Index Symbols | _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z Symbols --angles soprano-spinsys command line option --average-group soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --cell soprano-splitmols command line option --cell-indices soprano-splitmols command line option --center soprano-splitmols command line option --centre soprano-splitmols command line option --colormap soprano-plotnmr command line option --config soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --connectors soprano-plotnmr command line option --contour soprano-plotnmr command line option --contour-color soprano-plotnmr command line option --contour-levels soprano-plotnmr command line option --contour-linewidth soprano-plotnmr command line option --cross-terms soprano-spinsys command line option --cutoff soprano-dipolar command line option --default-vdw soprano-splitmols command line option --diag soprano-plotnmr command line option --dip soprano-spinsys command line option --dipolar-angles soprano-spinsys command line option --efg soprano-spinsys command line option --efg-angles soprano-spinsys command line option --efg-tag soprano-nmr command line option soprano-spinsys command line option --euler soprano-nmr command line option soprano-plotnmr command line option --exclude soprano-dipolar command line option soprano-nmr command line option --format soprano-spinsys command line option soprano-splitmols command line option --grad soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option --gradients soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option --grid soprano-plotnmr command line option --heatmap soprano-plotnmr command line option --include soprano-dipolar command line option soprano-nmr command line option --isonuclear soprano-dipolar command line option --isotopes soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option --jcoupling soprano-spinsys command line option --jcoupling-angles soprano-spinsys command line option --legend soprano-plotnmr command line option --marker-color soprano-plotnmr command line option --marker-linewidth soprano-plotnmr command line option --marker-symbol soprano-plotnmr command line option --markers soprano-plotnmr command line option --max-marker-size soprano-plotnmr command line option --mean-merge soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --merge soprano-dipolar command line option soprano-nmr command line option --ms soprano-spinsys command line option --ms-angles soprano-spinsys command line option --ms-iso soprano-spinsys command line option --ms-tag soprano-nmr command line option soprano-spinsys command line option --no-cell-indices soprano-splitmols command line option --no-connectors soprano-plotnmr command line option --no-contour soprano-plotnmr command line option --no-cross-terms soprano-spinsys command line option --no-diag soprano-plotnmr command line option --no-dip soprano-spinsys command line option --no-dipolar-angles soprano-spinsys command line option --no-efg soprano-spinsys command line option --no-efg-angles soprano-spinsys command line option --no-grid soprano-plotnmr command line option --no-heatmap soprano-plotnmr command line option --no-jcoupling soprano-spinsys command line option --no-jcoupling-angles soprano-spinsys command line option --no-legend soprano-plotnmr command line option --no-markers soprano-plotnmr command line option --no-mean-merge soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --no-ms soprano-spinsys command line option --no-ms-angles soprano-spinsys command line option --no-reduce soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --no-ticklabels soprano-plotnmr command line option --no-write soprano-splitmols command line option --obs soprano-spinsys command line option --observed-nucleus soprano-spinsys command line option --output soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option --output-dir soprano-splitmols command line option --output-format soprano-dipolar command line option soprano-nmr command line option --plot_type soprano-plotnmr command line option --precision soprano-dipolar command line option soprano-nmr command line option --program soprano-spinsys command line option --properties soprano-nmr command line option --q-order soprano-spinsys command line option --query soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option --rcut soprano-plotnmr command line option --reduce soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --ref soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option --references soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option --rss soprano-dipolar command line option --scale-marker-by soprano-plotnmr command line option --seedname soprano-splitmols command line option --select-i soprano-dipolar command line option soprano-spinsys command line option --select-j soprano-dipolar command line option soprano-spinsys command line option --shielding soprano-plotnmr command line option --sort-order soprano-dipolar command line option soprano-nmr command line option --sortby soprano-dipolar command line option soprano-nmr command line option --split soprano-spinsys command line option --subset soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --symprec soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option --ticklabels soprano-plotnmr command line option --vac soprano-splitmols command line option --vacuum soprano-splitmols command line option --vdw-custom soprano-splitmols command line option --vdw-scale soprano-splitmols command line option --vdw-set soprano-splitmols command line option --verbosity soprano command line option soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-splitmols command line option soprano-view command line option --view soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-splitmols command line option --xbroadening soprano-plotnmr command line option --xelement soprano-plotnmr command line option --xlim soprano-plotnmr command line option --yaxis-order soprano-plotnmr command line option --ybroadening soprano-plotnmr command line option --yelement soprano-plotnmr command line option --ylim soprano-plotnmr command line option -c soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-splitmols command line option soprano-view command line option -cmap soprano-plotnmr command line option -f soprano-dipolar command line option soprano-nmr command line option soprano-spinsys command line option soprano-splitmols command line option -g soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-view command line option -i soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option -m soprano-dipolar command line option soprano-nmr command line option -ms soprano-plotnmr command line option -o soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-splitmols command line option -p soprano-nmr command line option soprano-plotnmr command line option -s soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-splitmols command line option soprano-view command line option -v soprano command line option soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-spinsys command line option soprano-splitmols command line option soprano-view command line option -x soprano-plotnmr command line option -y soprano-plotnmr command line option _ __add__() (soprano.collection.collection.AtomsCollection method) __array__() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) __array_ufunc__() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) __call__() (soprano.properties.basic.basic.CalcEnergy method) (soprano.properties.basic.basic.LatticeABC method) (soprano.properties.basic.basic.LatticeCart method) (soprano.properties.basic.basic.NumAtoms method) (soprano.properties.castep.castep.CastepEnthalpy method) (soprano.properties.labeling.labeling.CarbonHybridationState method) (soprano.properties.labeling.labeling.HydrogenBondTypes method) (soprano.properties.labeling.labeling.MagresViewLabels method) (soprano.properties.labeling.labeling.MoleculeSites method) (soprano.properties.labeling.labeling.SiteLabels method) (soprano.properties.labeling.labeling.UniqueSites method) (soprano.properties.linkage.linkage.BondGraph method) (soprano.properties.linkage.linkage.Bonds method) (soprano.properties.linkage.linkage.CoordinationHistogram method) (soprano.properties.linkage.linkage.DihedralAngleList method) (soprano.properties.linkage.linkage.ElementPairs method) (soprano.properties.linkage.linkage.HydrogenBonds method) (soprano.properties.linkage.linkage.HydrogenBondsNumber method) (soprano.properties.linkage.linkage.LinkageList method) (soprano.properties.linkage.linkage.MoleculeCOM method) (soprano.properties.linkage.linkage.MoleculeCOMLinkage method) (soprano.properties.linkage.linkage.MoleculeMass method) (soprano.properties.linkage.linkage.MoleculeNumber method) (soprano.properties.linkage.linkage.MoleculeQuaternion method) (soprano.properties.linkage.linkage.MoleculeRelativeRotation method) (soprano.properties.linkage.linkage.Molecules method) (soprano.properties.linkage.linkage.MoleculeSpectralSort method) (soprano.properties.map.map.Remap method) (soprano.properties.map.map.RemapIndices method) (soprano.properties.nmr.dipolar.DipolarCoupling method) (soprano.properties.nmr.dipolar.DipolarCouplingList method) (soprano.properties.nmr.dipolar.DipolarDiagonal method) (soprano.properties.nmr.dipolar.DipolarEuler method) (soprano.properties.nmr.dipolar.DipolarRSS method) (soprano.properties.nmr.dipolar.DipolarTensor method) (soprano.properties.nmr.efg.EFGAnisotropy method) (soprano.properties.nmr.efg.EFGAsymmetry method) (soprano.properties.nmr.efg.EFGDiagonal method) (soprano.properties.nmr.efg.EFGEuler method) (soprano.properties.nmr.efg.EFGNQR method) (soprano.properties.nmr.efg.EFGQuadrupolarConstant method) (soprano.properties.nmr.efg.EFGQuadrupolarProduct method) (soprano.properties.nmr.efg.EFGQuaternion method) (soprano.properties.nmr.efg.EFGReducedAnisotropy method) (soprano.properties.nmr.efg.EFGSkew method) (soprano.properties.nmr.efg.EFGSpan method) (soprano.properties.nmr.efg.EFGTensor method) (soprano.properties.nmr.efg.EFGVzz method) (soprano.properties.nmr.isc.ISCDiagonal method) (soprano.properties.nmr.isc.JCAnisotropy method) (soprano.properties.nmr.isc.JCAsymmetry method) (soprano.properties.nmr.isc.JCDiagonal method) (soprano.properties.nmr.isc.JCEuler method) (soprano.properties.nmr.isc.JCIsotropy method) (soprano.properties.nmr.isc.JCouplingList method) (soprano.properties.nmr.isc.JCQuaternion method) (soprano.properties.nmr.isc.JCReducedAnisotropy method) (soprano.properties.nmr.isc.JCSkew method) (soprano.properties.nmr.isc.JCSpan method) (soprano.properties.nmr.isc.JCTensor method) (soprano.properties.nmr.isc.KTensor method) (soprano.properties.nmr.ms.MSAnisotropy method) (soprano.properties.nmr.ms.MSAsymmetry method) (soprano.properties.nmr.ms.MSDiagonal method) (soprano.properties.nmr.ms.MSEuler method) (soprano.properties.nmr.ms.MSIsotropy method) (soprano.properties.nmr.ms.MSQuaternion method) (soprano.properties.nmr.ms.MSReducedAnisotropy method) (soprano.properties.nmr.ms.MSShielding method) (soprano.properties.nmr.ms.MSShift method) (soprano.properties.nmr.ms.MSSkew method) (soprano.properties.nmr.ms.MSSpan method) (soprano.properties.nmr.ms.MSTensor method) (soprano.properties.nmr.spinsystem.NMRSites method) (soprano.properties.nmr.spinsystem.NMRSpinSystem method) (soprano.properties.order.order.BondOrder method) (soprano.properties.symmetry.symmetry.SymmetryDataset method) (soprano.properties.symmetry.symmetry.WyckoffPoints method) (soprano.properties.transform.transform.Mirror method) (soprano.properties.transform.transform.Rotate method) (soprano.properties.transform.transform.Translate method) __copy__() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __deepcopy__() (soprano.collection.collection.AtomsCollection method) (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __dir__() (soprano.nmr.tensor.TensorConvention method) __eq__() (soprano.nmr.site.Site method) (soprano.nmr.tensor.NMRTensor method) __get_pydantic_json_schema__() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) __getattr__() (soprano.collection.collection._AllCaller method) __getitem__() (soprano.collection.collection.AtomsCollection method) (soprano.selection.AtomSelection method) __hash__() (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) (soprano.nmr.tensor.NMRTensor method) __iter__() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __pretty__() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __pydantic_init_subclass__() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) __pydantic_on_complete__() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) __repr__() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) __repr_name__() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __repr_recursion__() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __rich_repr__() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) __str__() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) _AllCaller (class in soprano.collection.collection) _anisotropy() (in module soprano.nmr.utils) _asdict() (soprano.calculate.xrd.xrd.XraySpectrum method) (soprano.calculate.xrd.xrd.XraySpectrumData method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift method) (soprano.nmr.tensor.MagneticShielding.IUPACShielding method) (soprano.nmr.tensor.MagneticShielding.IUPACShift method) (soprano.nmr.tensor.MagneticShielding.MarylandShielding method) (soprano.nmr.tensor.MagneticShielding.MarylandShift method) (soprano.nmr.tensor.MagneticShielding.MehringShielding method) (soprano.nmr.tensor.MagneticShielding.MehringShift method) (soprano.properties.symmetry.symmetry.WyckoffPoint method) _asymmetry() (in module soprano.nmr.utils) _check_binary_op_params() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) _check_compatible() (soprano.nmr.tensor.ElectricFieldGradient class method) (soprano.nmr.tensor.MagneticShielding class method) (soprano.nmr.tensor.NMRTensor class method) _compute_bonds() (in module soprano.properties.linkage.linkage) _create_like() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) _dip_constant() (in module soprano.nmr.utils) _dip_tensor() (in module soprano.nmr.utils) _el_iso() (in module soprano.data.nmr) _ensure_open_sftp() (in module soprano.hpc.submitter.utils) _ensure_tensor_format() (in module soprano.nmr.utils) _equivalent_euler() (in module soprano.nmr.utils) _equivalent_relative_euler() (in module soprano.nmr.utils) _evals_sort() (in module soprano.nmr.utils) _evecs_2_quat() (in module soprano.nmr.utils) _evenq() (in module soprano.calculate.xrd.sel_rules) _find_wyckoff_points() (in module soprano.properties.symmetry.utils) _gauss_peak_default() (in module soprano.calculate.xrd.xrd) _get_isotope_list() (in module soprano.data.nmr) _get_referenced_eigenvalues() (soprano.nmr.tensor.MagneticShielding static method) _get_symmetry_dataset() (in module soprano.properties.symmetry.utils) _get_symmetry_ops() (in module soprano.properties.symmetry.utils) _get_tensor_array() (in module soprano.nmr.utils) _gradients_to_list() (in module soprano.nmr.utils) _handle_euler_edge_cases() (in module soprano.nmr.utils) _hash() (soprano.selection.AtomSelection method) _ifq() (in module soprano.calculate.xrd.sel_rules) _initialisation_params (soprano.nmr.tensor.ElectricFieldGradient property) (soprano.nmr.tensor.MagneticShielding property) (soprano.nmr.tensor.NMRTensor property) _integerq() (in module soprano.calculate.xrd.sel_rules) _J_constant() (in module soprano.nmr.utils) _leBail_rescale_I() (in module soprano.calculate.xrd.xrd) _loci_intersect() (in module soprano.properties.symmetry.utils) _main_loop() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) _make() (soprano.calculate.xrd.xrd.XraySpectrum class method) (soprano.calculate.xrd.xrd.XraySpectrumData class method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding class method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift class method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding class method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift class method) (soprano.nmr.tensor.MagneticShielding.IUPACShielding class method) (soprano.nmr.tensor.MagneticShielding.IUPACShift class method) (soprano.nmr.tensor.MagneticShielding.MarylandShielding class method) (soprano.nmr.tensor.MagneticShielding.MarylandShift class method) (soprano.nmr.tensor.MagneticShielding.MehringShielding class method) (soprano.nmr.tensor.MagneticShielding.MehringShift class method) (soprano.properties.symmetry.symmetry.WyckoffPoint class method) _matrix_to_euler() (in module soprano.nmr.utils) _normalise_euler_angles() (in module soprano.nmr.utils) _plot_annotations() (soprano.calculate.nmr.nmr.NMRPlot2D method) _putjob_remote() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) _rebuild_coupling_indices() (soprano.nmr.spin_system.SpinSystem method) _recalc() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) _references_to_list() (in module soprano.nmr.utils) _replace() (soprano.calculate.xrd.xrd.XraySpectrum method) (soprano.calculate.xrd.xrd.XraySpectrumData method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift method) (soprano.nmr.tensor.MagneticShielding.IUPACShielding method) (soprano.nmr.tensor.MagneticShielding.IUPACShift method) (soprano.nmr.tensor.MagneticShielding.MarylandShielding method) (soprano.nmr.tensor.MagneticShielding.MarylandShift method) (soprano.nmr.tensor.MagneticShielding.MehringShielding method) (soprano.nmr.tensor.MagneticShielding.MehringShift method) (soprano.properties.symmetry.symmetry.WyckoffPoint method) _Rwp_eval() (in module soprano.calculate.xrd.xrd) _setattr_handler() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) _skew() (in module soprano.nmr.utils) _span() (in module soprano.nmr.utils) _species_list_to_isotope_dict() (in module soprano.data.nmr) _species_list_to_isotope_list() (in module soprano.data.nmr) _split_species() (in module soprano.nmr.utils) _steinhardt_pars() (in module soprano.properties.order.order) _test_euler_rotation() (in module soprano.nmr.utils) _tryallanglestest() (in module soprano.nmr.utils) _valid_triples() (in module soprano.properties.order.order) _validate_df_output_extension() (in module soprano.scripts.cli_utils) _w99_field_definition() (in module soprano.calculate.gulp.w99) _write_spinsys_legacy() (in module soprano.calculate.nmr.simpson) _write_spinsys_spinsys() (in module soprano.calculate.nmr.simpson) _wyckoff_isohess() (in module soprano.properties.symmetry.utils) A abc2cart() (in module soprano.utils) add_note() (soprano.analyse.phylogen.genes.GeneError method) (soprano.calculate.gulp.w99.W99Error method) add_signal() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) add_site() (soprano.nmr.spin_system.SpinSystem method) additionGen() (in module soprano.collection.generate.defect) airssGen() (in module soprano.collection.generate.airss) all() (soprano.selection.AtomSelection static method) all_periodic() (in module soprano.utils) apply_df_filtering() (in module soprano.scripts.cli_utils) AtomsCollection (class in soprano.collection.collection) AtomSelection (class in soprano.selection) average_quaternions() (in module soprano.utils) average_quaternions_by_tags() (in module soprano.scripts.cli_utils) B B (soprano.calculate.nmr.nmr.NMRCalculator property) bondDistance() (in module soprano.measure) BondGraph (class in soprano.properties.linkage.linkage) BondOrder (class in soprano.properties.order.order) Bonds (class in soprano.properties.linkage.linkage) build_custom_vdw() (in module soprano.data.vdw) build_nmr_df() (in module soprano.scripts.nmr) C CalcEnergy (class in soprano.properties.basic.basic) calculate_distances() (in module soprano.calculate.nmr.utils) capitalize() (soprano.nmr.tensor.TensorConvention method) CarbonHybridationState (class in soprano.properties.labeling.labeling) cart2abc() (in module soprano.utils) casefold() (soprano.nmr.tensor.TensorConvention method) CastepEnthalpy (class in soprano.properties.castep.castep) CastepSubmitter (class in soprano.hpc.submitter.castep) center() (soprano.nmr.tensor.TensorConvention method) check_equivalent_sites_ms() (in module soprano.scripts.nmr) check_job() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) check_quadrupole_active() (in module soprano.nmr.tensor) check_tree() (soprano.collection.collection.AtomsCollection static method) chunkify() (soprano.collection.collection.AtomsCollection method) classify() (soprano.collection.collection.AtomsCollection method) clebsch_gordan() (in module soprano.utils) compute_asymmetric_distmat() (in module soprano.utils) confmat() (in module soprano.analyse.phylogen.metrics) contains_nmr_tensors() (in module soprano.nmr.tensor) context (soprano.hpc.submitter.utils.RemoteTarget property) CoordinationHistogram (class in soprano.properties.linkage.linkage) copy() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) count() (soprano.calculate.xrd.xrd.XraySpectrum method) (soprano.calculate.xrd.xrd.XraySpectrumData method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift method) (soprano.nmr.tensor.MagneticShielding.IUPACShielding method) (soprano.nmr.tensor.MagneticShielding.IUPACShift method) (soprano.nmr.tensor.MagneticShielding.MarylandShielding method) (soprano.nmr.tensor.MagneticShielding.MarylandShift method) (soprano.nmr.tensor.MagneticShielding.MehringShielding method) (soprano.nmr.tensor.MagneticShielding.MehringShift method) (soprano.nmr.tensor.TensorConvention method) (soprano.properties.symmetry.symmetry.WyckoffPoint method) Coupling (class in soprano.nmr.coupling) coupling_constant (soprano.nmr.coupling.DipolarCoupling property) coupling_list_to_mrsimulator() (in module soprano.nmr.coupling) Cq (soprano.nmr.tensor.ElectricFieldGradient property) create_mapping() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) D dataset_range() (soprano.calculate.xrd.xrd.XRDCalculator method) DebugQueueInterface (class in soprano.hpc.submitter.debug.debugqueue) defectGen() (in module soprano.collection.generate.defect) degeneracy (soprano.nmr.tensor.ElectricFieldGradient property) (soprano.nmr.tensor.MagneticShielding property) (soprano.nmr.tensor.NMRTensor property) delta (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding attribute) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift attribute) delta_11 (soprano.nmr.tensor.MagneticShielding.IUPACShift attribute) (soprano.nmr.tensor.MagneticShielding.MehringShift attribute) delta_22 (soprano.nmr.tensor.MagneticShielding.IUPACShift attribute) (soprano.nmr.tensor.MagneticShielding.MehringShift attribute) delta_33 (soprano.nmr.tensor.MagneticShielding.IUPACShift attribute) (soprano.nmr.tensor.MagneticShielding.MehringShift attribute) delta_iso (soprano.nmr.tensor.MagneticShielding.HaeberlenShift attribute) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift attribute) (soprano.nmr.tensor.MagneticShielding.IUPACShift attribute) (soprano.nmr.tensor.MagneticShielding.MarylandShift attribute) (soprano.nmr.tensor.MagneticShielding.MehringShift attribute) DihedralAngleList (class in soprano.properties.linkage.linkage) dipolar_coupling_from_distance_vector() (in module soprano.nmr.coupling) DipolarCoupling (class in soprano.nmr.coupling) (class in soprano.properties.nmr.dipolar) DipolarCouplingList (class in soprano.properties.nmr.dipolar) DipolarDiagonal (class in soprano.properties.nmr.dipolar) DipolarEuler (class in soprano.properties.nmr.dipolar) DipolarRSS (class in soprano.properties.nmr.dipolar) DipolarTensor (class in soprano.properties.nmr.dipolar) dq_buildup() (soprano.calculate.nmr.nmr.NMRCalculator method) E EFGAnisotropy (class in soprano.properties.nmr.efg) EFGAsymmetry (class in soprano.properties.nmr.efg) EFGDiagonal (class in soprano.properties.nmr.efg) EFGEuler (class in soprano.properties.nmr.efg) EFGNQR (class in soprano.properties.nmr.efg) EFGQuadrupolarConstant (class in soprano.properties.nmr.efg) EFGQuadrupolarProduct (class in soprano.properties.nmr.efg) EFGQuaternion (class in soprano.properties.nmr.efg) EFGReducedAnisotropy (class in soprano.properties.nmr.efg) EFGSkew (class in soprano.properties.nmr.efg) EFGSpan (class in soprano.properties.nmr.efg) EFGTensor (class in soprano.properties.nmr.efg) EFGVzz (class in soprano.properties.nmr.efg) ElectricFieldGradient (class in soprano.nmr.tensor) element (soprano.nmr.site.Site property) (soprano.nmr.tensor.MagneticShielding property) element_set (soprano.nmr.spin_system.SpinSystem property) ElementPairs (class in soprano.properties.linkage.linkage) encode() (soprano.nmr.tensor.TensorConvention method) endswith() (soprano.nmr.tensor.TensorConvention method) equivalent_euler_angles() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) equivalent_euler_to() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) equivalent_to() (soprano.calculate.nmr.utils.Peak2D method) eta (soprano.nmr.tensor.ElectricFieldGradient property) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding attribute) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift attribute) euclideanDistance() (in module soprano.measure) euler_angles() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) euler_to() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) evaluate() (soprano.analyse.phylogen.genes.Gene method) exp_dataset() (soprano.calculate.xrd.xrd.XRDCalculator method) expandtabs() (soprano.nmr.tensor.TensorConvention method) extract() (soprano.properties.basic.basic.CalcEnergy static method) (soprano.properties.basic.basic.LatticeABC static method) (soprano.properties.basic.basic.LatticeCart static method) (soprano.properties.basic.basic.NumAtoms static method) (soprano.properties.castep.castep.CastepEnthalpy static method) (soprano.properties.labeling.labeling.CarbonHybridationState static method) (soprano.properties.labeling.labeling.HydrogenBondTypes static method) (soprano.properties.labeling.labeling.MagresViewLabels static method) (soprano.properties.labeling.labeling.MoleculeSites static method) (soprano.properties.labeling.labeling.SiteLabels static method) (soprano.properties.labeling.labeling.UniqueSites static method) (soprano.properties.linkage.linkage.BondGraph static method) (soprano.properties.linkage.linkage.Bonds static method) (soprano.properties.linkage.linkage.CoordinationHistogram static method) (soprano.properties.linkage.linkage.DihedralAngleList static method) (soprano.properties.linkage.linkage.ElementPairs static method) (soprano.properties.linkage.linkage.HydrogenBonds static method) (soprano.properties.linkage.linkage.HydrogenBondsNumber static method) (soprano.properties.linkage.linkage.LinkageList static method) (soprano.properties.linkage.linkage.MoleculeCOM static method) (soprano.properties.linkage.linkage.MoleculeCOMLinkage static method) (soprano.properties.linkage.linkage.MoleculeMass static method) (soprano.properties.linkage.linkage.MoleculeNumber static method) (soprano.properties.linkage.linkage.MoleculeQuaternion static method) (soprano.properties.linkage.linkage.MoleculeRelativeRotation static method) (soprano.properties.linkage.linkage.Molecules static method) (soprano.properties.linkage.linkage.MoleculeSpectralSort static method) (soprano.properties.map.map.Remap static method) (soprano.properties.map.map.RemapIndices static method) (soprano.properties.nmr.dipolar.DipolarCoupling static method) (soprano.properties.nmr.dipolar.DipolarCouplingList static method) (soprano.properties.nmr.dipolar.DipolarDiagonal static method) (soprano.properties.nmr.dipolar.DipolarEuler static method) (soprano.properties.nmr.dipolar.DipolarRSS static method) (soprano.properties.nmr.dipolar.DipolarTensor static method) (soprano.properties.nmr.efg.EFGAnisotropy static method) (soprano.properties.nmr.efg.EFGAsymmetry static method) (soprano.properties.nmr.efg.EFGDiagonal static method) (soprano.properties.nmr.efg.EFGEuler static method) (soprano.properties.nmr.efg.EFGNQR static method) (soprano.properties.nmr.efg.EFGQuadrupolarConstant static method) (soprano.properties.nmr.efg.EFGQuadrupolarProduct static method) (soprano.properties.nmr.efg.EFGQuaternion static method) (soprano.properties.nmr.efg.EFGReducedAnisotropy static method) (soprano.properties.nmr.efg.EFGSkew static method) (soprano.properties.nmr.efg.EFGSpan static method) (soprano.properties.nmr.efg.EFGTensor static method) (soprano.properties.nmr.efg.EFGVzz static method) (soprano.properties.nmr.isc.ISCDiagonal static method) (soprano.properties.nmr.isc.JCAnisotropy static method) (soprano.properties.nmr.isc.JCAsymmetry static method) (soprano.properties.nmr.isc.JCDiagonal static method) (soprano.properties.nmr.isc.JCEuler static method) (soprano.properties.nmr.isc.JCIsotropy static method) (soprano.properties.nmr.isc.JCouplingList static method) (soprano.properties.nmr.isc.JCQuaternion static method) (soprano.properties.nmr.isc.JCReducedAnisotropy static method) (soprano.properties.nmr.isc.JCSkew static method) (soprano.properties.nmr.isc.JCSpan static method) (soprano.properties.nmr.isc.JCTensor static method) (soprano.properties.nmr.isc.KTensor static method) (soprano.properties.nmr.ms.MSAnisotropy static method) (soprano.properties.nmr.ms.MSAsymmetry static method) (soprano.properties.nmr.ms.MSDiagonal static method) (soprano.properties.nmr.ms.MSEuler static method) (soprano.properties.nmr.ms.MSIsotropy static method) (soprano.properties.nmr.ms.MSQuaternion static method) (soprano.properties.nmr.ms.MSReducedAnisotropy static method) (soprano.properties.nmr.ms.MSShielding static method) (soprano.properties.nmr.ms.MSShift static method) (soprano.properties.nmr.ms.MSSkew static method) (soprano.properties.nmr.ms.MSSpan static method) (soprano.properties.nmr.ms.MSTensor static method) (soprano.properties.nmr.spinsystem.NMRSites static method) (soprano.properties.nmr.spinsystem.NMRSpinSystem static method) (soprano.properties.order.order.BondOrder static method) (soprano.properties.symmetry.symmetry.SymmetryDataset static method) (soprano.properties.symmetry.symmetry.WyckoffPoints static method) (soprano.properties.transform.transform.Mirror static method) (soprano.properties.transform.transform.Rotate static method) (soprano.properties.transform.transform.Translate static method) extract_dipolar_couplings() (in module soprano.scripts.dipolar) extract_dipolar_RSS_couplings() (in module soprano.scripts.dipolar) F FILE soprano-spinsys command line option FILENAME soprano-splitmols command line option FILES soprano-dipolar command line option soprano-nmr command line option soprano-plotnmr command line option soprano-view command line option filter() (soprano.collection.collection.AtomsCollection method) filter_atoms_by_elements() (in module soprano.calculate.nmr.utils) filter_pairs_by_distance() (in module soprano.calculate.nmr.utils) find() (soprano.nmr.tensor.TensorConvention method) find_w99_atomtypes() (in module soprano.calculate.gulp.w99) find_XHn_groups() (in module soprano.scripts.cli_utils) finish_job() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) finish_run() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) format() (soprano.nmr.tensor.TensorConvention method) format_map() (soprano.nmr.tensor.TensorConvention method) fowles_mallows_index() (in module soprano.analyse.phylogen.metrics) fpos (soprano.properties.symmetry.symmetry.WyckoffPoint attribute) from_array() (soprano.selection.AtomSelection static method) from_bonds() (soprano.selection.AtomSelection static method) from_box() (soprano.selection.AtomSelection static method) from_dict() (soprano.nmr.site.Site class method) from_distance_vector() (soprano.nmr.coupling.DipolarCoupling class method) from_element() (soprano.selection.AtomSelection static method) from_input() (soprano.selection.AtomSelection static method) from_mrsimulator() (soprano.nmr.spin_system.SpinSystem method) from_selection_string() (soprano.selection.AtomSelection static method) from_sphere() (soprano.selection.AtomSelection static method) G gaussian() (in module soprano.calculate.nmr.utils) Gene (class in soprano.analyse.phylogen.genes) GeneDictionary (class in soprano.analyse.phylogen.genes) GeneError generate_contour_map() (in module soprano.calculate.nmr.utils) generate_peaks() (in module soprano.calculate.nmr.utils) genomes2png() (in module soprano.scripts.phylogen) get() (soprano.properties.basic.basic.CalcEnergy class method) (soprano.properties.basic.basic.LatticeABC class method) (soprano.properties.basic.basic.LatticeCart class method) (soprano.properties.basic.basic.NumAtoms class method) (soprano.properties.castep.castep.CastepEnthalpy class method) (soprano.properties.labeling.labeling.CarbonHybridationState class method) (soprano.properties.labeling.labeling.HydrogenBondTypes class method) (soprano.properties.labeling.labeling.MagresViewLabels class method) (soprano.properties.labeling.labeling.MoleculeSites class method) (soprano.properties.labeling.labeling.SiteLabels class method) (soprano.properties.labeling.labeling.UniqueSites class method) (soprano.properties.linkage.linkage.BondGraph class method) (soprano.properties.linkage.linkage.Bonds class method) (soprano.properties.linkage.linkage.CoordinationHistogram class method) (soprano.properties.linkage.linkage.DihedralAngleList class method) (soprano.properties.linkage.linkage.ElementPairs class method) (soprano.properties.linkage.linkage.HydrogenBonds class method) (soprano.properties.linkage.linkage.HydrogenBondsNumber class method) (soprano.properties.linkage.linkage.LinkageList class method) (soprano.properties.linkage.linkage.MoleculeCOM class method) (soprano.properties.linkage.linkage.MoleculeCOMLinkage class method) (soprano.properties.linkage.linkage.MoleculeMass class method) (soprano.properties.linkage.linkage.MoleculeNumber class method) (soprano.properties.linkage.linkage.MoleculeQuaternion class method) (soprano.properties.linkage.linkage.MoleculeRelativeRotation class method) (soprano.properties.linkage.linkage.Molecules class method) (soprano.properties.linkage.linkage.MoleculeSpectralSort class method) (soprano.properties.map.map.Remap class method) (soprano.properties.map.map.RemapIndices class method) (soprano.properties.nmr.dipolar.DipolarCoupling class method) (soprano.properties.nmr.dipolar.DipolarCouplingList class method) (soprano.properties.nmr.dipolar.DipolarDiagonal class method) (soprano.properties.nmr.dipolar.DipolarEuler class method) (soprano.properties.nmr.dipolar.DipolarRSS class method) (soprano.properties.nmr.dipolar.DipolarTensor class method) (soprano.properties.nmr.efg.EFGAnisotropy class method) (soprano.properties.nmr.efg.EFGAsymmetry class method) (soprano.properties.nmr.efg.EFGDiagonal class method) (soprano.properties.nmr.efg.EFGEuler class method) (soprano.properties.nmr.efg.EFGNQR class method) (soprano.properties.nmr.efg.EFGQuadrupolarConstant class method) (soprano.properties.nmr.efg.EFGQuadrupolarProduct class method) (soprano.properties.nmr.efg.EFGQuaternion class method) (soprano.properties.nmr.efg.EFGReducedAnisotropy class method) (soprano.properties.nmr.efg.EFGSkew class method) (soprano.properties.nmr.efg.EFGSpan class method) (soprano.properties.nmr.efg.EFGTensor class method) (soprano.properties.nmr.efg.EFGVzz class method) (soprano.properties.nmr.isc.ISCDiagonal class method) (soprano.properties.nmr.isc.JCAnisotropy class method) (soprano.properties.nmr.isc.JCAsymmetry class method) (soprano.properties.nmr.isc.JCDiagonal class method) (soprano.properties.nmr.isc.JCEuler class method) (soprano.properties.nmr.isc.JCIsotropy class method) (soprano.properties.nmr.isc.JCouplingList class method) (soprano.properties.nmr.isc.JCQuaternion class method) (soprano.properties.nmr.isc.JCReducedAnisotropy class method) (soprano.properties.nmr.isc.JCSkew class method) (soprano.properties.nmr.isc.JCSpan class method) (soprano.properties.nmr.isc.JCTensor class method) (soprano.properties.nmr.isc.KTensor class method) (soprano.properties.nmr.ms.MSAnisotropy class method) (soprano.properties.nmr.ms.MSAsymmetry class method) (soprano.properties.nmr.ms.MSDiagonal class method) (soprano.properties.nmr.ms.MSEuler class method) (soprano.properties.nmr.ms.MSIsotropy class method) (soprano.properties.nmr.ms.MSQuaternion class method) (soprano.properties.nmr.ms.MSReducedAnisotropy class method) (soprano.properties.nmr.ms.MSShielding class method) (soprano.properties.nmr.ms.MSShift class method) (soprano.properties.nmr.ms.MSSkew class method) (soprano.properties.nmr.ms.MSSpan class method) (soprano.properties.nmr.ms.MSTensor class method) (soprano.properties.nmr.spinsystem.NMRSites class method) (soprano.properties.nmr.spinsystem.NMRSpinSystem class method) (soprano.properties.order.order.BondOrder class method) (soprano.properties.symmetry.symmetry.SymmetryDataset class method) (soprano.properties.symmetry.symmetry.WyckoffPoints class method) (soprano.properties.transform.transform.Mirror class method) (soprano.properties.transform.transform.Rotate class method) (soprano.properties.transform.transform.Translate class method) get_array() (soprano.collection.collection.AtomsCollection method) (soprano.selection.AtomSelection method) get_atom_labels() (in module soprano.calculate.nmr.utils) get_bonding_distance() (in module soprano.utils) get_cluster_stats() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_clusters() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_column_list() (in module soprano.scripts.cli_utils) get_dipolar_couplings() (in module soprano.properties.nmr.spinsystem) get_distmat() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_duplicates() (in module soprano.scripts.cli_utils) get_efg_summary() (in module soprano.scripts.nmr) get_elbow_plot() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_energy() (in module soprano.calculate.nmr.utils) get_force_matrix() (in module soprano.calculate.nmr.utils) get_gene() (soprano.analyse.phylogen.genes.GeneDictionary class method) get_genome_matrices() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_genome_matrices_norm() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_genome_vectors() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_genome_vectors_norm() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_gulp_charges() (in module soprano.calculate.gulp.charges) get_hier_clusters() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_hier_tree() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_isotope_list_from_species() (in module soprano.data.nmr) get_j_couplings() (in module soprano.properties.nmr.spinsystem) get_kmeans_clusters() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_larmor_frequency() (soprano.calculate.nmr.nmr.NMRCalculator method) (soprano.nmr.tensor.ElectricFieldGradient method) get_linkage() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_matching_cols() (in module soprano.scripts.cli_utils) get_max_cluster_dist() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_missing_cols() (in module soprano.scripts.cli_utils) get_ms_summary() (in module soprano.scripts.nmr) get_pair_dipolar_couplings() (in module soprano.calculate.nmr.utils) get_pair_j_couplings() (in module soprano.calculate.nmr.utils) get_pairs() (soprano.calculate.nmr.nmr.NMRData2D method) get_peaks() (soprano.calculate.nmr.nmr.NMRData2D method) get_sel_rule_from_hall() (in module soprano.calculate.xrd.sel_rules) get_sel_rule_from_international() (in module soprano.calculate.xrd.sel_rules) get_sites() (in module soprano.properties.nmr.spinsystem) get_sklearn_clusters() (in module soprano.utils) (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) get_spin_system() (in module soprano.properties.nmr.spinsystem) get_symmetry_dataset() (in module soprano.properties.symmetry.backend) get_symmetry_ops_from_hall() (in module soprano.properties.symmetry.backend) get_total_forces() (in module soprano.calculate.nmr.utils) get_w99_energy() (in module soprano.calculate.gulp.w99) H haeberlen_shielding (soprano.nmr.tensor.MagneticShielding property) has() (soprano.collection.collection.AtomsCollection method) (soprano.selection.AtomSelection method) has_CH_bonds() (in module soprano.scripts.cli_utils) has_cif_labels() (in module soprano.utils) has_moyopy() (in module soprano.optional) has_reference() (in module soprano.nmr.tensor) has_spglib() (in module soprano.optional) has_symmetry_backend() (in module soprano.optional) help() (soprano.analyse.phylogen.genes.GeneDictionary class method) herzfeldberger_shielding (soprano.nmr.tensor.MagneticShielding property) hessian (soprano.properties.symmetry.symmetry.WyckoffPoint attribute) hkl (soprano.calculate.xrd.xrd.XraySpectrum attribute) hkl2d2_matgen() (in module soprano.utils) hkl_unique (soprano.calculate.xrd.xrd.XraySpectrum attribute) HydrogenBonds (class in soprano.properties.linkage.linkage) HydrogenBondsNumber (class in soprano.properties.linkage.linkage) HydrogenBondTypes (class in soprano.properties.labeling.labeling) I index() (soprano.calculate.xrd.xrd.XraySpectrum method) (soprano.calculate.xrd.xrd.XraySpectrumData method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding method) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding method) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift method) (soprano.nmr.tensor.MagneticShielding.IUPACShielding method) (soprano.nmr.tensor.MagneticShielding.IUPACShift method) (soprano.nmr.tensor.MagneticShielding.MarylandShielding method) (soprano.nmr.tensor.MagneticShielding.MarylandShift method) (soprano.nmr.tensor.MagneticShielding.MehringShielding method) (soprano.nmr.tensor.MagneticShielding.MehringShift method) (soprano.nmr.tensor.TensorConvention method) (soprano.properties.symmetry.symmetry.WyckoffPoint method) intensity (soprano.calculate.xrd.xrd.XraySpectrum attribute) (soprano.calculate.xrd.xrd.XraySpectrumData attribute) inv_plane_dist() (in module soprano.utils) invd (soprano.calculate.xrd.xrd.XraySpectrum attribute) is_pair (soprano.analyse.phylogen.genes.Gene property) is_quadrupole_active (soprano.nmr.tensor.ElectricFieldGradient property) is_string() (in module soprano.utils) isalnum() (soprano.nmr.tensor.TensorConvention method) isalpha() (soprano.nmr.tensor.TensorConvention method) isascii() (soprano.nmr.tensor.TensorConvention method) ISCDiagonal (class in soprano.properties.nmr.isc) ISCoupling (class in soprano.nmr.coupling) isdecimal() (soprano.nmr.tensor.TensorConvention method) isdigit() (soprano.nmr.tensor.TensorConvention method) isidentifier() (soprano.nmr.tensor.TensorConvention method) islower() (soprano.nmr.tensor.TensorConvention method) isnumeric() (soprano.nmr.tensor.TensorConvention method) isotope_selection() (in module soprano.scripts.cli_utils) (in module soprano.scripts.extract_nmr) isotope_set (soprano.nmr.spin_system.SpinSystem property) isprintable() (soprano.nmr.tensor.TensorConvention method) isspace() (soprano.nmr.tensor.TensorConvention method) istitle() (soprano.nmr.tensor.TensorConvention method) isupper() (soprano.nmr.tensor.TensorConvention method) iupac_shielding (soprano.nmr.tensor.MagneticShielding property) J J_anisotropy (soprano.nmr.coupling.ISCoupling property) J_asymmetry (soprano.nmr.coupling.ISCoupling property) J_eigenvectors (soprano.nmr.coupling.ISCoupling property) J_evals (soprano.nmr.coupling.ISCoupling property) J_reduced_anisotropy (soprano.nmr.coupling.ISCoupling property) JCAnisotropy (class in soprano.properties.nmr.isc) JCAsymmetry (class in soprano.properties.nmr.isc) JCDiagonal (class in soprano.properties.nmr.isc) JCEuler (class in soprano.properties.nmr.isc) JCIsotropy (class in soprano.properties.nmr.isc) JCoupling (in module soprano.nmr.coupling) JCouplingList (class in soprano.properties.nmr.isc) JCQuaternion (class in soprano.properties.nmr.isc) JCReducedAnisotropy (class in soprano.properties.nmr.isc) JCSkew (class in soprano.properties.nmr.isc) JCSpan (class in soprano.properties.nmr.isc) JCTensor (class in soprano.properties.nmr.isc) Jisotropy (soprano.nmr.coupling.ISCoupling property) join() (soprano.nmr.tensor.TensorConvention method) K kappa (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding attribute) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift attribute) (soprano.nmr.tensor.MagneticShielding.MarylandShielding attribute) (soprano.nmr.tensor.MagneticShielding.MarylandShift attribute) keyvalue_parser() (in module soprano.scripts.cli_utils) kill() (soprano.hpc.submitter.debug.debugqueue.DebugQueueInterface method) (soprano.hpc.submitter.queues.QueueInterface method) KTensor (class in soprano.properties.nmr.isc) L lambdax (soprano.calculate.xrd.xrd.XraySpectrum attribute) LatticeABC (class in soprano.properties.basic.basic) LatticeCart (class in soprano.properties.basic.basic) lebail_fit() (soprano.calculate.xrd.xrd.XRDCalculator method) LinkageList (class in soprano.properties.linkage.linkage) linspaceGen() (in module soprano.collection.generate.linspace) list() (soprano.hpc.submitter.debug.debugqueue.DebugQueueInterface method) (soprano.hpc.submitter.queues.QueueInterface method) list_distance() (in module soprano.utils) ljust() (soprano.nmr.tensor.TensorConvention method) load() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster static method) (soprano.collection.collection.AtomsCollection static method) load_genefile() (in module soprano.analyse.phylogen.genes) load_simpson_dat() (in module soprano.calculate.nmr.simpson) load_state() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) load_tree() (soprano.collection.collection.AtomsCollection static method) lorentzian() (in module soprano.calculate.nmr.utils) lower() (soprano.nmr.tensor.TensorConvention method) lstrip() (soprano.nmr.tensor.TensorConvention method) M MagneticShielding (class in soprano.nmr.tensor) MagneticShielding.HaeberlenShielding (class in soprano.nmr.tensor) MagneticShielding.HaeberlenShift (class in soprano.nmr.tensor) MagneticShielding.HerzfeldBergerShielding (class in soprano.nmr.tensor) MagneticShielding.HerzfeldBergerShift (class in soprano.nmr.tensor) MagneticShielding.IUPACShielding (class in soprano.nmr.tensor) MagneticShielding.IUPACShift (class in soprano.nmr.tensor) MagneticShielding.MarylandShielding (class in soprano.nmr.tensor) MagneticShielding.MarylandShift (class in soprano.nmr.tensor) MagneticShielding.MehringShielding (class in soprano.nmr.tensor) MagneticShielding.MehringShift (class in soprano.nmr.tensor) MagresViewLabels (class in soprano.properties.labeling.labeling) make_dipolar() (soprano.nmr.tensor.ElectricFieldGradient static method) (soprano.nmr.tensor.MagneticShielding static method) (soprano.nmr.tensor.NMRTensor static method) make_isotropic() (soprano.nmr.site.Site method) make_isotropic_like() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) maketrans() (soprano.nmr.tensor.TensorConvention static method) map() (soprano.collection.collection._AllCaller method) maryland_shielding (soprano.nmr.tensor.MagneticShielding property) max_distance_in_cell() (in module soprano.utils) mean() (soprano.nmr.tensor.ElectricFieldGradient class method) (soprano.nmr.tensor.MagneticShielding class method) (soprano.nmr.tensor.NMRTensor class method) (soprano.properties.basic.basic.CalcEnergy method) (soprano.properties.basic.basic.LatticeABC method) (soprano.properties.basic.basic.LatticeCart method) (soprano.properties.basic.basic.NumAtoms method) (soprano.properties.castep.castep.CastepEnthalpy method) (soprano.properties.labeling.labeling.CarbonHybridationState method) (soprano.properties.labeling.labeling.HydrogenBondTypes method) (soprano.properties.labeling.labeling.MagresViewLabels method) (soprano.properties.labeling.labeling.MoleculeSites method) (soprano.properties.labeling.labeling.SiteLabels method) (soprano.properties.labeling.labeling.UniqueSites method) (soprano.properties.linkage.linkage.BondGraph method) (soprano.properties.linkage.linkage.Bonds method) (soprano.properties.linkage.linkage.CoordinationHistogram method) (soprano.properties.linkage.linkage.DihedralAngleList method) (soprano.properties.linkage.linkage.ElementPairs method) (soprano.properties.linkage.linkage.HydrogenBonds method) (soprano.properties.linkage.linkage.HydrogenBondsNumber method) (soprano.properties.linkage.linkage.LinkageList method) (soprano.properties.linkage.linkage.MoleculeCOM method) (soprano.properties.linkage.linkage.MoleculeCOMLinkage method) (soprano.properties.linkage.linkage.MoleculeMass method) (soprano.properties.linkage.linkage.MoleculeNumber method) (soprano.properties.linkage.linkage.MoleculeQuaternion method) (soprano.properties.linkage.linkage.MoleculeRelativeRotation method) (soprano.properties.linkage.linkage.Molecules method) (soprano.properties.linkage.linkage.MoleculeSpectralSort method) (soprano.properties.map.map.Remap method) (soprano.properties.map.map.RemapIndices method) (soprano.properties.nmr.dipolar.DipolarCoupling method) (soprano.properties.nmr.dipolar.DipolarCouplingList method) (soprano.properties.nmr.dipolar.DipolarDiagonal method) (soprano.properties.nmr.dipolar.DipolarEuler method) (soprano.properties.nmr.dipolar.DipolarRSS method) (soprano.properties.nmr.dipolar.DipolarTensor method) (soprano.properties.nmr.efg.EFGAnisotropy method) (soprano.properties.nmr.efg.EFGAsymmetry method) (soprano.properties.nmr.efg.EFGDiagonal method) (soprano.properties.nmr.efg.EFGEuler method) (soprano.properties.nmr.efg.EFGNQR method) (soprano.properties.nmr.efg.EFGQuadrupolarConstant method) (soprano.properties.nmr.efg.EFGQuadrupolarProduct method) (soprano.properties.nmr.efg.EFGQuaternion method) (soprano.properties.nmr.efg.EFGReducedAnisotropy method) (soprano.properties.nmr.efg.EFGSkew method) (soprano.properties.nmr.efg.EFGSpan method) (soprano.properties.nmr.efg.EFGTensor method) (soprano.properties.nmr.efg.EFGVzz method) (soprano.properties.nmr.isc.ISCDiagonal method) (soprano.properties.nmr.isc.JCAnisotropy method) (soprano.properties.nmr.isc.JCAsymmetry method) (soprano.properties.nmr.isc.JCDiagonal method) (soprano.properties.nmr.isc.JCEuler method) (soprano.properties.nmr.isc.JCIsotropy method) (soprano.properties.nmr.isc.JCouplingList method) (soprano.properties.nmr.isc.JCQuaternion method) (soprano.properties.nmr.isc.JCReducedAnisotropy method) (soprano.properties.nmr.isc.JCSkew method) (soprano.properties.nmr.isc.JCSpan method) (soprano.properties.nmr.isc.JCTensor method) (soprano.properties.nmr.isc.KTensor method) (soprano.properties.nmr.ms.MSAnisotropy method) (soprano.properties.nmr.ms.MSAsymmetry method) (soprano.properties.nmr.ms.MSDiagonal method) (soprano.properties.nmr.ms.MSEuler method) (soprano.properties.nmr.ms.MSIsotropy method) (soprano.properties.nmr.ms.MSQuaternion method) (soprano.properties.nmr.ms.MSReducedAnisotropy method) (soprano.properties.nmr.ms.MSShielding method) (soprano.properties.nmr.ms.MSShift method) (soprano.properties.nmr.ms.MSSkew method) (soprano.properties.nmr.ms.MSSpan method) (soprano.properties.nmr.ms.MSTensor method) (soprano.properties.nmr.spinsystem.NMRSites method) (soprano.properties.nmr.spinsystem.NMRSpinSystem method) (soprano.properties.order.order.BondOrder method) (soprano.properties.symmetry.symmetry.SymmetryDataset method) (soprano.properties.symmetry.symmetry.WyckoffPoints method) (soprano.properties.transform.transform.Mirror method) (soprano.properties.transform.transform.Rotate method) (soprano.properties.transform.transform.Translate method) mehring_shielding (soprano.nmr.tensor.MagneticShielding property) merge_concatenate() (in module soprano.utils) merge_first() (in module soprano.utils) merge_mean() (in module soprano.utils) merge_peaks() (in module soprano.calculate.nmr.utils) merge_sites() (in module soprano.utils) merge_sum() (in module soprano.utils) merge_tagged_sites() (in module soprano.scripts.nmr) minimum_periodic() (in module soprano.utils) minimum_supcell() (in module soprano.utils) Mirror (class in soprano.properties.transform.transform) model_config (soprano.nmr.coupling.Coupling attribute) (soprano.nmr.coupling.DipolarCoupling attribute) (soprano.nmr.coupling.ISCoupling attribute) (soprano.nmr.site.Site attribute) (soprano.nmr.spin_system.SpinSystem attribute) model_construct() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) model_copy() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) model_dump() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) model_dump_json() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) model_extra (soprano.nmr.coupling.Coupling property) (soprano.nmr.coupling.DipolarCoupling property) (soprano.nmr.coupling.ISCoupling property) (soprano.nmr.site.Site property) (soprano.nmr.spin_system.SpinSystem property) model_fields_set (soprano.nmr.coupling.Coupling property) (soprano.nmr.coupling.DipolarCoupling property) (soprano.nmr.coupling.ISCoupling property) (soprano.nmr.site.Site property) (soprano.nmr.spin_system.SpinSystem property) model_json_schema() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) model_parametrized_name() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) model_post_init() (soprano.nmr.coupling.Coupling method) (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) model_rebuild() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) model_validate() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) model_validate_json() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) model_validate_strings() (soprano.nmr.coupling.Coupling class method) (soprano.nmr.coupling.DipolarCoupling class method) (soprano.nmr.coupling.ISCoupling class method) (soprano.nmr.site.Site class method) (soprano.nmr.spin_system.SpinSystem class method) module soprano soprano.analyse soprano.analyse.phylogen soprano.analyse.phylogen.genes soprano.analyse.phylogen.mapping soprano.analyse.phylogen.metrics soprano.analyse.phylogen.phylogenclust soprano.calculate soprano.calculate.gulp soprano.calculate.gulp.charges soprano.calculate.gulp.w99 soprano.calculate.nmr soprano.calculate.nmr.nmr soprano.calculate.nmr.simpson soprano.calculate.nmr.utils soprano.calculate.powder soprano.calculate.powder.powder soprano.calculate.powder.shrewd soprano.calculate.powder.triavg soprano.calculate.powder.zcw soprano.calculate.xrd soprano.calculate.xrd.sel_rules soprano.calculate.xrd.xrd soprano.collection soprano.collection.collection soprano.collection.generate soprano.collection.generate.airss soprano.collection.generate.defect soprano.collection.generate.linspace soprano.collection.generate.molneigh soprano.collection.generate.rattle soprano.collection.generate.transform soprano.data soprano.data.nmr soprano.data.vdw soprano.hpc soprano.hpc.submitter soprano.hpc.submitter.castep soprano.hpc.submitter.debug soprano.hpc.submitter.debug.debugqueue soprano.hpc.submitter.queues soprano.hpc.submitter.submit soprano.hpc.submitter.utils soprano.measure soprano.nmr soprano.nmr.coupling soprano.nmr.site soprano.nmr.spin_system soprano.nmr.tensor soprano.nmr.utils soprano.optional soprano.properties soprano.properties.atomsproperty soprano.properties.basic soprano.properties.basic.basic soprano.properties.castep soprano.properties.castep.castep soprano.properties.labeling soprano.properties.labeling.labeling soprano.properties.linkage soprano.properties.linkage.linkage soprano.properties.map soprano.properties.map.map soprano.properties.nmr soprano.properties.nmr.dipolar soprano.properties.nmr.efg soprano.properties.nmr.isc soprano.properties.nmr.ms soprano.properties.nmr.spinsystem soprano.properties.order soprano.properties.order.order soprano.properties.symmetry soprano.properties.symmetry.backend soprano.properties.symmetry.symmetry soprano.properties.symmetry.utils soprano.properties.transform soprano.properties.transform.transform soprano.rnd soprano.scripts soprano.scripts.cli soprano.scripts.cli_utils soprano.scripts.dipolar soprano.scripts.extract_nmr soprano.scripts.molecules soprano.scripts.msaverage soprano.scripts.nmr soprano.scripts.nmr_plot soprano.scripts.phylogen soprano.scripts.spinsys soprano.scripts.vasp2cell soprano.scripts.view soprano.selection soprano.utils molecularNeighbourhoodGen() (in module soprano.collection.generate.molneigh) MoleculeCOM (class in soprano.properties.linkage.linkage) MoleculeCOMLinkage (class in soprano.properties.linkage.linkage) MoleculeMass (class in soprano.properties.linkage.linkage) MoleculeNumber (class in soprano.properties.linkage.linkage) MoleculeQuaternion (class in soprano.properties.linkage.linkage) MoleculeRelativeRotation (class in soprano.properties.linkage.linkage) Molecules (class in soprano.properties.linkage.linkage) MoleculeSites (class in soprano.properties.labeling.labeling) MoleculeSpectralSort (class in soprano.properties.linkage.linkage) MSAnisotropy (class in soprano.properties.nmr.ms) MSAsymmetry (class in soprano.properties.nmr.ms) MSDiagonal (class in soprano.properties.nmr.ms) MSEuler (class in soprano.properties.nmr.ms) MSIsotropy (class in soprano.properties.nmr.ms) MSQuaternion (class in soprano.properties.nmr.ms) MSReducedAnisotropy (class in soprano.properties.nmr.ms) MSShielding (class in soprano.properties.nmr.ms) MSShift (class in soprano.properties.nmr.ms) MSSkew (class in soprano.properties.nmr.ms) MSSpan (class in soprano.properties.nmr.ms) MSTensor (class in soprano.properties.nmr.ms) N n_couplings (soprano.nmr.spin_system.SpinSystem property) n_sites (soprano.nmr.spin_system.SpinSystem property) next_job() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) nmr_extract_atoms() (in module soprano.scripts.nmr) nmr_extract_multi() (in module soprano.scripts.nmr) nmr_gamma() (in module soprano.data.nmr) nmr_quadrupole() (in module soprano.data.nmr) nmr_spin() (in module soprano.data.nmr) NMRCalculator (class in soprano.calculate.nmr.nmr) NMRData2D (class in soprano.calculate.nmr.nmr) NMRPlot2D (class in soprano.calculate.nmr.nmr) NMRSites (class in soprano.properties.nmr.spinsystem) NMRSpinSystem (class in soprano.properties.nmr.spinsystem) NMRTensor (class in soprano.nmr.tensor) norm_confmat() (in module soprano.analyse.phylogen.metrics) NQR (soprano.nmr.tensor.ElectricFieldGradient property) NumAtoms (class in soprano.properties.basic.basic) O omega (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding attribute) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShift attribute) (soprano.nmr.tensor.MagneticShielding.MarylandShielding attribute) (soprano.nmr.tensor.MagneticShielding.MarylandShift attribute) operations (soprano.properties.symmetry.symmetry.WyckoffPoint attribute) optimise_annotations() (in module soprano.calculate.nmr.utils) P partition() (soprano.nmr.tensor.TensorConvention method) PAS (soprano.nmr.tensor.ElectricFieldGradient property) (soprano.nmr.tensor.MagneticShielding property) (soprano.nmr.tensor.NMRTensor property) Peak2D (class in soprano.calculate.nmr.utils) peak_f_args (soprano.calculate.xrd.xrd.XRDCalculator property) peak_func (soprano.calculate.xrd.xrd.XRDCalculator property) periodic_bridson() (in module soprano.utils) PhylogenCluster (class in soprano.analyse.phylogen.phylogenclust) plot() (soprano.calculate.nmr.nmr.NMRPlot2D method) PlotSettings (class in soprano.calculate.nmr.nmr) pos (soprano.properties.symmetry.symmetry.WyckoffPoint attribute) powder_peaks() (soprano.calculate.xrd.xrd.XRDCalculator method) Pq (soprano.nmr.tensor.ElectricFieldGradient property) process_pairs() (in module soprano.calculate.nmr.utils) progbar() (in module soprano.utils) Q QueueInterface (class in soprano.hpc.submitter.queues) R random_combination() (in module soprano.rnd) rattleGen() (in module soprano.collection.generate.rattle) recursive_mol_label() (in module soprano.utils) redefine_unit_cell() (in module soprano.scripts.molecules) reload_as_molecular_crystal() (in module soprano.scripts.cli_utils) Remap (class in soprano.properties.map.map) RemapIndices (class in soprano.properties.map.map) remote_target (soprano.hpc.submitter.debug.debugqueue.DebugQueueInterface property) (soprano.hpc.submitter.queues.QueueInterface property) RemoteTarget (class in soprano.hpc.submitter.utils) RemoteTargetContext (class in soprano.hpc.submitter.utils) remove_coupling() (soprano.nmr.spin_system.SpinSystem method) remove_signal() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) remove_site() (soprano.nmr.spin_system.SpinSystem method) removeprefix() (soprano.nmr.tensor.TensorConvention method) removesuffix() (soprano.nmr.tensor.TensorConvention method) rep_alg() (in module soprano.utils) replace() (soprano.nmr.tensor.TensorConvention method) replace_folder() (in module soprano.utils) requireSpglib() (in module soprano.optional) resolve_backend() (in module soprano.properties.symmetry.backend) rfind() (soprano.nmr.tensor.TensorConvention method) rindex() (soprano.nmr.tensor.TensorConvention method) rjust() (soprano.nmr.tensor.TensorConvention method) Rotate (class in soprano.properties.transform.transform) rotation_to() (soprano.nmr.tensor.ElectricFieldGradient method) (soprano.nmr.tensor.MagneticShielding method) (soprano.nmr.tensor.NMRTensor method) rpartition() (soprano.nmr.tensor.TensorConvention method) rsplit() (soprano.nmr.tensor.TensorConvention method) rstrip() (soprano.nmr.tensor.TensorConvention method) run_calculators() (soprano.collection.collection.AtomsCollection method) run_cmd() (soprano.hpc.submitter.utils.RemoteTargetContext method) S safe_communicate() (in module soprano.utils) safe_input() (in module soprano.utils) save() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) (soprano.collection.collection.AtomsCollection method) save_collection() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) save_state() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) save_tree() (soprano.collection.collection.AtomsCollection method) seedname() (in module soprano.utils) set_array() (soprano.collection.collection.AtomsCollection method) (soprano.selection.AtomSelection method) set_calculators() (soprano.collection.collection.AtomsCollection method) set_element_isotope() (soprano.calculate.nmr.nmr.NMRCalculator method) set_genes() (soprano.analyse.phylogen.phylogenclust.PhylogenCluster method) set_gradient() (soprano.nmr.tensor.MagneticShielding method) set_isotopes() (soprano.calculate.nmr.nmr.NMRCalculator method) set_larmor_frequency() (soprano.calculate.nmr.nmr.NMRCalculator method) set_parameters() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) set_peak_func() (soprano.calculate.xrd.xrd.XRDCalculator method) set_powder() (soprano.calculate.nmr.nmr.NMRCalculator method) set_reference() (soprano.calculate.nmr.nmr.NMRCalculator method) (soprano.nmr.tensor.MagneticShielding method) set_remote_host() (soprano.hpc.submitter.debug.debugqueue.DebugQueueInterface method) (soprano.hpc.submitter.queues.QueueInterface method) set_single_crystal() (soprano.calculate.nmr.nmr.NMRCalculator method) setup_job() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) shift_asymmetry (soprano.nmr.tensor.MagneticShielding property) shift_span (soprano.nmr.tensor.MagneticShielding property) sigma_11 (soprano.nmr.tensor.MagneticShielding.IUPACShielding attribute) (soprano.nmr.tensor.MagneticShielding.MehringShielding attribute) sigma_22 (soprano.nmr.tensor.MagneticShielding.IUPACShielding attribute) (soprano.nmr.tensor.MagneticShielding.MehringShielding attribute) sigma_33 (soprano.nmr.tensor.MagneticShielding.IUPACShielding attribute) (soprano.nmr.tensor.MagneticShielding.MehringShielding attribute) sigma_iso (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding attribute) (soprano.nmr.tensor.MagneticShielding.HerzfeldBergerShielding attribute) (soprano.nmr.tensor.MagneticShielding.IUPACShielding attribute) (soprano.nmr.tensor.MagneticShielding.MarylandShielding attribute) (soprano.nmr.tensor.MagneticShielding.MehringShielding attribute) silence_stdio() (in module soprano.utils) SimpsonSequence (class in soprano.calculate.nmr.simpson) Site (class in soprano.nmr.site) SiteLabels (class in soprano.properties.labeling.labeling) soprano module soprano command line option --verbosity -v soprano-dipolar command line option --average-group --config --cutoff --exclude --include --isonuclear --isotopes --merge --output --output-format --precision --query --rss --select-i --select-j --sort-order --sortby --symprec --verbosity --view -c -f -g -i -m -o -v FILES soprano-nmr command line option --average-group --config --efg-tag --euler --exclude --grad --gradients --include --isotopes --mean-merge --merge --ms-tag --no-mean-merge --no-reduce --output --output-format --precision --properties --query --reduce --ref --references --sort-order --sortby --subset --symprec --verbosity --view -c -f -g -i -m -o -p -s -v FILES soprano-plotnmr command line option --average-group --colormap --config --connectors --contour --contour-color --contour-levels --contour-linewidth --diag --euler --grad --gradients --grid --heatmap --isotopes --legend --marker-color --marker-linewidth --marker-symbol --markers --max-marker-size --mean-merge --no-connectors --no-contour --no-diag --no-grid --no-heatmap --no-legend --no-markers --no-mean-merge --no-reduce --no-ticklabels --output --plot_type --query --rcut --reduce --ref --references --scale-marker-by --shielding --subset --symprec --ticklabels --verbosity --view --xbroadening --xelement --xlim --yaxis-order --ybroadening --yelement --ylim -c -cmap -g -i -ms -o -p -s -v -x -y FILES soprano-spinsys command line option --angles --average-group --config --cross-terms --dip --dipolar-angles --efg --efg-angles --efg-tag --format --grad --gradients --isotopes --jcoupling --jcoupling-angles --mean-merge --ms --ms-angles --ms-iso --ms-tag --no-cross-terms --no-dip --no-dipolar-angles --no-efg --no-efg-angles --no-jcoupling --no-jcoupling-angles --no-mean-merge --no-ms --no-ms-angles --no-reduce --obs --observed-nucleus --output --program --q-order --reduce --ref --references --select-i --select-j --split --subset --symprec --verbosity --view -c -f -g -i -o -s -v FILE soprano-splitmols command line option --cell --cell-indices --center --centre --default-vdw --format --no-cell-indices --no-write --output-dir --seedname --vac --vacuum --vdw-custom --vdw-scale --vdw-set --verbosity --view -c -f -o -s -v FILENAME soprano-view command line option --average-group --config --mean-merge --no-mean-merge --no-reduce --reduce --subset --symprec --verbosity -c -g -s -v FILES soprano.analyse module soprano.analyse.phylogen module soprano.analyse.phylogen.genes module soprano.analyse.phylogen.mapping module soprano.analyse.phylogen.metrics module soprano.analyse.phylogen.phylogenclust module soprano.calculate module soprano.calculate.gulp module soprano.calculate.gulp.charges module soprano.calculate.gulp.w99 module soprano.calculate.nmr module soprano.calculate.nmr.nmr module soprano.calculate.nmr.simpson module soprano.calculate.nmr.utils module soprano.calculate.powder module soprano.calculate.powder.powder module soprano.calculate.powder.shrewd module soprano.calculate.powder.triavg module soprano.calculate.powder.zcw module soprano.calculate.xrd module soprano.calculate.xrd.sel_rules module soprano.calculate.xrd.xrd module soprano.collection module soprano.collection.collection module soprano.collection.generate module soprano.collection.generate.airss module soprano.collection.generate.defect module soprano.collection.generate.linspace module soprano.collection.generate.molneigh module soprano.collection.generate.rattle module soprano.collection.generate.transform module soprano.data module soprano.data.nmr module soprano.data.vdw module soprano.hpc module soprano.hpc.submitter module soprano.hpc.submitter.castep module soprano.hpc.submitter.debug module soprano.hpc.submitter.debug.debugqueue module soprano.hpc.submitter.queues module soprano.hpc.submitter.submit module soprano.hpc.submitter.utils module soprano.measure module soprano.nmr module soprano.nmr.coupling module soprano.nmr.site module soprano.nmr.spin_system module soprano.nmr.tensor module soprano.nmr.utils module soprano.optional module soprano.properties module soprano.properties.atomsproperty module soprano.properties.basic module soprano.properties.basic.basic module soprano.properties.castep module soprano.properties.castep.castep module soprano.properties.labeling module soprano.properties.labeling.labeling module soprano.properties.linkage module soprano.properties.linkage.linkage module soprano.properties.map module soprano.properties.map.map module soprano.properties.nmr module soprano.properties.nmr.dipolar module soprano.properties.nmr.efg module soprano.properties.nmr.isc module soprano.properties.nmr.ms module soprano.properties.nmr.spinsystem module soprano.properties.order module soprano.properties.order.order module soprano.properties.symmetry module soprano.properties.symmetry.backend module soprano.properties.symmetry.symmetry module soprano.properties.symmetry.utils module soprano.properties.transform module soprano.properties.transform.transform module soprano.rnd module soprano.scripts module soprano.scripts.cli module soprano.scripts.cli_utils module soprano.scripts.dipolar module soprano.scripts.extract_nmr module soprano.scripts.molecules module soprano.scripts.msaverage module soprano.scripts.nmr module soprano.scripts.nmr_plot module soprano.scripts.phylogen module soprano.scripts.spinsys module soprano.scripts.vasp2cell module soprano.scripts.view module soprano.selection module soprano.utils module sort_peaks() (in module soprano.calculate.nmr.utils) sortdf() (in module soprano.scripts.cli_utils) sorted_byarray() (soprano.collection.collection.AtomsCollection method) SpacegroupDataset (class in soprano.properties.symmetry.backend) spec_simul() (soprano.calculate.xrd.xrd.XRDCalculator method) spectrum_1d() (soprano.calculate.nmr.nmr.NMRCalculator method) sph_harm() (in module soprano.properties.order.order) spherical_repr (soprano.nmr.tensor.ElectricFieldGradient property) (soprano.nmr.tensor.MagneticShielding property) (soprano.nmr.tensor.NMRTensor property) SpinSystem (class in soprano.nmr.spin_system) split() (soprano.nmr.tensor.TensorConvention method) splitlines() (soprano.nmr.tensor.TensorConvention method) start_run() (soprano.hpc.submitter.castep.CastepSubmitter method) (soprano.hpc.submitter.submit.Submitter method) startswith() (soprano.nmr.tensor.TensorConvention method) stop() (soprano.hpc.submitter.castep.CastepSubmitter static method) (soprano.hpc.submitter.submit.Submitter static method) strip() (soprano.nmr.tensor.TensorConvention method) styled_plot() (in module soprano.calculate.nmr.utils) submit() (soprano.hpc.submitter.debug.debugqueue.DebugQueueInterface method) (soprano.hpc.submitter.queues.QueueInterface method) Submitter (class in soprano.hpc.submitter.submit) subset() (soprano.selection.AtomSelection method) substitutionGen() (in module soprano.collection.generate.defect) supcell_gridgen() (in module soprano.utils) swapcase() (soprano.nmr.tensor.TensorConvention method) swing_twist_decomp() (in module soprano.utils) SymmetryDataset (class in soprano.properties.symmetry.symmetry) T tag_functional_groups() (in module soprano.scripts.nmr) tensor_mean_property() (in module soprano.properties.nmr.efg) (in module soprano.properties.nmr.ms) TensorConvention (class in soprano.nmr.tensor) theta2 (soprano.calculate.xrd.xrd.XraySpectrum attribute) (soprano.calculate.xrd.xrd.XraySpectrumData attribute) title() (soprano.nmr.tensor.TensorConvention method) to_mrsimulator() (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) to_simpson() (soprano.nmr.coupling.DipolarCoupling method) (soprano.nmr.coupling.ISCoupling method) (soprano.nmr.site.Site method) (soprano.nmr.spin_system.SpinSystem method) to_string() (soprano.nmr.spin_system.SpinSystem method) transformGen() (in module soprano.collection.generate.transform) Translate (class in soprano.properties.transform.transform) translate() (soprano.nmr.tensor.TensorConvention method) tree2json() (in module soprano.scripts.phylogen) U unique() (soprano.selection.AtomSelection static method) UniqueSites (class in soprano.properties.labeling.labeling) update_site() (soprano.nmr.spin_system.SpinSystem method) upper() (soprano.nmr.tensor.TensorConvention method) V validate() (soprano.selection.AtomSelection method) validate_species() (soprano.nmr.site.Site static method) vdw_radius() (in module soprano.data.vdw) viewimages() (in module soprano.scripts.cli_utils) Vzz (soprano.nmr.tensor.ElectricFieldGradient property) W W99Error wigner_3j() (in module soprano.utils) with_traceback() (soprano.analyse.phylogen.genes.GeneError method) (soprano.calculate.gulp.w99.W99Error method) write() (soprano.nmr.spin_system.SpinSystem method) write_input() (soprano.calculate.nmr.simpson.SimpsonSequence method) write_molecules() (in module soprano.scripts.molecules) write_spinsys() (in module soprano.calculate.nmr.simpson) WyckoffPoint (class in soprano.properties.symmetry.symmetry) WyckoffPoints (class in soprano.properties.symmetry.symmetry) X XraySpectrum (class in soprano.calculate.xrd.xrd) XraySpectrumData (class in soprano.calculate.xrd.xrd) XRDCalculator (class in soprano.calculate.xrd.xrd) Z zeta (soprano.nmr.tensor.ElectricFieldGradient property) (soprano.nmr.tensor.MagneticShielding.HaeberlenShielding attribute) (soprano.nmr.tensor.MagneticShielding.HaeberlenShift attribute) zfill() (soprano.nmr.tensor.TensorConvention method)
