Index

_

__atnum2symbol__ (in module shnitsel.io.helpers) __build_conjugated_smarts() (in module shnitsel.geo.geomatch) __call__() (Converter method) __codata_version__ (in module shnitsel.units.definitions) __collect_tuples() (in module shnitsel.geo.geomatch) __delattr__() (Proxy method) __get_all_angles() (in module shnitsel.geo.geomatch) __get_all_atoms() (in module shnitsel.geo.geomatch) __get_all_bonds() (in module shnitsel.geo.geomatch) __get_all_dihedrals() (in module shnitsel.geo.geomatch) __get_angles_by_indices() (in module shnitsel.geo.geomatch) __get_atoms_by_indices() (in module shnitsel.geo.geomatch) __get_bond_info() (in module shnitsel.geo.geomatch) __get_bonds_by_indices() (in module shnitsel.geo.geomatch) __get_color_atoms() (in module shnitsel.geo.geomatch) __get_color_bonds() (in module shnitsel.geo.geomatch) __get_dihedrals_by_indices() (in module shnitsel.geo.geomatch) __get_highlight_molimg() (in module shnitsel.geo.geomatch) __get_img_multiple_mols() (in module shnitsel.geo.geomatch) __getattribute__() (Proxy method) __hash__() (Proxy method) __level_to_geo() (in module shnitsel.geo.geomatch) __match_bla_chromophor() (in module shnitsel.geo.geomatch) __match_pattern() (in module shnitsel.geo.geomatch) __name__ (Converter attribute) __nonzero__() (Proxy method) __repr__() (Proxy method) __setattr__() (Proxy method) __SHNITSEL_READERS (in module shnitsel.io.shnitsel.parse) __slots__ (Proxy attribute) __str__() (Proxy method) __symbol2atnum__ (in module shnitsel.io.helpers) _amount_unit_scales (in module shnitsel.units.definitions) _assign_descriptor_coords() (in module shnitsel.geo.geocalc) _bokeh_package_available (in module shnitsel.vis.plot.select) _charge_unit_scales (in module shnitsel.units.definitions) _check_matches() (in module shnitsel.geo.geocalc) _check_matching_dimensions() (in module shnitsel.data.shnitsel_db.combiner_methods) _check_matching_var_meta() (in module shnitsel.data.shnitsel_db.combiner_methods) _collect_metadata() (in module shnitsel.io.ase.write) _colon_whitespace_pattern (in module shnitsel.io.pyrai2md.parse) _combine_compounds_stacked() (in module shnitsel.geo.analogs) _combine_compounds_unstacked() (in module shnitsel.geo.analogs) _compare_dicts_of_values() (in module shnitsel.data.shnitsel_db.combiner_methods) _CONVERTERS (in module shnitsel.units.conversion) _coordinate_meta_keys (in module shnitsel.data.shnitsel_db.combiner_methods) _copy_data() (Datasheet method), [1] (DatasheetPage method) _create_class_proxy() (Proxy class method) _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.shnitsel_db) (in module shnitsel.data.shnitsel_db.datatree_level) _decode_shnitsel_v1_1_dataset() (in module shnitsel.io.shnitsel.parse) _decode_shnitsel_v1_2_datatree() (in module shnitsel.io.shnitsel.parse) _default_bond_length_thresholds_angstrom (in module shnitsel.clean.filter_geo) _default_energy_thresholds_eV (in module shnitsel.clean.filter_energy) _default_trajid_pattern_regex (in module shnitsel.io.format_reader_base) _dict_to_thresholds() (in module shnitsel.clean.filter_geo) _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) _empty_results() (in module shnitsel.geo.geocalc) _energy_unit_scales (in module shnitsel.units.definitions)

_fields (in module shnitsel._contracts) _find_atom_pairs() (in module shnitsel.geo.analogs) _float_pattern (in module shnitsel.io.pyrai2md.parse) _force_unit_scales (in module shnitsel.units.definitions) _get_fosc() (in module shnitsel.analyze.spectra) _ignore_none (ConsistentValue attribute) _int_pattern (in module shnitsel.io.pyrai2md.parse) _json_deserialize_ndarray() (in module shnitsel.io.ase.parse) _length_unit_scales (in module shnitsel.units.definitions) _lengths_for_searches() (in module shnitsel.clean.filter_geo) _merge_traj_metadata() (in module shnitsel.data.shnitsel_db.combiner_methods) _method_needs (ShnitselAccessor attribute) _methods (DataArrayAccessor attribute) (DatasetAccessor attribute) (ShnitselAccessor attribute) _nacs_unit_scales (in module shnitsel.units.definitions) _ndarray_of_tuples() (in module shnitsel.geo.geocalc) _ndarray_to_json_ser() (in module shnitsel.io.ase.write) _newton_reader (in module shnitsel.io.read) _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) _optional_shnitsel_attributes (in module trajectory_verification) _optional_shnitsel_variables (in module trajectory_verification) _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) _per_traj() (in module shnitsel.io.read) _positions() (in module shnitsel.geo.geocalc) _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) _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) _required_shnitsel_attributes (in module trajectory_verification) _required_shnitsel_variables (in module trajectory_verification) _selected_on_change() (FrameSelector method) (TrajSelector method) _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) _socs_unit_scale (in module shnitsel.units.definitions) _special_names (Proxy attribute) _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) _Trajectory (class in shnitsel.data.trajectory_format) _transition_identification_re (in module shnitsel.io.sharc.parse_initial_conditions) _true_on_all_leaves() (in module trajectory_verification) _val (ConsistentValue attribute) _velocity_unit_scales (in module shnitsel.units.definitions) _weak (ConsistentValue attribute) _wrap_single_trajectory() (in module shnitsel.data.trajectory_format_wrapper)

A

add_as_tree_method() (in module shnitsel.data.shnitsel_db.db_function_decorator) add_trajectory_group() (CompoundGroup method), [1] (ShnitselDBRoot method) aggregate_xr_over_levels() (in module shnitsel.data.shnitsel_db_helpers) amount_units (class in shnitsel.units.definitions) angle() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.geo.geocalc) angle_() (in module shnitsel.geo.geocalc) angle_cos_sin_() (in module shnitsel.geo.geocalc) Angstrom (distance attribute) API() (in module shnitsel.__api_info) apply_dataset_meta_from_db_metadata() (in module shnitsel.io.ase.parse) apply_trajectory_setup_properties() (ShnitselDBRoot method) ase_time_units (time attribute), [1] assign_cutoffs() (in module shnitsel.clean.common) assign_fosc() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.spectra)

assign_levels() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) assign_mask() (in module shnitsel.clean.common) assign_optional_settings() (in module trajectory_setup) assign_required_settings() (in module trajectory_setup) 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)

B

binning_with_min_entries() (in module shnitsel.vis.plot.pca_biplot) biplot_kde() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.kde) bkapp() (FrameSelector method) (TrajSelector method) Bohr (distance attribute)

Bohr_per_atu (velocity attribute) Bohr_per_fs (velocity attribute) bond_length_filtranda() (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.filter_geo) broaden_gauss() (in module shnitsel.analyze.spectra) build_shnitsel_db() (in module shnitsel.data.shnitsel_db_format)

C

calc_all() (Datasheet method), [1] (DatasheetPage method) calc_angle() (in module shnitsel.vis.plot.pca_biplot) calc_classical_populations() (DatasetAccessor method) (in module shnitsel.analyze.populations) calc_confidence_interval() (DataArrayAccessor method) (in module shnitsel.analyze.stats) calc_confidence_interval_in_array_dimensions() (in module shnitsel.analyze.stats) calc_dist() (in module shnitsel.vis.plot.pca_biplot) calc_pops (in module shnitsel.analyze.populations) calc_spectra() (in module shnitsel.analyze.spectra) calc_truncation_maximum() (in module shnitsel.vis.datasheet.figures.hist) can (DatasheetPage attribute) case_sensitive_mapping (Converter attribute) center() (in module shnitsel.analyze.generic) center_geoms() (in module shnitsel.geo.geocalc) centertext() (in module shnitsel.vis.datasheet.figures.common) charge (class in shnitsel.units.definitions) (DatasheetPage attribute) (unit_dimensions attribute) check_dims() (in module shnitsel.io.sharc.parse_initial_conditions) check_matching_dimensions() (in module shnitsel.io.read) check_matching_var_meta() (in module shnitsel.io.read) check_path_for_format_info() (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) circbins() (in module shnitsel.vis.plot.pca_biplot) cluster_general() (in module shnitsel.vis.plot.pca_biplot) cluster_loadings() (in module shnitsel.vis.plot.pca_biplot) collect_trajectories() (CompoundGroup method), [1] (in module shnitsel.data.shnitsel_db_format) (TrajectoryData method), [1] (TrajectoryGroup method), [1] combine_analogs() (in module shnitsel.geo.analogs) compare_dicts_of_values() (in module shnitsel.io.read) completed (NewtonXSettingsResult attribute) (RequiredTrajectorySettings attribute) compound_name (CompoundInfo attribute), [1] CompoundGroup (class in shnitsel.data.shnitsel_db) (class in shnitsel.data.shnitsel_db.db_compound_group) CompoundInfo (class in shnitsel.data.shnitsel_db) (class in shnitsel.data.shnitsel_db.db_compound_group) concat_subtree() (in module shnitsel.data.shnitsel_db.db_function_decorator) concat_trajs() (in module shnitsel.data.shnitsel_db.combiner_methods) (in module shnitsel.io.read)

confidence_interval_aggregate_last_dim() (in module shnitsel.analyze.stats) ConsistentValue (class in shnitsel.io.helpers) conversions (Converter attribute) convert_all_units_to_shnitsel_defaults() (in module shnitsel.units.conversion) convert_charge (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_shnitsel_tree() (in module shnitsel.data.shnitsel_db_format) 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_value() (Converter method) convert_velocity (in module shnitsel.units.conversion) Converter (class in shnitsel.units.conversion) coords (Needs attribute) coords_or_vars (Needs attribute) 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_mask_from_dataset() (in module shnitsel.clean) (in module shnitsel.clean.common) cum_mask_from_filtranda() (in module shnitsel.clean) (in module shnitsel.clean.common) cum_max_quantiles() (in module shnitsel.clean) (in module shnitsel.clean.common) custom_ylgnr (in module shnitsel.vis.colormaps) cutoffs_from_dataset() (in module shnitsel.clean.common) cutoffs_from_filtranda() (in module shnitsel.clean.common) cutoffs_from_mask() (in module shnitsel.clean.common)

D

da (FrameSelector attribute) da_or_data_var() (in module shnitsel.clean.common) DAManualAccessor (class in shnitsel._accessors) data (Trajres attribute) data_source (Datasheet attribute), [1] data_vars (Needs attribute) DATAARRAY_ACCESSOR_NAME (in module shnitsel._accessors) (in module shnitsel._state) DATAARRAY_ACCESSOR_REGISTERED (in module shnitsel._state) DataArrayAccessor (class in shnitsel._generated_accessors) dataclass_from_dict() (in module shnitsel.data.helpers) DATASET_ACCESSOR_NAME (in module shnitsel._accessors) (in module shnitsel._state) DATASET_ACCESSOR_REGISTERED (in module shnitsel._state) dataset_to_tree_method() (in module shnitsel.data.shnitsel_db.db_function_decorator) DatasetAccessor (class in shnitsel._generated_accessors) DatasetOrArray (in module shnitsel._contracts) (in module shnitsel.core.typedefs) (in module shnitsel.data.multi_indices) 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) DataTreeLevel_keys (in module shnitsel.data.shnitsel_db.datatree_level) db_from_trajs() (in module shnitsel.data.shnitsel_db.combiner_methods) (in module shnitsel.io.read) dcross() (in module shnitsel.geo.geocalc) ddot() (in module shnitsel.geo.geocalc) Debye (dipole attribute), [1] decode_attrs() (in module shnitsel.io.shnitsel.parse) default() (NumpyDataEncoder method) default_mol() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.bridges)

default_state_name_assigner() (in module shnitsel.io.helpers) default_state_type_assigner() (in module shnitsel.io.helpers) defined (ConsistentValue attribute) delta_E (DatasheetPage property) delta_t (NewtonXSettingsResult attribute) (RequiredTrajectorySettings attribute) (ShMetadataKeys attribute) df (FrameSelector attribute) df_selection (FrameSelector property) dihedral() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.geo.geocalc) dihedral_() (in module shnitsel.geo.geocalc) DimName (in module shnitsel.core.typedefs) dims (Needs attribute) 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 shnitsel.io.helpers) dipole (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) dispatch_cut() (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 shnitsel.geo.geocalc) dnorm() (in module shnitsel.geo.geocalc) ds_broaden_gauss() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.spectra) DSManualAccessor (class in shnitsel._accessors) dummy_leading_dim (in module shnitsel.io.ase.parse)

E

e (charge attribute) Eh (energy attribute), [1] Eh_per_Angstrom (force attribute), [1] Eh_per_Bohr (force attribute), [1] encode_attrs() (in module shnitsel.io.shnitsel.write) energy (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) energy_file_path (PyrAI2mdFormatInformation attribute) energy_filtranda() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.filter_energy) ensure_stacked() (in module shnitsel.clean.common) ensure_unstacked() (in module shnitsel.clean.common)

error_reporting (LoadingParameters attribute) est_level (MetaInformation attribute) (OptionalTrajectorySettings attribute) (ShMetadataKeys attribute) eV (energy attribute), [1] (socs attribute) eV_per_Angstrom (force attribute), [1] eV_per_Bohr (force attribute), [1] eval_kdes() (in module shnitsel.vis.plot.kde) expand_midx() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) extrude() (in module shnitsel.vis.plot.common)

F

femto_seconds (time attribute), [1] figax() (in module shnitsel.vis.plot.common) figaxs_defaults() (in module shnitsel.vis.datasheet.figures.common) filter_by_length() (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.filter_geo) filter_cluster_coords() (in module shnitsel.vis.plot.pca_biplot) filter_compounds() (ShnitselDBRoot method) filter_state_combinations() (StateSelection method) filter_states() (StateSelection method) filter_trajectories() (CompoundGroup method), [1] (ShnitselDBRoot method) finalize_icond_dataset() (in module shnitsel.io.sharc.parse_initial_conditions) finalize_loaded_trajectory() (in module trajectory_finalization) find_candidates_in_directory() (FormatReader method) (NewtonXFormatReader method) (PyrAI2mdFormatReader method) (SHARCFormatReader method) (ShnitselFormatReader method) fit_and_eval_kdes() (in module shnitsel.vis.plot.kde) fit_kdes() (in module shnitsel.vis.plot.kde) flag_angles() (in module shnitsel.geo.geomatch) flag_atoms() (in module shnitsel.geo.geomatch) flag_bats() (in module shnitsel.geo.geomatch) flag_bats_multiple() (in module shnitsel.geo.geomatch) flag_bla_chromophor() (in module shnitsel.geo.geomatch)

flag_bonds() (in module shnitsel.geo.geomatch) flag_dihedrals() (in module shnitsel.geo.geomatch) flag_exact() (in module shnitsel.geo.geomatch_exact) flag_nonredundant() (in module shnitsel.geo.nonred) 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) force (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) format_inchi() (in module shnitsel.vis.datasheet.figures.structure) format_name (FormatInformation attribute) FormatInformation (class in shnitsel.io.format_reader_base) FormatReader (class in shnitsel.io.format_reader_base) fosc_time (DatasheetPage property) frame3D() (DataArrayAccessor method) (in module shnitsel.vis.plot.p3mhelpers) 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) full_dihedral_() (in module shnitsel.geo.geocalc)

G

get_atom_number_from_symbol() (in module shnitsel.io.helpers) get_bats() (DataArrayAccessor method) (in module shnitsel.geo.geocalc) get_bats_matching() (in module shnitsel.geo.geomatch_exact) get_bla_chromophor() (in module shnitsel.geo.geocalc) get_bond_angles() (DataArrayAccessor method) (in module shnitsel.geo.geocalc) get_bond_lengths() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.geo.geocalc) get_bond_torsions() (DataArrayAccessor method) (in module shnitsel.geo.geocalc) get_clusters_coords() (in module shnitsel.vis.plot.pca_biplot) get_compound_info() (CompoundGroup method), [1] get_current_raw() (_Trajectory method) get_default_input_attributes() (in module shnitsel.units.defaults) get_dipoles_per_xyz() (in module shnitsel.io.xyz) (in module shnitsel.io.xyz.parse) get_fosc() (in module shnitsel.analyze.spectra) get_group_info() (TrajectoryGroup method), [1] 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_mask() (in module shnitsel.vis.plot.pca_biplot) get_original_raw() (_Trajectory method)

get_per_state() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.stats) get_pyramids() (DataArrayAccessor method) (in module shnitsel.geo.geocalc) get_smiles_order_ignoring_h() (in module shnitsel.geo.nonred) get_spectra_groups() (in module shnitsel.analyze.spectra) get_spectrum() (in module shnitsel.analyze.spectra) get_standardized_pairwise_dists (in module shnitsel.analyze.generic) get_statecomb_coordinate() (in module trajectory_setup) get_subfigures() (DatasheetPage static method) get_symbol_from_atom_number() (in module shnitsel.io.helpers) get_trajectories_with_path() (in module shnitsel.data.shnitsel_db_helpers) get_triangular() (in module shnitsel.io.helpers) get_units_with_defaults() (FormatReader method) (NewtonXFormatReader method) (PyrAI2mdFormatReader method) (SHARCFormatReader method) (ShnitselFormatReader method) get_unstacked_coord() (in module shnitsel.clean.common) get_xx_yy() (in module shnitsel.vis.plot.kde) group_attributes (GroupInfo attribute), [1] group_name (GroupInfo attribute), [1] group_subtree_by_metadata() (in module shnitsel.data.shnitsel_db.grouping_methods) groupable (Needs attribute) GroupInfo (class in shnitsel.data.shnitsel_db) (class in shnitsel.data.shnitsel_db.db_trajectory_group)

H

Hartree (energy attribute), [1] (socs attribute) Hartree_per_Angstrom (force attribute), [1] Hartree_per_Bohr (force attribute), [1]

has_forces (OptionalTrajectorySettings attribute) (ShMetadataKeys attribute) has_required_properties() (in module trajectory_verification) highlight_pairs() (in module shnitsel.rd) hops (DatasheetPage property)

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) identify_or_check_input_kind() (in module shnitsel.io.read) identify_pyramids() (in module shnitsel.geo.geocalc) idx (IcondPath attribute) inchi (DatasheetPage property) InconsistentAttributeError init_from_dataset() (StateSelection class method) inlabel() (in module shnitsel.vis.plot.common) (in module shnitsel.vis.plot.spectra3d) input_format (MetaInformation attribute) (RequiredTrajectorySettings attribute) input_format_version (MetaInformation attribute) (RequiredTrajectorySettings attribute)

input_type (MetaInformation attribute) (RequiredTrajectorySettings attribute) (ShMetadataKeys attribute) input_units (LoadingParameters attribute) inter_state (DatasheetPage property) INTERFACE_READERS (in module shnitsel.io.sharc.qm_helpers) internal() (in module shnitsel.__api_info) InterState (in module shnitsel.core.typedefs) is_level() (CompoundGroup method), [1] (ShnitselDBRoot method) (TrajectoryData method), [1] (TrajectoryGroup method), [1] is_multi_trajectory (OptionalTrajectorySettings attribute) is_permitted_traj_result() (in module trajectory_verification) is_stacked() (in module shnitsel.clean.common) is_variable_assigned() (in module variable_flagging)

J

J (energy attribute), [1]

K

kabsch() (DataArrayAccessor method) (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] KindType (in module shnitsel.io.helpers) kJ (energy attribute), [1]

L

layer_subtree() (in module shnitsel.data.shnitsel_db.db_function_decorator) layer_trajs() (in module shnitsel.data.shnitsel_db.combiner_methods) (in module shnitsel.io.read) LDA (in module shnitsel.analyze.lda) lda() (DataArrayAccessor method) (in module shnitsel.analyze.lda) length (in module shnitsel.units) (in module shnitsel.units.definitions) (unit_dimensions attribute)

linear_discriminat_analysis (in module shnitsel.analyze.lda) list_analogs() (in module shnitsel.geo.analogs) list_iconds() (in module shnitsel.io.sharc.parse_initial_conditions) list_of_iconds (SHARCMultiInitialFormatInformation attribute) list_subtree() (in module shnitsel.data.shnitsel_db.db_function_decorator) LoadingParameters (class in shnitsel.io.helpers) log_file_path (PyrAI2mdFormatInformation attribute) long_name (VariableInfoAttributes attribute)

M

magma_rw (in module shnitsel.vis.colormaps) main() (in module convert_to_shnitsel) (in module merge_shnitsel_files) make_uniform_path() (in module shnitsel.io.helpers) map_over_trajectories() (CompoundGroup method), [1] (ShnitselDBRoot method) (TrajectoryData method), [1] (TrajectoryGroup method), [1] mark_variable_assigned() (in module variable_flagging) max_ts (RequiredTrajectorySettings attribute) mdiff() (DataArrayAccessor method) (in module shnitsel.data.multi_indices) merge_shnitsel_files module merge_traj_metadata() (in module shnitsel.io.read) merge_with() (CompoundGroup method), [1] (ShnitselDBRoot method) (TrajectoryGroup method), [1] MetaInformation (class in shnitsel.data.shnitsel_db_format) 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 (OptionalTrajectorySettings attribute) MissingValue (class in shnitsel.data.tree) module convert_to_shnitsel merge_shnitsel_files molcas_opt shnitsel, [1] shnitsel.__api_info shnitsel._accessors shnitsel._contracts shnitsel._generated_accessors shnitsel._state shnitsel.analyze shnitsel.analyze.generic 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.core shnitsel.core.typedefs shnitsel.data shnitsel.data.helpers shnitsel.data.multi_indices shnitsel.data.proxy_class shnitsel.data.shnitsel_db shnitsel.data.shnitsel_db.combiner_methods shnitsel.data.shnitsel_db.datatree_level shnitsel.data.shnitsel_db.db_compound_group shnitsel.data.shnitsel_db.db_function_decorator shnitsel.data.shnitsel_db.db_trajectory_data shnitsel.data.shnitsel_db.db_trajectory_group shnitsel.data.shnitsel_db.grouping_methods shnitsel.data.shnitsel_db.helpers shnitsel.data.shnitsel_db.node_base shnitsel.data.shnitsel_db_format shnitsel.data.shnitsel_db_helpers shnitsel.data.trajectory_format shnitsel.data.trajectory_format_wrapper shnitsel.data.trajectory_variable_description shnitsel.data.tree shnitsel.filtering shnitsel.filtering.state_selection shnitsel.geo shnitsel.geo.analogs shnitsel.geo.geocalc shnitsel.geo.geomatch shnitsel.geo.geomatch_exact shnitsel.geo.nonred shnitsel.io shnitsel.io.ase shnitsel.io.ase.parse shnitsel.io.ase.write shnitsel.io.format_reader_base shnitsel.io.helpers 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.hist shnitsel.vis.datasheet.figures.nacs_hist shnitsel.vis.datasheet.figures.per_state_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.vmd shnitsel.xarray trajectory_finalization trajectory_setup trajectory_verification variable_flagging

mol (amount_units attribute) (DatasheetPage property) mol_skeletal (DatasheetPage property) mol_to_numbered_smiles() (in module shnitsel.rd) mol_to_png() (in module shnitsel.vis.datasheet.figures.structure) molcas_opt module mpl_imshow_png() (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) MultiplicityLabel (in module shnitsel.filtering.state_selection)

N

nacs (class in shnitsel.units.definitions) (unit_dimensions attribute) name (ConsistentValue attribute) (Datasheet attribute), [1] (DatasheetPage attribute) (Needs attribute) 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) 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) noodle (DatasheetPage property) norm() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.generic) normal() (in module shnitsel.geo.geocalc) not_dims (Needs attribute) num_atoms (NewtonXSettingsResult attribute) num_doublets (RequiredTrajectorySettings attribute) num_singlets (RequiredTrajectorySettings attribute) num_states (NewtonXSettingsResult attribute) num_steps (NewtonXSettingsResult attribute) num_triplets (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) (in module shnitsel.clean) (in module shnitsel.clean.common) one_per_Bohr (nacs attribute)

one_per_cm (nacs attribute) (socs attribute) one_per_m (nacs attribute) OptionalTrajectorySettings (class in trajectory_setup) outlabel() (in module shnitsel.vis.plot.common)

P

P (in module shnitsel._contracts) pairwise_dists_pca() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.pca) Param (in module shnitsel.__api_info) (in module shnitsel.data.shnitsel_db.db_function_decorator) 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) PathOptionsType (in module shnitsel.io.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_line_plot() (in module shnitsel.vis.plot.polychrom) pcm_plots() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.spectra3d) per_state (DatasheetPage property) PerState (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) 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_dip_trans_histograms() (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_kdes() (in module shnitsel.vis.plot.kde) plot_loadings() (in module shnitsel.vis.plot.pca_biplot) plot_many() (in module shnitsel.vis.plot.time) plot_nacs_histograms() (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.nacs_hist) plot_noodle() (DatasheetPage method) plot_noodleplot() (in module shnitsel.vis.plot.pca_biplot) plot_noodleplot_lines() (in module shnitsel.vis.plot.pca_biplot) plot_per_state_histograms() (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.per_state_hist) plot_populations_graph() (in module shnitsel.vis.datasheet.figures.time) plot_separated_spectra_and_hists() (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_separated_spectra_and_hists_groundstate() (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_shaded() (in module shnitsel.vis.plot.time) plot_single() (in module shnitsel.vis.plot.time) plot_spectra() (in module shnitsel.vis.datasheet.figures.dip_trans_hist) plot_structure() (DatasheetPage method) (in module shnitsel.vis.datasheet.figures.structure) plot_time_interstate_error() (in module shnitsel.vis.datasheet.figures.time) plot_timeplots() (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) positions_file_path (NewtonXFormatInformation attribute) principal_component_analysis (in module shnitsel.analyze.pca) Proxy (class in shnitsel.data.proxy_class) public (in module shnitsel.__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) pyramid_() (in module shnitsel.geo.geocalc)

Q

quantity_name (Converter attribute)

R

R (in module shnitsel.data.shnitsel_db_helpers) random_trajid_assigner() (in module shnitsel.io.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_folder_multi() (in module shnitsel.io.read) read_from_path() (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) read_trajectory() (FormatReader method) READERS (in module shnitsel.io.read) relativize() (in module shnitsel.analyze.generic) replace_total() (in module shnitsel.analyze.generic) RequiredTrajectorySettings (class in trajectory_setup) RetType (in module shnitsel.__api_info) (in module shnitsel.data.shnitsel_db.db_function_decorator) rotational_procrustes() (in module shnitsel.geo.geocalc) rotational_procrustes_() (in module shnitsel.geo.geocalc)

S

sanity_check() (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.filter_energy) save_split() (in module shnitsel.data.helpers) seconds (time attribute), [1] sel_trajids() (DataArrayAccessor method) (in module shnitsel.data.multi_indices) sel_trajs() (DataArray.st method) (DataArrayAccessor method) (Dataset.st method) (DatasetAccessor method) (in module shnitsel.data.multi_indices) selected_frame_indices (FrameSelector attribute) selection (FrameSelector property) sep_ground_excited_spectra() (in module shnitsel.analyze.spectra) separate_angles() (in module shnitsel.vis.plot.pca_biplot) set_atom_props() (in module shnitsel.rd) set_axes() (in module shnitsel.vis.plot.time) set_compound_info() (ShnitselDBRoot method) set_sharc_state_type_and_name_defaults() (in module shnitsel.io.sharc.qm_helpers) set_state_defaults() (in module trajectory_finalization) set_variable_attributes() (in module shnitsel.data.trajectory_variable_description) setup_frames() (in module shnitsel.data.helpers) 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) ShMetadataKeys (class in shnitsel.data.shnitsel_db.grouping_methods) shnitsel module, [1] shnitsel.__api_info module shnitsel._accessors module shnitsel._contracts module shnitsel._generated_accessors module shnitsel._state module shnitsel.analyze module shnitsel.analyze.generic 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.core module shnitsel.core.typedefs module shnitsel.data module shnitsel.data.helpers module shnitsel.data.multi_indices module shnitsel.data.proxy_class module shnitsel.data.shnitsel_db module shnitsel.data.shnitsel_db.combiner_methods module shnitsel.data.shnitsel_db.datatree_level module shnitsel.data.shnitsel_db.db_compound_group module shnitsel.data.shnitsel_db.db_function_decorator module shnitsel.data.shnitsel_db.db_trajectory_data module shnitsel.data.shnitsel_db.db_trajectory_group module shnitsel.data.shnitsel_db.grouping_methods module shnitsel.data.shnitsel_db.helpers module shnitsel.data.shnitsel_db.node_base module shnitsel.data.shnitsel_db_format module shnitsel.data.shnitsel_db_helpers module shnitsel.data.trajectory_format module shnitsel.data.trajectory_format_wrapper module shnitsel.data.trajectory_variable_description module shnitsel.data.tree module shnitsel.filtering module shnitsel.filtering.state_selection module shnitsel.geo module shnitsel.geo.analogs module shnitsel.geo.geocalc module shnitsel.geo.geomatch module shnitsel.geo.geomatch_exact module shnitsel.geo.nonred module shnitsel.io module shnitsel.io.ase module shnitsel.io.ase.parse module shnitsel.io.ase.write module shnitsel.io.format_reader_base module shnitsel.io.helpers 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.hist module shnitsel.vis.datasheet.figures.nacs_hist module shnitsel.vis.datasheet.figures.per_state_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.vmd module shnitsel.xarray module shnitsel_blue (in module shnitsel.vis.plot.filtration) shnitsel_magenta (in module shnitsel.vis.plot.filtration) shnitsel_yellow (in module shnitsel.vis.plot.filtration) ShnitselAccessor (class in shnitsel._accessors) ShnitselDB (in module shnitsel.data.shnitsel_db_format) ShnitselDBRoot (class in shnitsel.data.shnitsel_db_format) ShnitselFormatInformation (class in shnitsel.io.shnitsel.format_reader) ShnitselFormatReader (class in shnitsel.io.shnitsel.format_reader) ShnitselNode (class in shnitsel.data.shnitsel_db.node_base) single_hist() (in module shnitsel.vis.datasheet.figures.dip_trans_hist) ski_plots() (in module shnitsel.vis.plot) (in module shnitsel.vis.plot.spectra3d) smiles (DatasheetPage property) smiles_map() (DataArrayAccessor method) (in module shnitsel.bridges) socs (class in shnitsel.units.definitions) (unit_dimensions attribute) software (ShMetadataKeys attribute) spectra (DatasheetPage property) spectra_all_times() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.analyze.spectra) 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) st_yellow (in module shnitsel.geo.geomatch) stack_trajs() (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 (StateSelection attribute) state_combination_names (StateSelection attribute) state_combinations (StateSelection attribute) state_names (LoadingParameters attribute) (StateSelection attribute) state_types (LoadingParameters attribute) (StateSelection attribute) StateCombination (in module shnitsel.filtering.state_selection) StateId (in module shnitsel.filtering.state_selection) states (StateSelection attribute) StateSelection (class in shnitsel.filtering.state_selection) structure_atXYZ (DatasheetPage property) structure_skeletal (DatasheetPage attribute) subtract_combinations() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.analyze.generic) suitable (ShnitselAccessor attribute) symbols (in module shnitsel.vis.datasheet.figures.common)

T

T (in module shnitsel._contracts) (in module shnitsel.data.helpers) (in module shnitsel.data.shnitsel_db.db_compound_group) (in module shnitsel.data.shnitsel_db.db_function_decorator) (in module shnitsel.data.shnitsel_db.db_trajectory_data) (in module shnitsel.data.shnitsel_db.db_trajectory_group) (in module shnitsel.data.shnitsel_db_format) (in module shnitsel.data.shnitsel_db_helpers) (in module shnitsel.io.shnitsel.parse) t_max (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 (ShMetadataKeys attribute) theory_basis_set (MetaInformation attribute) (OptionalTrajectorySettings attribute) time (class in shnitsel.units) (class in shnitsel.units.definitions) (unit_dimensions attribute) time_grouped_confidence_interval() (DataArrayAccessor method) (in module shnitsel.analyze.stats) timeplot() (in module shnitsel.vis.plot.time) title (FrameSelector attribute) to_be (Needs attribute) to_groupname() (ShMetadataKeys method) to_mol() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.bridges) to_xyz() (DataArray.st method) (DataArrayAccessor method) (in module shnitsel.bridges) traj3D() (DataArrayAccessor method) (in module shnitsel.vis.plot.p3mhelpers) traj_list_to_child_mapping() (in module shnitsel.data.shnitsel_db.helpers) 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) Trajectory (in module shnitsel.data.trajectory_format) trajectory_finalization module trajectory_id (LoadingParameters attribute) trajectory_input_path (OptionalTrajectorySettings attribute) trajectory_setup module trajectory_verification module TrajectoryData (class in shnitsel.data.shnitsel_db) (class in shnitsel.data.shnitsel_db.db_trajectory_data) TrajectoryGroup (class in shnitsel.data.shnitsel_db) (class in shnitsel.data.shnitsel_db.db_trajectory_group) trajid (FormatInformation attribute) Trajid (in module shnitsel.io.read) trajid (OptionalTrajectorySettings attribute) 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) transect() (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.common) tree_to_frames() (in module shnitsel.data.tree) true_upto() (DataArrayAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.common) truncate() (Dataset.st method) (DatasetAccessor method) (in module shnitsel.clean) (in module shnitsel.clean.common) truncate_from_above() (in module shnitsel.vis.datasheet.figures.hist) ts_to_time() (in module shnitsel.data.helpers)

U

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() (DatasetAccessor method) (in module shnitsel.data.multi_indices) Unstacked (in module shnitsel.core.typedefs) 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) velocity (class in shnitsel.units.definitions) (unit_dimensions attribute) verify_trajectory_format() (in module trajectory_verification) version (FormatInformation attribute) (ShMetadataKeys attribute)

W

webgl (FrameSelector attribute) wrap_trajectory() (in module shnitsel.data.trajectory_format_wrapper) write_ase_db() (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

xname (FrameSelector attribute)

Y

yname (FrameSelector attribute)