T1T2ne_NS module

class t1t2ne.scripts.t1t2ne_ns.NSCmd[source]

Bases: BaseCommand

DESCRIPTION: str = 'With this module, you can estimate the optimal number of scans for your NMR experiments based on the desired signal-to-noise ratio (SNR) and relaxation properties of the sample.\nThe module reads a reference spectrum, then computes its SNR, and finally estimates the number of scans needed to achieve a target SNR for the T1, T2, and heteronuclear NOE experiments.'
SHORT_HELP: str = 'Helps you select a reasonable number of scans for the dynamics experiments.'
static add_arguments(parser)[source]

Aggiunge gli argomenti specifici di questo comando al parser.

static run(args: Namespace) → None[source]

Esegue la logica del comando.

t1t2ne.scripts.t1t2ne_ns.estimate_snr(CO)[source]

Provides an estimate of the expected signal-to-noise ratio (SNR) per scan for a single peak in the HSQC spectrum based on the average :math:` au_c` provided. The function fits the NH region of the 1D spectrum (or of the HSQC reference) to a skew normal distribution - or the integral of the spectrum - to estimate the area of a single peak, which is then used to estimate the intensity of a single peak in the HSQC spectrum. The noise is estimated from a region of the spectrum without peaks. The function prints the estimated SNR per scan for a single peak and updates the references attribute of the CO object with the references used for the calculations.

Parameters:

CO (Conf_Optns object) –

The configuration object containing the necessary information to load the data and perform the analysis. The CO object should have the following attributes:

  • B_0 : float The magnetic field strength in Tesla.

  • S2 : list of float The order parameters to use for the calculation of tau_c. In IDP mode, two values should be provide, else only one.

  • tau : list of float The correlation times to use for the calculation of tau_c. In IDP mode, two values should be provide, else only one.

  • hsqc : str, optional The experiment number of the HSQC reference spectrum to use for the SNR estimation.

  • tract : str, optional The experiment number of the TRACT spectrum to use for the SNR estimation.

  • T : float, optional The temperature in Kelvin, used to recompute tau_c based on temperature.

  • nres : int, optional The number of non-proline residues in the protein. If not provided, it will be estimated from the molecular weight using a rough estimate of 110 Da per residue and multiplying by 0.937 to account for the fact that prolines do not have an amide proton and therefore do not contribute to the signal in the HSQC spectrum.

Returns:

The function prints the estimated SNR per scan for a single peak, suggests a number of scans for the three experiments, and updates the references attribute of the CO object with the references used for the calculations.

Return type:

None

t1t2ne.scripts.t1t2ne_ns.suggest_scans(CO, SNR)[source]

Suggest a number of scans given the expected reduction in SNR

Parameters:

  • CO (Conf_Optns object) –

    The configuration object containing the necessary information to perform the analysis. The CO object should have the following attributes:

    • xred : list of float The percent residual signal for the longest delay of the experiment, or NOE efficiency as percentage. Accepts a list, computes the optimal number of scans for each value.

  • SNR (float) – The estimated signal-to-noise ratio per scan for a single peak.

Returns:

The function prints the suggested number of scans for each experiment in the list.

Return type:

None