T1T2ne_MAKELISTS module

class t1t2ne.scripts.t1t2ne_makelists.MakeListsCmd[source]

Bases: BaseCommand

Make lists of values for the protein dynamics experiments

DESCRIPTION: str = 'With this module, the lists of values for the protein dynamics experiments are created, and the heteronuclear NOE expected value is printed.\nIn the standard operation mode, the tau_c or MW are used to compute the optimal lists.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 = 'Make lists of values for the protein dynamics experiments'
static add_arguments(parser)[source]

Adds the arguments for the MakeLists command to the parser.

static run(args)[source]

Runs the MakeLists command.

t1t2ne.scripts.t1t2ne_makelists.create_lists(CO, R1, R2)[source]

Creates vdlist and vclist for T1 and T2 experiments based on the computed R1 and R2 values. The vdlist is created so that the longest delay of the T1 experiment corresponds to a residual signal intensity of T1red, which is a user-defined percentage reduction. Defaults to 5%. The vclist is created so that the longest CPMG block of the T2 experiment corresponds to a residual signal intensity of T2red, which is a user-defined percentage reduction. Defaults to 10%. The user can choose to create the lists in logarithmic or linear scale. In logscale, the protocol suggested by F. Ferrage in his protocol is used.

Parameters:

  • CO (Conf_Optns object) –

    The configuration object containing the necessary information to load the data and perform the analysis. The following attributes of the CO object are used in this function:

    • B_0 : float The magnetic field strength in Tesla.

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

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

    • nT : list of int The number of increments for the T1 and T2 experiments. nT[0] corresponds to T1 and nT[1] corresponds to T2. If only one value is provided, it is used for both

    • xred: list of float The percent residual signal for the longest delay of the experiments. If only one value is provided, it is used for both T1 and T2. If not provided, defaults to 5% for T1 and 10% for T2.

    The following options of the CO object are also used in this function:

    • large : bool, optional Whether to create the lists for the “large” sequence, which is optimized for short T2 times. If True, the d21 value is set to 450 us and only 8 cycles per CPMG block are used instead of 16. Default is False.

    • small : bool, optional Whether to create the lists for the “.idp” sequence, which is optimized for long T2 times. If True, the d21 value is set to 600 us. Default is False.

    • logscale : bool, optional Whether to create the lists in logarithmic scale. If True, the protocol suggested by F. Ferrage is used. Default is True.

    • randomize : bool, optional Whether to randomize the order of the values in the lists. Default is False.

  • R1 (float) – The R1 relaxation rate in s^-1.

  • R2 (float) – The R2 relaxation rate in s^-1.

Returns:

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

Return type:

None