T1T2ne_SETUPTRACT module

class t1t2ne.scripts.t1t2ne_setuptract.SetupTractCmd

Bases: BaseCommand

DESCRIPTION: str = 'With this module, the vdlist for a TRACT experiment is set up.In the standard operation mode, the tau_c or MW are used to compute the optimal vdlist.S2 is assumed to be 0.9 for the standard operation mode.The IDP mode requires input of the molecular weight of the protein to estimate the correlation time of the slow motion.\nOptionally, the length of the correlation window can be provided as an estimate for the intermediate correlation time.\nIf not provided, it assumes a correlation time of 1.6 ns for the intermediate motion.Two S2 values are expected in the IDP mode. If not provided, they are assumed to be 0.15 for the slow motion and 0.35 for the intermediate motion.'

SHORT_HELP: str = 'Setup the vdlist for a TRACT experiment'

static add_arguments(parser)

Aggiunge gli argomenti specifici di questo comando al parser.

static run(args)

Esegue la logica del comando.

t1t2ne.scripts.t1t2ne_setuptract.d_optimal_criterion(t, lam1, lam2)

Returns -log det(FIM); minimize this.

t1t2ne.scripts.t1t2ne_setuptract.decode(u, t_max, n, min_gap)

Map unconstrained u in [0,1]^n to sorted times with min_gap enforced.

t1t2ne.scripts.t1t2ne_setuptract.suggest_tract_vdlist(CO)

Suggests a vdlist for the TRACT experiment based on the computed average \(\tau_c\) from the MW. The longest delay of the vdlist is set to 2 times the Rb relaxation time, which corresponds to a reduction of the signal intensity of about 86%. The vdlist is logarithmically spaced from 20 us to the longest delay. The user can choose the number of increments in the vdlist. The function prints the suggested vdlist in Bruker-readable format 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. It is expected that the CO object has the following attributes: - B_0: the magnetic field strength in Tesla - tau: the average correlation time in seconds, calculated from the MW or provided by the user - list of 3 values for the IDP model, 2 values for the non-IDP model - S2: the order parameter S2 to use for the calculation - list of 2 values for the IDP model, 1 value for the non-IDP model - nucs: the nuclei to use for the calculation of the relaxation rates. Default is [‘1H’, ‘15N’]. - r: the length of the 1H-15N bond in meters. Default is 1.02e-10 m. - Deltasigma: the chemical shift anisotropy of the 15N nucleus. Default is -160 ppm. - theta: the angle between the 1H-15N bond and the principal axis of the CSA tensor in radians. Default is 17 degrees converted to radians. - nT: the number of increments in the suggested vdlist. Default is 8.

Returns:

The function prints the suggested vdlist in Bruker-readable format and updates the references attribute of the CO object with the references used for the calculations.

Return type:

None