hqs_nmr.postprocessing

NMR spectra postprocessing routines.

Functions

adapt_spectrum_by_j_coupling(...)

Adapt a spectrum with respect to a shift in a J-coupling.

create_new_molecule(molecule_parameters, ...)

Create a new molecular NMR parameter representation, with adapted shifts.

fit_spline_to_vector_function()

Fit spline to real or complex vector function.

get_fitted_greens_function(greens_function)

Calculate a spline fit of a Green's function after rediscretizing the frequencies.

j_coupling_adaptation_parameters(...)

Determine all parameters needed to adapt a Green's function with respect to some J-coupling.

prepare_j_coupling_adaptation(...)

Calculate the Green's function and all parameters needed to perform a J-coupling adaptation.

prepare_shifting(greens_function[, ...])

Prepare splines and rediscretized frequency points for shifting the shifts.

rediscretize_frequency_range(omegas_ppm[, ...])

Rediscretize the frequency range for the spline fits.

shift_greens_function(shifts, ...)

Shift Green's function using spline fit.
hqs_nmr.postprocessing.prepare_shifting(greens_function: NMRGreensFunction1D, num_omegas_spline: int = 2000, offset: float = 1e-12) → tuple[ndarray, list[CubicSpline], list[CubicSpline]][source]

Prepare splines and rediscretized frequency points for shifting the shifts.

Parameters:

  • greens_function – Green’s function calculated using hqs_nmr.

  • num_omegas_spline – Number of frequency points added to the rediscretized.

  • 2000. (frequencies. Defaults to)

  • offset – Small factor to avoid division by zero. Defaults to 1e-12.

Returns:

Original omegas with added linear discretization in ppm. splines_real: List with splines fitting the real part entries of the Green’s function. splines_complex: List with splines fitting the imaginary part entries of the Green’s function.

Return type:

rediscretized_omegas_ppm

hqs_nmr.postprocessing.shift_greens_function(shifts: ndarray, greens_function: NMRGreensFunction1D, rediscretized_omegas_ppm: ndarray, splines_real: list[CubicSpline], splines_imag: list[CubicSpline], number_relevant_spins: int) → NMRSpectrum1D[source]

Shift Green’s function using spline fit.

Parameters:

  • shifts – The shifts of the magnetic shifts.

  • greens_function – Green’s function that is supposed to be shifted.

  • rediscretized_omegas_ppm – Rediscretized frequency points in ppm.

  • splines_real – Splines for the real part of the Green’s function.

  • splines_imag – Splines for the imaginary part of the Green’s function.

  • number_relevant_spins – Number of times the homo-isotope appears in the molecule.

Returns:

Normalized and shifted spectrum.

hqs_nmr.postprocessing.rediscretize_frequency_range(omegas_ppm: ndarray, num_omegas_spline: int = 2000) → ndarray[source]

Rediscretize the frequency range for the spline fits.

Add an additional linear discretization to the current distribution.

Parameters:

  • omegas_ppm – Frequency discretization without the linear discretization.

  • num_omegas_spline – Minimal number of points in the linear discretization.

Returns.:

Vector with new discretization.

hqs_nmr.postprocessing.fit_spline_to_vector_function(parameters: ndarray, vector_function: ndarray[tuple[int, ...], dtype[floating]]) → list[CubicSpline][source]
hqs_nmr.postprocessing.fit_spline_to_vector_function(parameters: ndarray, vector_function: ndarray[tuple[int, ...], dtype[complexfloating]]) → tuple[list[CubicSpline], list[CubicSpline]]

Fit spline to real or complex vector function.

Parameters:

  • parameters – Parameters at which the vector function was evaluated.

  • vector_function – Values of the vector function.

Returns:

If the vector function is real, it returns one list with a spline associated with each vector function entry, otherwise it returns one list for the real and one for the complex part.

hqs_nmr.postprocessing.create_new_molecule(molecule_parameters: NMRParameters, shifts_of_Jz_ppm: np.ndarray) → NMRParameters[source]

Create a new molecular NMR parameter representation, with adapted shifts.

Parameters:

  • molecule_parameters – Molecular NMR parameters that should be adapted.

  • shifts_of_Jz_ppm – Shifts of the magnetic shifts in ppm.

Returns:

Molecular NMR parameters with the adapted shifts.

hqs_nmr.postprocessing.get_fitted_greens_function(greens_function: NMRGreensFunction1D, num_omegas_spline: int = 2000, offset: float = 1e-12) → tuple[ndarray, ndarray][source]

Calculate a spline fit of a Green’s function after rediscretizing the frequencies.

Args.:

greens_function: Green’s function to fit. num_omegas_spline: Number of frequency points added to the rediscretized frequencies. Defaults to 2000. offset: Small factor to avoid division by zero when fitting the Green’s function. Defaults to 1e-12.

Returns:

Rediscretized frequency range and fitted Green’s function.

hqs_nmr.postprocessing.j_coupling_adaptation_parameters(result_greens_function: NMRResultGreensFunction1D, result_eom_greens_function: NMRResultGreensFunction1D, result_eom_correction_greens_function: NMRResultGreensFunction1D) → dict[str, Any][source]

Determine all parameters needed to adapt a Green’s function with respect to some J-coupling.

Note that all Green’s functions used here should be non normalized.

Args.:

result_greens_function: Green’s function that should be adapted. result_eom_greens_function: EOM Green’s function associated with the standard NMR Green’s function. result_eom_correction_greens_function: EOM Green’s function to correct the standard NMR Green’s function.

Returns:

A dictionary with all necessary parameters.

hqs_nmr.postprocessing.prepare_j_coupling_adaptation(molecule_parameters: NMRParameters, calculation_parameters: NMRCalculationParameters, adaptation_indices: tuple[int, int] | list[tuple[int, int]]) → tuple[NMRResultGreensFunction1D, dict[str, Any]][source]

Calculate the Green’s function and all parameters needed to perform a J-coupling adaptation.

Args.:

molecule_parameters: The NMR parameters of the molecule, which should be adapted. calculation_parameters: The NMR calculation parameters as defined for a standard NMR Green’s function calculation. adaptation_indices: Tuple or list of tuple of all J-coupling which are supposed to be adapted at once.

Returns:

The result of a standard Green’s function calculation using the input parameters and a dictionary with all necessary parameters to perform a J-coupling adaptation.

hqs_nmr.postprocessing.adapt_spectrum_by_j_coupling(delta_j_coupling: float, rediscretized_omegas_rad_per_s: ndarray, rediscretized_omegas_ppm: ndarray, broadening_rad_per_s: float | ndarray, sz_terms_rad_per_s: ndarray, greens_function: ndarray, eom_greens_function: ndarray, eom_correction_greens_function: ndarray) → ndarray[source]

Adapt a spectrum with respect to a shift in a J-coupling.

Which J-coupling is shifted depends on the EOM correction Green’s function.

Parameters:

  • delta_j_coupling – Shift of the J-coupling.

  • rediscretized_omegas_rad_per_s – Rediscretized frequency range in rad per s.

  • rediscretized_omegas_ppm – Rediscretized frequency range in ppm.

  • broadening_rad_per_s – Artificial broadening (half of the fwhm) in rad per s. If a vector is handed over a spin-dependent broadening is assumed.

  • sz_terms_rad_per_s – Array with the coefficients of the I^z terms in the Hamiltonian.

  • greens_function – The spin contributions of the Green’s function to be adapted.

  • eom_greens_function – The spin contributions of the EOM Green’s function associated with

  • function. (the standard Green's)

  • eom_correction_greens_function – The spin contributions of the EOM correction Green’s

  • function.

Returns:

The normalized Green’s function spin contributions with the adapted J-coupling taken into account.