shnitsel._generated_accessors ============================= .. py:module:: shnitsel._generated_accessors Classes ------- .. autoapisummary:: shnitsel._generated_accessors.DataArrayAccessor shnitsel._generated_accessors.DatasetAccessor Module Contents --------------- .. py:class:: DataArrayAccessor(obj) Bases: :py:obj:`shnitsel._accessors.DAManualAccessor` .. py:attribute:: _methods :value: ['norm', 'subtract_combinations', 'pairwise_dists_pca', 'sudi', 'hop_indices', 'relativize',... .. py:method:: norm(dim = 'direction', keep_attrs = None) Wrapper for :py:func:`shnitsel.core.postprocess.norm`. .. py:method:: subtract_combinations(dim, labels = False) Wrapper for :py:func:`shnitsel.core.postprocess.subtract_combinations`. .. py:method:: pairwise_dists_pca(**kwargs) Wrapper for :py:func:`shnitsel.core.postprocess.pairwise_dists_pca`. .. py:method:: sudi() Wrapper for :py:func:`shnitsel.core.postprocess.sudi`. .. py:method:: hop_indices() Wrapper for :py:func:`shnitsel.core.postprocess.hop_indices`. .. py:method:: relativize(**sel) Wrapper for :py:func:`shnitsel.core.postprocess.relativize`. .. py:method:: ts_to_time(delta_t = None, old = 'drop') Wrapper for :py:func:`shnitsel.core.postprocess.ts_to_time`. .. py:method:: keep_norming(exclude = None) Wrapper for :py:func:`shnitsel.core.postprocess.keep_norming`. .. py:method:: calc_ci(confidence = 0.95) Wrapper for :py:func:`shnitsel.core.postprocess.calc_ci`. .. py:method:: time_grouped_ci(confidence = 0.9) Wrapper for :py:func:`shnitsel.core.postprocess.time_grouped_ci`. .. py:method:: to_xyz(comment='#') Wrapper for :py:func:`shnitsel.core.postprocess.to_xyz`. .. py:method:: traj_to_xyz() Wrapper for :py:func:`shnitsel.core.postprocess.traj_to_xyz`. .. py:method:: dihedral(i, j, k, l, deg = False, full = False) Wrapper for :py:func:`shnitsel.core.postprocess.dihedral`. .. py:method:: angle(i, j, k, deg = False) Wrapper for :py:func:`shnitsel.core.postprocess.angle`. .. py:method:: distance(i, j) Wrapper for :py:func:`shnitsel.core.postprocess.distance`. .. py:method:: trajs_with_hops() Wrapper for :py:func:`shnitsel.core.postprocess.trajs_with_hops`. .. py:method:: get_hop_types() Wrapper for :py:func:`shnitsel.core.postprocess.get_hop_types`. .. py:method:: to_mol(charge=None, covFactor=1.2, to2D=True, molAtomMapNumber=None, atomNote=None, atomLabel=None) Wrapper for :py:func:`shnitsel.core.postprocess.to_mol`. .. py:method:: default_mol() Wrapper for :py:func:`shnitsel.core.postprocess.default_mol`. .. py:method:: convert_energy(to) Wrapper for :py:func:`shnitsel.core.postprocess.convert_energy`. .. py:method:: convert_forces(to) Wrapper for :py:func:`shnitsel.core.postprocess.convert_forces`. .. py:method:: convert_dipoles(to) Wrapper for :py:func:`shnitsel.core.postprocess.convert_dipoles`. .. py:method:: convert_length(to) Wrapper for :py:func:`shnitsel.core.postprocess.convert_length`. .. py:method:: flatten_levels(idx_name, levels, new_name = None, position = 0, renamer = None) Wrapper for :py:func:`shnitsel.core.xrhelpers.flatten_levels`. .. py:method:: expand_midx(midx_name, level_name, value) Wrapper for :py:func:`shnitsel.core.xrhelpers.expand_midx`. .. py:method:: assign_levels(levels = None, **levels_kwargs) Wrapper for :py:func:`shnitsel.core.xrhelpers.assign_levels`. .. py:method:: mgroupby(levels) Wrapper for :py:func:`shnitsel.core.xrhelpers.mgroupby`. .. py:method:: msel(**kwargs) Wrapper for :py:func:`shnitsel.core.xrhelpers.msel`. .. py:method:: sel_trajs(trajids_or_mask, invert=False) Wrapper for :py:func:`shnitsel.core.xrhelpers.sel_trajs`. .. py:method:: sel_trajids(trajids, invert=False) Wrapper for :py:func:`shnitsel.core.xrhelpers.sel_trajids`. .. py:method:: smiles_map(charge=0, covFactor=1.5) Wrapper for :py:func:`shnitsel.core.filter_unphysical.smiles_map`. .. py:method:: last_time_where() Wrapper for :py:func:`shnitsel.core.filtre.last_time_where`. .. py:method:: get_bond_lengths(bond_types=None, mol=None) Wrapper for :py:func:`shnitsel.core.geom.get_bond_lengths`. .. py:method:: get_bond_angles(angle_types=None, mol=None, deg=False) Wrapper for :py:func:`shnitsel.core.geom.get_bond_angles`. .. py:method:: get_bond_torsions(quadruple_types=None, mol=None, signed=False, deg=False) Wrapper for :py:func:`shnitsel.core.geom.get_bond_torsions`. .. py:method:: get_bats(mol=None, signed=False, deg=False) Wrapper for :py:func:`shnitsel.core.geom.get_bats`. .. py:method:: kabsch(reference_or_indexers = None, **indexers_kwargs) Wrapper for :py:func:`shnitsel.core.geom.kabsch`. .. py:method:: FrameSelector(xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True) Wrapper for :py:func:`shnitsel.core.plot.select.FrameSelector`. .. py:method:: TrajSelector(xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True) Wrapper for :py:func:`shnitsel.core.plot.select.TrajSelector`. .. py:method:: frame3D() Wrapper for :py:func:`shnitsel.core.plot.p3mhelpers.frame3D`. .. py:method:: frames3Dgrid() Wrapper for :py:func:`shnitsel.core.plot.p3mhelpers.frames3Dgrid`. .. py:method:: traj3D() Wrapper for :py:func:`shnitsel.core.plot.p3mhelpers.traj3D`. .. py:method:: trajs3Dgrid(trajids = None, loop='forward') Wrapper for :py:func:`shnitsel.core.plot.p3mhelpers.trajs3Dgrid`. .. py:method:: pca(dim, n_components = 2, return_pca_object = False) Wrapper for :py:func:`shnitsel.core.ml.pca`. .. py:method:: lda(dim, cats, n_components=2) Wrapper for :py:func:`shnitsel.core.ml.lda`. .. py:method:: pls(yda, n_components=2, common_dim=None) Wrapper for :py:func:`shnitsel.core.ml.pls`. .. py:class:: DatasetAccessor(obj) Bases: :py:obj:`shnitsel._accessors.DSManualAccessor` .. py:attribute:: _methods :value: ['pca_and_hops', 'validate', 'ts_to_time', 'setup_frames', 'assign_fosc', 'broaden_gauss',... .. py:method:: pca_and_hops() Wrapper for :py:func:`shnitsel.core.postprocess.pca_and_hops`. .. py:method:: validate() Wrapper for :py:func:`shnitsel.core.postprocess.validate`. .. py:method:: ts_to_time(delta_t = None, old = 'drop') Wrapper for :py:func:`shnitsel.core.postprocess.ts_to_time`. .. py:method:: setup_frames(to_time = None, convert_to_eV = None, convert_e_kin_to_eV = None, relativize_energy = None, relativize_selector=None) Wrapper for :py:func:`shnitsel.core.postprocess.setup_frames`. .. py:method:: assign_fosc() Wrapper for :py:func:`shnitsel.core.postprocess.assign_fosc`. .. py:method:: broaden_gauss(fosc, agg_dim = 'frame', width = 0.5, nsamples = 1000, xmax = None) Wrapper for :py:func:`shnitsel.core.postprocess.broaden_gauss`. .. py:method:: get_per_state() Wrapper for :py:func:`shnitsel.core.postprocess.get_per_state`. .. py:method:: get_inter_state() Wrapper for :py:func:`shnitsel.core.postprocess.get_inter_state`. .. py:method:: calc_pops() Wrapper for :py:func:`shnitsel.core.postprocess.calc_pops`. .. py:method:: find_hops() Wrapper for :py:func:`shnitsel.core.postprocess.find_hops`. .. py:method:: default_mol() Wrapper for :py:func:`shnitsel.core.postprocess.default_mol`. .. py:method:: flatten_levels(idx_name, levels, new_name = None, position = 0, renamer = None) Wrapper for :py:func:`shnitsel.core.xrhelpers.flatten_levels`. .. py:method:: expand_midx(midx_name, level_name, value) Wrapper for :py:func:`shnitsel.core.xrhelpers.expand_midx`. .. py:method:: assign_levels(levels = None, **levels_kwargs) Wrapper for :py:func:`shnitsel.core.xrhelpers.assign_levels`. .. py:method:: mgroupby(levels) Wrapper for :py:func:`shnitsel.core.xrhelpers.mgroupby`. .. py:method:: msel(**kwargs) Wrapper for :py:func:`shnitsel.core.xrhelpers.msel`. .. py:method:: save_frames(path, complevel=9) Wrapper for :py:func:`shnitsel.core.xrhelpers.save_frames`. .. py:method:: sel_trajs(trajids_or_mask, invert=False) Wrapper for :py:func:`shnitsel.core.xrhelpers.sel_trajs`. .. py:method:: unstack_trajs() Wrapper for :py:func:`shnitsel.core.xrhelpers.unstack_trajs`. .. py:method:: stack_trajs() Wrapper for :py:func:`shnitsel.core.xrhelpers.stack_trajs`. .. py:method:: iconds_to_frames() Wrapper for :py:func:`shnitsel.core.parse.sharc_icond.iconds_to_frames`. .. py:method:: spectra_all_times() Wrapper for :py:func:`shnitsel.core.plot.spectra3d.spectra_all_times`. .. py:method:: energy_filtranda() Wrapper for :py:func:`shnitsel.core.filtre.energy_filtranda`. .. py:method:: get_cutoffs() Wrapper for :py:func:`shnitsel.core.filtre.get_cutoffs`. .. py:method:: truncate(cutoffs) Wrapper for :py:func:`shnitsel.core.filtre.truncate`. .. py:method:: write_ase(db_path, kind, keys = None, preprocess = True) Wrapper for :py:func:`shnitsel.core.ase.write_ase`. .. py:method:: pls_ds(xname, yname, n_components=2) Wrapper for :py:func:`shnitsel.core.ml.pls_ds`.