfo attribute) MultiplicityLabel (in module shnitsel.core.typedefs) MultiplicityLabelValues (in module shnitsel.core.typedefs) MultiPlot (class in shnitsel.vis.support.multi_plot) MultiSeriesDataset (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.multi_series) MultiSeriesLayered (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.multi_layered) MultiSeriesStacked (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.multi_stacked)

N

nacs (class in shnitsel.units.definitions) (DataSeries property), [1] (InterState property), [1] (unit_dimensions attribute) nacs_norm (InterState property), [1] name (ConsistentValue attribute) (Datasheet attribute), [1] (DatasheetPage attribute) (Needs attribute) (StateCombInfo attribute) (StateInfo attribute) (TreeNode property), [1] nano_meter (distance attribute) nano_seconds (time attribute), [1] nans() (in module shnitsel.io.sharc.parse_initial_conditions) ndarray_to_json_ser() (in module shnitsel.io.shnitsel.write) Needs (class in shnitsel._contracts) needs() (in module shnitsel._contracts) NewChildType (in module shnitsel.data.tree.compound) (in module shnitsel.data.tree.data_group) (in module shnitsel.data.tree.data_leaf) (in module shnitsel.data.tree.node) (in module shnitsel.data.tree.tree) NewDataType (in module shnitsel.data.tree.node) Newton (force attribute), [1] newtonx_version (NewtonXSettingsResult attribute) NewtonXFormatInformation (class in shnitsel.io.newtonx.format_reader)

NewtonXFormatReader (class in shnitsel.io.newtonx.format_reader) NewtonXSettingsResult (class in shnitsel.io.newtonx.parse) NodeType (in module shnitsel.data.tree.support_functions) (in module trajectory_finalization) non_degenerate() (StateSelection method), [1] non_redundant() (StructureSelection method), [1] noncumulative_mask (Filtration property) norm() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.generic) normal() (in module algebra) normalize() (in module algebra) normalize_dataset() (in module trajectory_finalization) not_dims (Needs attribute) num_atoms (NewtonXSettingsResult attribute) num_doublets (DataSeries property), [1] (RequiredTrajectorySettings attribute) num_singlets (DataSeries property), [1] (RequiredTrajectorySettings attribute) num_states (NewtonXSettingsResult attribute) (TrajectoryGroupingMetadata attribute) num_steps (NewtonXSettingsResult attribute) num_triplets (DataSeries property), [1] (RequiredTrajectorySettings attribute) numbered_smiles_to_mol() (in module shnitsel.bridges) NumpyDataEncoder (class in shnitsel.io.shnitsel.write) nx_log_path (NewtonXFormatInformation attribute)

O

omit() (DatasetAccessor method) (Filtration method) (in module shnitsel.clean.common) one_per_Bohr (nacs attribute) one_per_cm (nacs attribute) (socs attribute)

one_per_m (nacs attribute) only() (StructureSelection method), [1] OptionalTrajectorySettings (class in trajectory_setup) OriginType (in module shnitsel.analyze.pca) outlabel() (in module shnitsel.vis.plot.common)

P

P (in module shnitsel._contracts) pages (Datasheet property), [1] Param (in module shnitsel.core._api_info) parse_dyn_out() (in module shnitsel.io.newtonx.parse) parse_en_data() (in module shnitsel.io.newtonx.parse) parse_input_settings() (in module shnitsel.io.sharc.parse_trajectory) parse_md_energies() (in module shnitsel.io.pyrai2md.parse) parse_molcas_log() (in module molcas_opt) parse_newtonx() (in module shnitsel.io.newtonx) (in module shnitsel.io.newtonx.parse) parse_nx_log_data() (in module shnitsel.io.newtonx.parse) parse_nx_misc_input_settings() (in module shnitsel.io.newtonx.parse) parse_observables_from_log() (in module shnitsel.io.pyrai2md.parse) parse_output_listings() (in module shnitsel.io.sharc.parse_trajectory) parse_output_log() (in module shnitsel.io.sharc.parse_trajectory) parse_output_settings() (in module shnitsel.io.sharc.parse_trajectory) parse_pyrai2md() (in module shnitsel.io.pyrai2md) (in module shnitsel.io.pyrai2md.parse) parse_QM_in() (in module shnitsel.io.sharc.parse_initial_conditions) parse_QM_log() (in module shnitsel.io.sharc.parse_initial_conditions) parse_QM_log_geom() (in module shnitsel.io.sharc.parse_initial_conditions) parse_QM_out() (in module shnitsel.io.sharc.parse_initial_conditions) parse_settings_from_nx_log() (in module shnitsel.io.newtonx.parse) parse_trajout_dat() (in module shnitsel.io.sharc.parse_trajectory) parse_trajout_xyz() (in module shnitsel.io.sharc.parse_trajectory) parse_xyz() (in module shnitsel.io.xyz) (in module shnitsel.io.xyz.parse) path (FormatInformation attribute) (IcondPath attribute) (Trajres attribute) (TreeNode property), [1] PathOptionsType (in module helpers) PCA (in module shnitsel.analyze.pca) pca() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.pca) pca_and_hops() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.pca) pca_data (DatasheetPage property) pca_direct() (in module shnitsel.analyze.pca) pca_explanation (DatasheetPage property) pca_full_data (DatasheetPage property) pca_info (DatasheetPage property) pca_line_plot() (in module shnitsel.vis.plot.polychrom) pca_mapped_dimension (PCAResult property) pca_pipeline (PCAResult property) PCAResult (class in shnitsel.analyze.pca) pcm_plots() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.spectra3d) per_state (DataSeries property), [1] (DatasheetPage property) PerState (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.per_state) (in module shnitsel.core.typedefs) pick_clusters() (in module shnitsel.vis.plot.pca_biplot) pico_meter (distance attribute) pico_seconds (time attribute), [1] plot() (Datasheet method), [1] (DatasheetPage method) (MultiPlot method) (Visualizable method) plot_bin_edges() (in module shnitsel.vis.plot.pca_biplot) plot_cdf_for_kde() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.kde) plot_ci() (in module shnitsel.vis.plot.time) plot_clusters() (in module shnitsel.vis.plot.pca_biplot) plot_clusters2 (in module shnitsel.vis.plot.pca_biplot) plot_clusters3 (in module shnitsel.vis.plot.pca_biplot) plot_clusters_grid() (in module shnitsel.vis.plot.pca_biplot) plot_clusters_insets() (in module shnitsel.vis.plot.pca_biplot) plot_coupling_page() (DatasheetPage method)

plot_dip_trans_histograms() (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_energy_bands() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.energy_bands) plot_energy_histogram() (in module shnitsel.vis.datasheet.figures.soc_trans_hist) plot_individual_source() (MultiPlot static method) plot_loadings() (in module shnitsel.vis.plot.pca_biplot) plot_many() (in module shnitsel.vis.plot.time) plot_nacs_histograms() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.nacs_hist) plot_noodle() (Datasheet method), [1] (DatasheetPage method) plot_noodleplot() (in module shnitsel.vis.plot.pca_biplot) plot_pca_structure() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.structure) plot_per_state_histograms() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.per_state_hist) plot_populations() (Filtration method) plot_populations_graph() (in module shnitsel.vis.datasheet.figures.time) plot_separated_spectra_and_hists() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_separated_spectra_and_hists_groundstate() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_separated_spectra_and_soc_dip_hists() (in module shnitsel.vis.datasheet.figures.soc_trans_hist) plot_separated_spectra_and_soc_dip_hists_groundstate() (in module shnitsel.vis.datasheet.figures.soc_trans_hist) plot_shaded() (in module shnitsel.vis.plot.time) plot_single() (in module shnitsel.vis.plot.time) plot_soc_or_dip_trans_histograms() (in module shnitsel.vis.datasheet.figures.soc_trans_hist) plot_socs_histograms() (in module shnitsel.vis.datasheet.figures.socs_hist) plot_spectra() (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_structure() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.structure) plot_thresholds() (Filtration method) plot_time_interstate_error() (in module shnitsel.vis.datasheet.figures.time) plot_timeplots() (Datasheet method), [1] (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.time) pls() (DataArrayAccessor method) (in module shnitsel.analyze.pls) pls_ds() (DatasetAccessor method) (in module shnitsel.analyze.pls) pops (DatasheetPage property) PopulationStatistics (class in shnitsel.analyze.populations) positions module positions (DataSeries property), [1] positions_file_path (NewtonXFormatInformation attribute) principal_component_analysis (in module shnitsel.analyze.pca) principal_components (PCAResult property) project_array() (PCAResult method) projected_inputs (PCAResult property) ProvidesDelayedData (class in shnitsel.data.tree.data_leaf) Proxy (class in shnitsel.data.proxy_class) public (in module shnitsel.core._api_info) pwdists() (DataArrayAccessor method) (in module shnitsel.analyze.generic) PyrAI2mdFormatInformation (class in shnitsel.io.pyrai2md.format_reader) PyrAI2mdFormatReader (class in shnitsel.io.pyrai2md.format_reader) pyramidalization_angle() (DataArrayAccessor method) (in module pyramids) pyramids module pyramids (StructureSelection attribute), [1] pyramids_selected (StructureSelection attribute), [1] pyramids_types (StructureSelection attribute), [1] PyramidsDescriptor (in module shnitsel.filtering.structure_selection)

Q

quantity_name (Converter attribute)

R

R (in module shnitsel.data.shnitsel_db_helpers) random_trajid_assigner() (in module helpers) read() (in module shnitsel) (in module shnitsel.io) (in module shnitsel.io.read) read_ase() (in module shnitsel.io.ase) (in module shnitsel.io.ase.parse) read_columbus_qm_info() (in module shnitsel.io.sharc.qm_helpers) read_data() (FormatReader method) read_folder_multi() (in module shnitsel.io.read) read_from_path() (ASEFormatReader method) (FormatReader method) (NewtonXFormatReader method) (PyrAI2mdFormatReader method) (SHARCFormatReader method) (ShnitselFormatReader method) read_iconds_individual() (in module shnitsel.io.sharc.parse_initial_conditions) read_molcas_qm_info() (in module shnitsel.io.sharc.qm_helpers) read_pyrai2md_settings_from_log() (in module shnitsel.io.pyrai2md.parse) read_shnitsel_file() (in module shnitsel.io.shnitsel) (in module shnitsel.io.shnitsel.parse) read_single() (in module shnitsel.io.read) read_traj() (in module shnitsel.io.sharc) (in module shnitsel.io.sharc.parse_trajectory)

Readable (in module shnitsel.data.xr_io_registry) register_custom_xr_input_type() (in module shnitsel.data.xr_io_registry) register_format_reader() (in module shnitsel.io.format_registry) REGISTERED_READERS (in module shnitsel.io.format_registry) relative (PopulationStatistics property) relativize() (in module shnitsel.analyze.generic) render_meta_page() (DatasheetPage method) replace_total() (in module shnitsel.analyze.generic) RequiredTrajectorySettings (class in trajectory_setup) ResDataType (in module shnitsel.data.tree.support_functions) ResType (in module shnitsel.data.tree.compound) (in module shnitsel.data.tree.data_group) (in module shnitsel.data.tree.data_leaf) (in module shnitsel.data.tree.node) (in module shnitsel.data.tree.tree) (in module shnitsel.data.xr_io_compatibility) results (PCAResult property) ResultType (in module shnitsel.analyze.pca) RetType (in module shnitsel.core._api_info) root (TreeNode property), [1] root_children_section (in module shnitsel.data.tree.tree_vis) rotational_procrustes() (in module shnitsel.geo.alignment) rotational_procrustes_np() (in module shnitsel.geo.alignment)

S

same_multiplicity_transitions() (StateSelection method), [1] sanity_check() (DatasetAccessor method) (in module shnitsel.clean) save_split() (in module shnitsel.data.helpers) seconds (time attribute), [1] sel() (in module shnitsel.data.tree.selection) (ShnitselDataset method), [1] (TreeNode method), [1] sel_trajs() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) select (StructureSelection attribute), [1] select() (StateSelection method), [1] select_all() (StructureSelection method), [1] select_angles() (StructureSelection method), [1] select_angles_by_atoms() (StructureSelection method), [1] select_atoms() (StructureSelection method), [1] select_atoms_idx() (StructureSelection method), [1] select_bats() (StructureSelection method), [1] select_BLA_chromophor() (StructureSelection method), [1] select_bonds() (StructureSelection method), [1] select_bonds_by_atoms() (StructureSelection method), [1] select_bonds_idx() (StructureSelection method), [1] select_dihedrals() (StructureSelection method), [1] select_dihedrals_by_atoms() (StructureSelection method), [1] select_pw_dists() (StructureSelection method), [1] select_pyramids() (StructureSelection method), [1] select_pyramids_by_atoms() (StructureSelection method), [1] select_state_combinations() (StateSelection method), [1] select_states() (StateSelection method), [1] selected_frame_indices (FrameSelector attribute) selection (FrameSelector property) SelfEffacingClass (class in shnitsel.xarray) set_atom_props() (in module shnitsel.rd) set_charge() (ShnitselDataset method), [1] set_compound_info() (ShnitselDBRoot method), [1] set_sharc_state_type_and_name_defaults() (in module shnitsel.data.state_helpers) set_state_charges() (StateSelection method), [1] set_state_combination_names() (StateSelection method), [1] set_state_combinations() (StateSelection method), [1] set_state_defaults() (in module trajectory_finalization) set_state_names() (StateSelection method), [1] set_state_types() (StateSelection method), [1] set_variable_attributes() (in module shnitsel.data.trajectory_variable_description) setup_defaults() (in module shnitsel.data.xr_io_registry) setup_frames() (in module shnitsel.data.helpers) setup_queue_handler() (in module messages) shapes_from_metadata() (in module shnitsel.io.ase.parse) SHARCDynamicFormatInformation (class in shnitsel.io.sharc.format_reader) SHARCFormatReader (class in shnitsel.io.sharc.format_reader) SHARCInitialFormatInformation (class in shnitsel.io.sharc.format_reader) SHARCMultiInitialFormatInformation (class in shnitsel.io.sharc.format_reader) shnitsel module, [1] shnitsel._accessors module shnitsel._contracts module shnitsel._generated_accessors module shnitsel._state module shnitsel.analyze module shnitsel.analyze.generic module shnitsel.analyze.hops module shnitsel.analyze.lda module shnitsel.analyze.pca module shnitsel.analyze.pls module shnitsel.analyze.populations module shnitsel.analyze.spectra module shnitsel.analyze.stats module shnitsel.bridges module shnitsel.clean module shnitsel.clean.common module shnitsel.clean.dispatch_plots module shnitsel.clean.filter_energy module shnitsel.clean.filter_geo module shnitsel.clean.filtration_class module shnitsel.core module shnitsel.core._api_info module shnitsel.core.feature_detection module shnitsel.core.typedefs module shnitsel.data module shnitsel.data.atom_helpers module shnitsel.data.charge_helpers module shnitsel.data.dataset_containers module shnitsel.data.dataset_containers.data_series module shnitsel.data.dataset_containers.dataset_vis module shnitsel.data.dataset_containers.frames module shnitsel.data.dataset_containers.inter_state module shnitsel.data.dataset_containers.multi_layered module shnitsel.data.dataset_containers.multi_series module shnitsel.data.dataset_containers.multi_stacked module shnitsel.data.dataset_containers.per_state module shnitsel.data.dataset_containers.shared module shnitsel.data.dataset_containers.trajectory module shnitsel.data.dataset_containers.trajectory_collection module shnitsel.data.dataset_containers.xr_conversion module shnitsel.data.helpers module shnitsel.data.multi_indices module shnitsel.data.proxy_class module shnitsel.data.shnitsel_db module shnitsel.data.shnitsel_db.db_function_decorator module shnitsel.data.shnitsel_db_helpers module shnitsel.data.state_helpers module shnitsel.data.traj_combiner_methods module shnitsel.data.trajectory_grouping_params module shnitsel.data.trajectory_variable_description module shnitsel.data.tree module shnitsel.data.tree.child_support_functions module shnitsel.data.tree.compound module shnitsel.data.tree.data_group module shnitsel.data.tree.data_leaf module shnitsel.data.tree.datatree_level module shnitsel.data.tree.node module shnitsel.data.tree.selection module shnitsel.data.tree.support_functions module shnitsel.data.tree.tree module shnitsel.data.tree.tree_completion module shnitsel.data.tree.tree_vis module shnitsel.data.tree.xr_conversion module shnitsel.data.xr_io_compatibility module shnitsel.data.xr_io_registry module shnitsel.filtering module shnitsel.filtering.helpers module shnitsel.filtering.state_selection module shnitsel.filtering.structure_selection module shnitsel.geo module shnitsel.geo.alignment module shnitsel.geo.analogs module shnitsel.geo.geocalc module shnitsel.io module shnitsel.io.ase module shnitsel.io.ase.format_reader module shnitsel.io.ase.parse module shnitsel.io.ase.write module shnitsel.io.format_reader_base module shnitsel.io.format_registry module shnitsel.io.newtonx module shnitsel.io.newtonx.format_reader module

shnitsel.io.newtonx.parse module shnitsel.io.pyrai2md module shnitsel.io.pyrai2md.format_reader module shnitsel.io.pyrai2md.parse module shnitsel.io.read module shnitsel.io.sharc module shnitsel.io.sharc.format_reader module shnitsel.io.sharc.parse_initial_conditions module shnitsel.io.sharc.parse_trajectory module shnitsel.io.sharc.qm_helpers module shnitsel.io.shnitsel module shnitsel.io.shnitsel.format_reader module shnitsel.io.shnitsel.parse module shnitsel.io.shnitsel.write module shnitsel.io.xyz module shnitsel.io.xyz.parse module shnitsel.rd module shnitsel.units module shnitsel.units.conversion module shnitsel.units.defaults module shnitsel.units.definitions module shnitsel.vis module shnitsel.vis.colormaps module shnitsel.vis.datasheet module shnitsel.vis.datasheet.datasheet module shnitsel.vis.datasheet.datasheet_page module shnitsel.vis.datasheet.figures module shnitsel.vis.datasheet.figures.common module shnitsel.vis.datasheet.figures.dip_trans_hist module shnitsel.vis.datasheet.figures.energy_bands module shnitsel.vis.datasheet.figures.hist module shnitsel.vis.datasheet.figures.nacs_hist module shnitsel.vis.datasheet.figures.per_state_hist module shnitsel.vis.datasheet.figures.soc_trans_hist module shnitsel.vis.datasheet.figures.socs_hist module shnitsel.vis.datasheet.figures.structure module shnitsel.vis.datasheet.figures.time module shnitsel.vis.plot module shnitsel.vis.plot.common module shnitsel.vis.plot.filtration module shnitsel.vis.plot.kde module shnitsel.vis.plot.p3mhelpers module shnitsel.vis.plot.pca_biplot module shnitsel.vis.plot.polychrom module shnitsel.vis.plot.select module shnitsel.vis.plot.spectra3d module shnitsel.vis.plot.time module shnitsel.vis.static module shnitsel.vis.static.css module shnitsel.vis.static.html module shnitsel.vis.support module shnitsel.vis.support.ipython_visualization module shnitsel.vis.support.multi_plot module shnitsel.vis.support.visualizeable module shnitsel.vis.vmd module shnitsel.xarray module shnitsel_blue (in module shnitsel.vis.plot.filtration) shnitsel_dataset_repr() (in module shnitsel.data.dataset_containers.dataset_vis) shnitsel_magenta (in module shnitsel.vis.plot.filtration) shnitsel_yellow (in module shnitsel.vis.plot.filtration) ShnitselAccessor (class in shnitsel._accessors) ShnitselDataset (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.shared) ShnitselDB (in module shnitsel.data.tree) (in module shnitsel.data.tree.tree) ShnitselDBRoot (class in shnitsel.data.tree) (class in shnitsel.data.tree.tree) ShnitselDerivedDataset (class in shnitsel.data.dataset_containers.shared) ShnitselFormatInformation (class in shnitsel.io.shnitsel.format_reader) ShnitselFormatReader (class in shnitsel.io.shnitsel.format_reader) single_dip_trans_hist() (in module shnitsel.vis.datasheet.figures.dip_trans_hist) (in module shnitsel.vis.datasheet.figures.soc_trans_hist) single_soc_trans_hist() (in module shnitsel.vis.datasheet.figures.soc_trans_hist) single_trans_hist() (in module shnitsel.vis.datasheet.figures.soc_trans_hist) singlet_state_pattern_re (in module shnitsel.data.state_helpers) singlets_only() (StateSelection method), [1] sizes (ShnitselDataset property), [1] ski_plots() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.spectra3d) SMARTSstring (in module shnitsel.filtering.structure_selection) smiles (DatasheetPage property) smiles_map() (DataArrayAccessor method) (in module shnitsel.bridges) socs (class in shnitsel.units.definitions) (DataSeries property), [1] (InterState property), [1] (unit_dimensions attribute) socs_norm (InterState property), [1] spectra (DatasheetPage property) spectra_excited (DatasheetPage property) spectra_ground (DatasheetPage property) spectra_groups (DatasheetPage property) spectra_times (DatasheetPage attribute) SpectraDictType (in module shnitsel.core.typedefs) split_for_saving() (in module shnitsel.data.helpers) stack_trajs() (DataArrayAccessor method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) Stacked (in module shnitsel.core.typedefs) standard_shnitsel_units (in module shnitsel.units) (in module shnitsel.units.definitions) standard_units_of_formats (in module shnitsel.units) (in module shnitsel.units.definitions) state_charges (ShnitselDataset property), [1] (StateSelection attribute), [1] state_colors (StateSelection attribute), [1] state_combination_colors (StateSelection attribute), [1] state_combination_names (StateSelection attribute), [1] state_combinations (StateSelection attribute), [1] state_combinations_base (StateSelection attribute), [1] state_degeneracy_group (ShnitselDataset property), [1] (StateSelection attribute), [1] state_diagonal (ShnitselDataset property), [1] state_ids (ShnitselDataset property), [1] state_info() (StateSelection method), [1] state_magnetic_number (ShnitselDataset property), [1] state_name_to_tex_label() (in module shnitsel.data.state_helpers) state_names (LoadingParameters attribute) (ShnitselDataset property), [1] (StateSelection attribute), [1] state_selection (DatasheetPage attribute) state_selection_provided (DatasheetPage attribute) state_types (LoadingParameters attribute) (ShnitselDataset property), [1] (StateSelection attribute), [1] StateCombination (in module shnitsel.core.typedefs) (in module shnitsel.filtering) StateCombInfo (class in shnitsel.core.typedefs) StateId (in module shnitsel.core.typedefs) (in module shnitsel.filtering) StateInfo (class in shnitsel.core.typedefs) states (StateSelection attribute), [1] states_base (StateSelection attribute), [1] StateSelection (class in shnitsel.filtering) (class in shnitsel.filtering.state_selection) StateSelectionDescriptor (in module shnitsel.filtering) (in module shnitsel.filtering.state_selection) StateTypeSpecifier (in module shnitsel.core.typedefs) STATIC_FILES (in module shnitsel.data.tree.tree_vis) struc_sel() (DSManualAccessor method) structure_atXYZ (DatasheetPage property) structure_selection (DatasheetPage attribute) structure_selection_provided (DatasheetPage attribute) structure_skeletal (DatasheetPage attribute) StructureMapping (class in shnitsel.geo.analogs) StructureSelection (class in shnitsel.filtering) (class in shnitsel.filtering.structure_selection) StructureSelectionDescriptor (in module shnitsel.filtering) (in module shnitsel.filtering.structure_selection) subgroups (DataGroup property), [1] subject_original (Filtration attribute) subleaves (DataGroup property), [1] subtract_combinations() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.generic) suitable (ShnitselAccessor attribute) summarize_attrs() (in module shnitsel.data.tree.tree_vis) summarize_tree_children() (in module shnitsel.data.tree.tree_vis) SUPPORTED_COORD_KEYS (in module shnitsel.io.ase.parse) SupportsFromXrConversion (class in shnitsel.data.xr_io_compatibility) SupportsToXrConversion (class in shnitsel.data.xr_io_compatibility) symbols (in module shnitsel.vis.datasheet.figures.per_state_hist)

T

T (in module helpers) (in module shnitsel._contracts) (in module shnitsel.data.helpers) (in module shnitsel.data.tree.node) (in module shnitsel.io.shnitsel.parse) t_max (DataSeries property), [1] (NewtonXSettingsResult attribute) (RequiredTrajectorySettings attribute) targets (Converter attribute) text_backgroundcolor (in module shnitsel.vis.plot.filtration) text_color (in module shnitsel.vis.plot.filtration) theory_basis_set (DataSeries property), [1] (MetaInformation attribute), [1] (OptionalTrajectorySettings attribute) (TrajectoryGroupingMetadata attribute) thresholds (Filtration attribute) time (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) time_grouped_confidence_interval() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.stats) timeplot() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.time) title (FrameSelector attribute) to_be (Needs attribute) to_dataarray() (EnergyFiltrationThresholds method) (GeometryFiltrationThresholds method) to_layered() (TreeNode method), [1] to_mol() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.bridges) to_stacked() (TreeNode method), [1] to_xyz() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.bridges) traj3D() (DataArrayAccessor method) (in module shnitsel.vis.plot.p3mhelpers) traj_to_xyz() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.bridges) (in module shnitsel.vis.vmd) traj_vmd() (DataArrayAccessor method) (in module shnitsel.vis.vmd) trajectories (TrajectoryCollection property) Trajectory (class in shnitsel.data.dataset_containers) (class in shnitsel.data.dataset_containers.trajectory) trajectory_finalization module trajectory_groupable (Filtration attribute)

trajectory_id (DataSeries property), [1] (LoadingParameters attribute) (OptionalTrajectorySettings attribute) trajectory_input_path (DataSeries property), [1] (OptionalTrajectorySettings attribute) (Trajectory property), [1] trajectory_setup module trajectory_verification module TrajectoryCollection (class in shnitsel.data.dataset_containers.trajectory_collection) TrajectoryGroupingMetadata (class in shnitsel.data.trajectory_grouping_params) TrajectoryOrFrames (in module shnitsel.analyze.hops) (in module shnitsel.clean.common) (in module shnitsel.clean.filter_energy) (in module shnitsel.clean.filter_geo) trajid (DataSeries property), [1] (FormatInformation attribute) (Frames property), [1] Trajres (class in shnitsel.io.read) trajs3Dgrid() (DataArrayAccessor method) (in module shnitsel.vis.plot.p3mhelpers) TrajSelector (class in shnitsel.vis.plot.select) TrajSelector() (DataArrayAccessor method) (DatasetAccessor method) TrajType (in module shnitsel.data.shnitsel_db_helpers) (in module shnitsel.io.format_reader_base) (in module trajectory_setup) transect() (DatasetAccessor method) (Filtration method) (in module shnitsel.clean.common) tree_merge() (in module shnitsel.data.tree) (in module shnitsel.data.tree.support_functions) tree_node_sections() (in module shnitsel.data.tree.tree_vis) tree_repr() (in module shnitsel.data.tree.tree_vis) tree_to_xarray_datatree() (in module shnitsel.data.tree) (in module shnitsel.data.tree.xr_conversion) tree_zip() (in module shnitsel.data.tree) (in module shnitsel.data.tree.support_functions) TreeNode (class in shnitsel.data.tree) (class in shnitsel.data.tree.node) triplet_state_pattern_re (in module shnitsel.data.state_helpers) triplets_only() (StateSelection method), [1] true_upto() (DataArrayAccessor method) (in module shnitsel.clean.common) truncate() (Dataset.st method) (DatasetAccessor method) (Filtration method) (in module shnitsel.clean.common) truncate_from_above() (in module shnitsel.vis.datasheet.figures.hist)

U

union (StateSelection attribute), [1] (StructureSelection attribute), [1] unit_dimensions (class in shnitsel.units.definitions) unit_info (VariableInfoAttributes attribute) unitdim (UnitInfo attribute) UnitInfo (class in shnitsel.data.trajectory_variable_description) units (UnitInfo attribute)

unstack_trajs() (DataArrayAccessor method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) Unstacked (in module shnitsel.core.typedefs) unstacked_trajectory_dim (Filtration attribute) unsuitable (ShnitselAccessor attribute) unwrap_single_entry_in_tree() (in module shnitsel.data.shnitsel_db_helpers)

V

v (ConsistentValue property) validate() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.helpers) validity_populations() (in module shnitsel.vis.plot.filtration) variable_flagging module

VariableInfoAttributes (class in shnitsel.data.trajectory_variable_description) velocities (DataSeries property), [1] velocity (class in shnitsel.units.definitions) (unit_dimensions attribute) verify_trajectory_format() (in module trajectory_verification) version (FormatInformation attribute) Visualizable (class in shnitsel.vis.support.visualizeable)

W

webgl (FrameSelector attribute) wrap_dataset() (in module shnitsel.data.dataset_containers) write_ase_db() (Dataset.st method) (DatasetAccessor method) (in module shnitsel), [1] (in module shnitsel.io) (in module shnitsel.io.ase) (in module shnitsel.io.ase.write)

write_shnitsel_file() (DatasetAccessor method) (in module shnitsel), [1] (in module shnitsel.io) (in module shnitsel.io.shnitsel) (in module shnitsel.io.shnitsel.write)

X

xarray_datatree_to_shnitsel_tree() (in module shnitsel.data.tree) (in module shnitsel.data.tree.xr_conversion) xname (FrameSelector attribute)

xr_dataset_to_shnitsel_format() (in module shnitsel.data.dataset_containers.xr_conversion) xr_obj (FrameSelector attribute) XRAttrType (in module shnitsel.io.shnitsel.parse)

Y

yname (FrameSelector attribute)