Exemplo n.º 1
0
    def test_value_set_r1_rit(self):
        """Test of the pipe_control.value.set() function."""

        # Set the current data pipe to 'mf'.
        pipes.switch('relax_disp')

        # Set variables.
        exp_type = 'R1rho'
        frq = 800.1 * 1E6

        # Set an experiment type to the pipe.
        set_exp_type(spectrum_id='test', exp_type=exp_type)

        # Set a frequency to loop through.
        spectrometer.set_frequency(id='test', frq=frq, units='Hz')

        # Generate dic key.
        r20_key = generate_r20_key(exp_type=exp_type, frq=frq)

        # Set first similar to r2.
        value.set(val=None, param='r2')
        self.assertEqual(cdp.mol[0].res[0].spin[0].r2[r20_key], 10.0)

        # Then set for r1.
        value.set(val=None, param='r1')
        print(cdp.mol[0].res[0].spin[0])
        self.assertEqual(cdp.mol[0].res[0].spin[0].r1[r20_key], 2.0)
Exemplo n.º 2
0
    def test_value_set_r1_rit(self):
        """Test of the pipe_control.value.set() function."""

        # Set the current data pipe to 'mf'.
        pipes.switch('relax_disp')

        # Set variables.
        exp_type = 'R1rho'
        frq = 800.1 * 1E6

        # Set an experiment type to the pipe.
        set_exp_type(spectrum_id='test', exp_type=exp_type)

        # Set a frequency to loop through.
        spectrometer.set_frequency(id='test', frq=frq, units='Hz')

        # Generate dic key.
        r20_key = generate_r20_key(exp_type=exp_type, frq=frq)

        # Set first similar to r2.
        value.set(val=None, param='r2')
        self.assertEqual(cdp.mol[0].res[0].spin[0].r2[r20_key], 10.0)

        # Then set for r1.
        value.set(val=None, param='r1')
        print(cdp.mol[0].res[0].spin[0])
        self.assertEqual(cdp.mol[0].res[0].spin[0].r1[r20_key], 2.0)
Exemplo n.º 3
0
        relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)

        # Relaxation dispersion CPMG constant time delay T (in s).
        relax_disp.relax_time(spectrum_id=new_id, time=relax_time)

        # Set the CPMG frequency.
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir=DATA_PATH, spin_id=spin_id, disp_point_col=7, data_col=10, error_col=9)

# Change the model.
relax_disp.select_model('NS MMQ 3-site linear')

# The R20 keys.
r20_1h_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=400e6)
r20_1h_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_1h_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_1h_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=1000e6)
r20_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=400e6)
r20_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=1000e6)
r20_zq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=400e6)
r20_zq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_zq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_zq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=1000e6)
r20_dq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=400e6)
r20_dq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_dq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_dq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=1000e6)
Exemplo n.º 4
0
        # Set the offset.
        relax_disp.spin_lock_offset(spectrum_id=new_id, offset=-frequency_to_ppm(frq=offset, B0=H_frq, isotope='15N'))

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=':1', offset_col=6, data_col=10, error_col=9)

# Load the R1 data.
relax_data.read(ri_id='600MHz', ri_type='R1', frq=600e6, file='R1_600MHz.out', dir='..', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6, file='R1_800MHz.out', dir='..', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)

# Change the model.
relax_disp.select_model('NS R1rho 3-site linear')

# The R20 keys.
r20_600_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=600e6)
r20_800_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)

# Manually set the parameter values.
spin = cdp.mol[0].res[0].spin[0]
spin.r2 = {
    r20_600_key:   8.000284037933310,
    r20_800_key:   9.000296050530716,
}
spin.pA = 0.850029879276267
spin.pB = 0.049922261890898
spin.pC = 0.100047858832835
spin.kex_AB = 500.991549690434681
spin.kex_AC = 0.0
spin.kex_BC = 2003.189830166320235
spin.dw_AB = -2.991465198310455
Exemplo n.º 5
0
def loop_parameters(spins=None):
    """Generator function for looping of the parameters of the cluster.

    @keyword spins: The list of spin data containers for the block.
    @type spins:    list of SpinContainer instances
    @return:        The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).
    @rtype:         str, int, int, str
    """

    # Make sure that the R1 parameter is correctly set up.
    r1_setup()

    # The parameter index.
    param_index = -1

    # The R2eff model.
    if cdp.model_type == 'R2eff':
        # Loop over the spins.
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # Yield the two parameters.
            params = ['r2eff', 'i0']
            for i in range(2):
                # First increment the indices.
                param_index += 1

                # Yield the data.
                yield params[i], param_index, spin_index, None

    # All other models.
    else:
        # First the R1 fit parameter (one per spin per field strength).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The R1 parameter.
            if 'r1' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r1', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

        # Then the R2 parameters (one per spin per field strength).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The R2 parameter.
            if 'r2' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r2', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

            # The R2A parameter.
            if 'r2a' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r2a', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

            # The R2B parameter.
            if 'r2b' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r2b', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

        # Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per spin).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # Yield the data.
            if 'phi_ex' in spins[spin_index].params:
                param_index += 1
                yield 'phi_ex', param_index, spin_index, None
            if 'phi_ex_B' in spins[spin_index].params:
                param_index += 1
                yield 'phi_ex_B', param_index, spin_index, None
            if 'phi_ex_C' in spins[spin_index].params:
                param_index += 1
                yield 'phi_ex_C', param_index, spin_index, None
            if 'padw2' in spins[spin_index].params:
                param_index += 1
                yield 'padw2', param_index, spin_index, None
            if 'dw' in spins[spin_index].params:
                param_index += 1
                yield 'dw', param_index, spin_index, None
            if 'dw_AB' in spins[spin_index].params:
                param_index += 1
                yield 'dw_AB', param_index, spin_index, None
            if 'dw_BC' in spins[spin_index].params:
                param_index += 1
                yield 'dw_BC', param_index, spin_index, None
            if 'dw_AC' in spins[spin_index].params:
                param_index += 1
                yield 'dw_AC', param_index, spin_index, None

        # Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            if 'dwH' in spins[spin_index].params:
                param_index += 1
                yield 'dwH', param_index, spin_index, None
            if 'dwH_AB' in spins[spin_index].params:
                param_index += 1
                yield 'dwH_AB', param_index, spin_index, None
            if 'dwH_BC' in spins[spin_index].params:
                param_index += 1
                yield 'dwH_BC', param_index, spin_index, None
            if 'dwH_AC' in spins[spin_index].params:
                param_index += 1
                yield 'dwH_AC', param_index, spin_index, None

        # All other parameters (one per spin cluster).
        for param in spins[0].params:
            if not param in ['r1', 'r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', 'dwH_BC', 'dwH_AB']:
                param_index += 1
                yield param, param_index, None, None
Exemplo n.º 6
0
        relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)

        # Relaxation dispersion CPMG constant time delay T (in s).
        relax_disp.relax_time(spectrum_id=new_id, time=relax_time)

        # Set the CPMG frequency.
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)

# Change the model.
relax_disp.select_model('MMQ CR72')

# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key7 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key8 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key9 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6)
r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6)
r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
Exemplo n.º 7
0
        relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)

        # Relaxation dispersion CPMG constant time delay T (in s).
        relax_disp.relax_time(spectrum_id=new_id, time=relax_time)

        # Set the CPMG frequency.
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)

# Change the model.
relax_disp.select_model('NS MMQ 2-site')

# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key7 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key8 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key9 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=600e6)
r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=800e6)
r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
Exemplo n.º 8
0
    pipe.switch(pipe_name=pipe_name)
    print("\nModel: %s" % (model))

    # Loop over the spins.
    for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
        # Generate spin string.
        spin_string = generate_spin_string(spin=cur_spin, mol_name=mol_name, res_num=resi, res_name=resn)

        # Loop over the parameters.
        print("\nOptimised parameters for spin: %s" % (spin_string))
        for param in cur_spin.params + ['chi2']:
            # Get the value.
            if param in ['r1', 'r2']:
                for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
                    # Generate the R20 key.
                    r20_key = generate_r20_key(exp_type=exp_type, frq=frq)

                    # Get the value.
                    value = getattr(cur_spin, param)[r20_key]

                    # Print value.
                    print("%-10s %-6s %-6s %3.8f" % ("Parameter:", param, "Value:", value))

            # For all other parameters.
            else:
                # Get the value.
                value = getattr(cur_spin, param)

                # Print value.
                print("%-10s %-6s %-6s %3.8f" % ("Parameter:", param, "Value:", value))
Exemplo n.º 9
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    # NS : r2a = r2b
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D)
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR)
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_EXPANDED)

    # NS full : r2a = r2b
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D_FULL)
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR_FULL)

    # The model.
    model_analyse = model_analyse_list[10]

    ## Experiments
    # Exp 1
    sfrq_1 = 500.0*1E6
    r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1)
    time_T2_1 = 0.05
    ncycs_1 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 40, 50]
    # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
    #r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
    r2eff_errs_1 = [0.0] * len(ncycs_1)
    exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1]

    sfrq_2 = 600.0*1E6
    r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2)
    time_T2_2 = 0.06
    ncycs_2 = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 40, 60]
    # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
    #r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
    r2eff_errs_2 = [0.0] * len(ncycs_2)
    exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2]
Exemplo n.º 10
0
def loop_parameters(spins=None):
    """Generator function for looping of the parameters of the cluster.

    @keyword spins: The list of spin data containers for the block.
    @type spins:    list of SpinContainer instances
    @return:        The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).
    @rtype:         str, int, int, str
    """

    # Make sure that the R1 parameter is correctly set up.
    r1_setup()

    # The parameter index.
    param_index = -1

    # The R2eff model.
    if cdp.model_type == 'R2eff':
        # Loop over the spins.
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # Yield the two parameters.
            params = ['r2eff', 'i0']
            for i in range(2):
                # First increment the indices.
                param_index += 1

                # Yield the data.
                yield params[i], param_index, spin_index, None

    # All other models.
    else:
        # First the R1 fit parameter (one per spin per field strength).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The R1 parameter.
            if 'r1' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r1', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

        # Then the R2 parameters (one per spin per field strength).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The R2 parameter.
            if 'r2' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r2', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

            # The R2A parameter.
            if 'r2a' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r2a', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

            # The R2B parameter.
            if 'r2b' in spins[spin_index].params:
                for exp_type, frq in loop_exp_frq():
                    param_index += 1
                    yield 'r2b', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq)

        # Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per spin).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # Yield the data.
            if 'phi_ex' in spins[spin_index].params:
                param_index += 1
                yield 'phi_ex', param_index, spin_index, None
            if 'phi_ex_B' in spins[spin_index].params:
                param_index += 1
                yield 'phi_ex_B', param_index, spin_index, None
            if 'phi_ex_C' in spins[spin_index].params:
                param_index += 1
                yield 'phi_ex_C', param_index, spin_index, None
            if 'padw2' in spins[spin_index].params:
                param_index += 1
                yield 'padw2', param_index, spin_index, None
            if 'dw' in spins[spin_index].params:
                param_index += 1
                yield 'dw', param_index, spin_index, None
            if 'dw_AB' in spins[spin_index].params:
                param_index += 1
                yield 'dw_AB', param_index, spin_index, None
            if 'dw_BC' in spins[spin_index].params:
                param_index += 1
                yield 'dw_BC', param_index, spin_index, None
            if 'dw_AC' in spins[spin_index].params:
                param_index += 1
                yield 'dw_AC', param_index, spin_index, None

        # Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            if 'dwH' in spins[spin_index].params:
                param_index += 1
                yield 'dwH', param_index, spin_index, None
            if 'dwH_AB' in spins[spin_index].params:
                param_index += 1
                yield 'dwH_AB', param_index, spin_index, None
            if 'dwH_BC' in spins[spin_index].params:
                param_index += 1
                yield 'dwH_BC', param_index, spin_index, None
            if 'dwH_AC' in spins[spin_index].params:
                param_index += 1
                yield 'dwH_AC', param_index, spin_index, None

        # All other parameters (one per spin cluster).
        for param in spins[0].params:
            if not param in ['r1', 'r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', 'dwH_BC', 'dwH_AB']:
                param_index += 1
                yield param, param_index, None, None
Exemplo n.º 11
0
    # NS : r2a = r2b
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D)
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR)
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_EXPANDED)

    # NS full : r2a = r2b
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_3D_FULL)
    model_analyse_list.append(MODEL_NS_CPMG_2SITE_STAR_FULL)

    # The model.
    model_analyse = model_analyse_list[0]

    ## Experiments
    # Exp 1
    sfrq_1 = 599.8908617*1E6
    r20_key_1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_1)
    time_T2_1 = 0.06
    ncycs_1 = [28, 4, 32, 60, 2, 10, 16, 8, 20, 50, 18, 40, 6, 12, 24]
    # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
    #r2eff_errs_1 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
    r2eff_errs_1 = [0.0] * len(ncycs_1)
    exp_1 = [sfrq_1, time_T2_1, ncycs_1, r2eff_errs_1]

    sfrq_2 = 499.8908617*1E6
    r20_key_2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq_2)
    time_T2_2 = 0.04
    ncycs_2 = [20, 16, 10, 36, 2, 12, 4, 22, 18, 40, 14, 26, 8, 32, 24, 6, 28 ]
    # Here you define the direct R2eff errors (rad/s), as being added or subtracted for the created R2eff point in the corresponding ncyc cpmg frequence.
    #r2eff_errs_2 = [0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05, -0.05, 0.05]
    r2eff_errs_2 = [0.0] * len(ncycs_2)
    exp_2 = [sfrq_2, time_T2_2, ncycs_2, r2eff_errs_2]
Exemplo n.º 12
0
def loop_parameters(spins=None):
    """Generator function for looping of the model parameters of the cluster.

    @keyword spins: The list of spin data containers for the block.
    @type spins:    list of SpinContainer instances
    @return:        The parameter name, the parameter index (for the parameter vector), the spin index (for the cluster), and the R20 parameter key (for R20, R20A, and R20B parameters stored as dictionaries).
    @rtype:         str, int, int, str
    """

    # Make sure that the R1 parameter is correctly set up.
    r1_setup()

    # The parameter index.
    param_index = -1

    # The R2eff model.
    if cdp.model_type == 'R2eff':
        # Loop over the spins.
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # One or two parameters.
            params = ['r2eff']
            if has_exponential_exp_type():
                params = ['r2eff', 'i0']

            # Yield the parameters.
            for param in params:
                # First increment the indices.
                param_index += 1

                # Yield the data.
                yield param, param_index, spin_index, None

    # All other models.
    else:
        # First the R1 fit parameter (one per spin per field strength).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The parameters.
            for param in PARAMS_R1:
                if param in spins[spin_index].params:
                    for exp_type, frq in loop_exp_frq():
                        param_index += 1
                        yield param, param_index, spin_index, generate_r20_key(
                            exp_type=exp_type, frq=frq)

        # Then the R2 parameters (one per spin per field strength).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The parameters.
            for param in PARAMS_R20:
                if param in spins[spin_index].params:
                    for exp_type, frq in loop_exp_frq():
                        param_index += 1
                        yield param, param_index, spin_index, generate_r20_key(
                            exp_type=exp_type, frq=frq)

        # Then the chemical shift difference parameters (one per spin).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # Yield the data.
            for param in PARAMS_CHEM_SHIFT_DIFF:
                if param in spins[spin_index].params:
                    param_index += 1
                    yield param, param_index, spin_index, None

        # Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # Yield the data.
            for param in PARAMS_CHEM_SHIFT_DIFF_MMQ:
                if param in spins[spin_index].params:
                    param_index += 1
                    yield param, param_index, spin_index, None

        # All other parameters (one per spin cluster).
        for spin_index in range(len(spins)):
            # Skip deselected spins.
            if not spins[spin_index].select:
                continue

            # The parameters.
            for param in spins[0].params:
                if not param in PARAMS_SPIN:
                    param_index += 1
                    yield param, param_index, None, None

            # No more spins.
            break
Exemplo n.º 13
0
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id,
                               file=file,
                               dir='..',
                               spin_id=spin_id,
                               disp_point_col=1,
                               data_col=2,
                               error_col=3)

# Change the model.
relax_disp.select_model('NS MMQ 2-site')

# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)

# Manually set the parameter values.
spin_N = cdp.mol[0].res[0].spin[1]
spin_N.r2 = {
    r20_key1: 8.412998,
    r20_key2: 8.847946,
    r20_key3: 10.329567,
    r20_key4: 6.779626,
    r20_key5: 7.089813,
    r20_key6: 5.610770
Exemplo n.º 14
0
    def test_tp02_data_to_tp02(self):
        """Test the GUI analysis with the relaxation dispersion 'TP02' model fitting to the 'TP02' synthetic data."""

        # The paths to the data files.
        data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'dispersion' + sep + 'r1rho_off_res_tp02' + sep

        # Simulate the new analysis wizard, selecting the fixed time CPMG experiment.
        analysis = self.new_analysis_wizard(analysis_type='disp')

        # Change the results directory.
        analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir))

        # Create the sequence data.
        self._execute_uf(uf_name='spin.create',
                         res_name='Trp',
                         res_num=1,
                         spin_name='N')
        interpreter.flush()
        self._execute_uf(uf_name='spin.create',
                         res_name='Trp',
                         res_num=2,
                         spin_name='N')
        interpreter.flush()
        self._execute_uf(uf_name='sequence.display')
        interpreter.flush()

        # Set up the nuclear isotopes.
        analysis.spin_isotope()
        uf_store['spin.isotope'].page.SetValue('spin_id', '')
        uf_store['spin.isotope'].wizard._go_next()
        interpreter.flush()  # Required because of the asynchronous uf call.

        # Load the chemical shift data.
        self._execute_uf(uf_name='chemical_shift.read',
                         file='ref_500MHz.list',
                         dir=data_path)
        interpreter.flush()

        # The spectral data.
        frq = [500, 800]
        frq_label = ['500MHz', '800MHz']
        error = 200000.0
        data = []
        spin_lock = [
            None, 1000.0, 1500.0, 2000.0, 2500.0, 3000.0, 3500.0, 4000.0,
            4500.0, 5000.0, 5500.0, 6000.0
        ]
        for frq_index in range(len(frq)):
            for spin_lock_index in range(len(spin_lock)):
                # The reference.
                if spin_lock[spin_lock_index] == None:
                    id = 'ref_%s' % frq_label[frq_index]
                    file = "ref_%s.list" % frq_label[frq_index]

                # Normal data.
                else:
                    id = "nu_%s_%s" % (spin_lock[spin_lock_index],
                                       frq_label[frq_index])
                    file = "nu_%s_%s.list" % (spin_lock[spin_lock_index],
                                              frq_label[frq_index])

                # Append the data.
                data.append(
                    [id, file, spin_lock[spin_lock_index], frq[frq_index]])

        # Load the R1 data.
        for frq_index in range(len(frq)):
            label = 'R1_%s' % frq_label[frq_index]
            self._execute_uf(uf_name='relax_data.read',
                             ri_id=label,
                             ri_type='R1',
                             frq=frq[frq_index] * 1e6,
                             file='%s.out' % label,
                             dir=data_path,
                             mol_name_col=1,
                             res_num_col=2,
                             res_name_col=3,
                             spin_num_col=4,
                             spin_name_col=5,
                             data_col=6,
                             error_col=7)
            interpreter.flush()

        # Set up the peak intensity wizard.
        analysis.peak_wizard_launch(None)
        wizard = analysis.peak_wizard

        # The spectra.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='read',
                              file=data_path + file,
                              spectrum_id=id,
                              int_method='height',
                              dim=1)
            wizard._apply(None)
        wizard._skip(None)

        # The error type.
        page = wizard.get_page(wizard.page_indices['err_type'])
        page.selection = 'rmsd'
        wizard._go_next(None)

        # Baseplane RMSD.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='rmsd', spectrum_id=id, error=error)
            wizard._apply(None)
        wizard._skip(None)

        # The experiment type.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='exp_type',
                              spectrum_id=id,
                              exp_type='R1rho')
            wizard._apply(None)
        wizard._skip(None)

        # Set the spectrometer frequency.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='spectrometer_frequency',
                              id=id,
                              frq=H_frq,
                              units='MHz')
            wizard._apply(None)
        wizard._skip(None)

        # Set the relaxation times.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='relax_time', spectrum_id=id, time=0.1)
            wizard._apply(None)
        wizard._skip(None)

        # Set the relaxation dispersion spin-lock field strength (nu1).
        for id, file, field, H_frq in data:
            wizard.setup_page(page='spin_lock_field',
                              spectrum_id=id,
                              field=field)
            wizard._apply(None)
        wizard._skip(None)

        # Set the spin-lock offset.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='spin_lock_offset',
                              spectrum_id=id,
                              offset=110.0)
            wizard._apply(None)
        wizard._skip(None)

        # Flush all wx events (to allow the spectrum list GUI element to populate all its rows).
        wx.Yield()

        # Simulate right clicking in the spectrum list element to test the popup menu.
        analysis.peak_intensity.on_right_click(Fake_right_click())

        # Simulate the popup menu entries to catch bugs there (just apply the user functions with the currently set values).
        # FIXME: skipping the checks for certain wxPython bugs.
        if status.relax_mode != 'gui' and wx.version(
        ) != '2.9.4.1 gtk2 (classic)':
            analysis.peak_intensity.action_relax_disp_spin_lock_field(item=4)
            uf_store['relax_disp.spin_lock_field'].wizard._go_next()
            interpreter.flush()
            analysis.peak_intensity.action_relax_disp_exp_type(item=5)
            uf_store['relax_disp.exp_type'].wizard._go_next()
            interpreter.flush()
            analysis.peak_intensity.action_relax_disp_relax_time(item=0)
            uf_store['relax_disp.relax_time'].wizard._go_next()
            interpreter.flush()
            analysis.peak_intensity.action_spectrometer_frq(item=10)
            uf_store['spectrometer.frequency'].wizard._go_next()
            interpreter.flush()

        # Deselect all but the 'TP02' model.
        models = [MODEL_R2EFF, MODEL_NOREX, MODEL_TP02]
        for i in range(len(analysis.model_field.models_stripped)):
            if analysis.model_field.models_stripped[i] in models:
                analysis.model_field.select[i] = True
            else:
                analysis.model_field.select[i] = False
        analysis.model_field.modify()

        # Set the grid search size and number of MC sims.
        analysis.grid_inc.SetValue(4)
        analysis.mc_sim_num.SetValue(3)

        # Optimisation speedups.
        analysis.opt_func_tol = 1e-10
        analysis.opt_max_iterations = 10000

        # Execute relax.
        analysis.execute(
            wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED,
                            analysis.button_exec_relax.GetId()))

        # Wait for execution to complete.
        analysis.thread.join()

        # Flush all wx events.
        wx.Yield()

        # Exceptions in the thread.
        self.check_exceptions()

        # Check the relax controller.
        # FIXME: skipping the checks for certain wxPython bugs.
        if status.relax_mode != 'gui' and wx.version(
        ) != '2.9.4.1 gtk2 (classic)':
            self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(),
                             100)
            self.assertEqual(self.app.gui.controller.main_gauge.GetValue(),
                             100)

        # The original parameters.
        r1rho_prime = [[10.0, 15.0], [12.0, 18.0]]
        pA = 0.7654321
        kex = 1234.56789
        delta_omega = [7.0, 9.0]

        # The R20 keys.
        r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6)
        r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)

        # Switch to the 'TP02' model data pipe, then check for each spin.
        switch("%s - %s" % ('TP02', get_bundle()))
        spin_index = 0
        for spin, spin_id in spin_loop(return_id=True):
            # Printout.
            print("\nSpin %s." % spin_id)

            # Check the fitted parameters.
            self.assertAlmostEqual(spin.r2[r20_key1] / 10,
                                   r1rho_prime[spin_index][0] / 10, 4)
            self.assertAlmostEqual(spin.r2[r20_key2] / 10,
                                   r1rho_prime[spin_index][1] / 10, 4)
            self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3)
            self.assertAlmostEqual(spin.kex / 1000.0, kex / 1000.0, 3)

            # Increment the spin index.
            spin_index += 1
Exemplo n.º 15
0
    def test_tp02_data_to_tp02(self):
        """Test the GUI analysis with the relaxation dispersion 'TP02' model fitting to the 'TP02' synthetic data."""

        # The paths to the data files.
        data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_off_res_tp02'+sep

        # Simulate the new analysis wizard, selecting the fixed time CPMG experiment.
        analysis = self.new_analysis_wizard(analysis_type='disp')

        # Change the results directory.
        analysis.field_results_dir.SetValue(str_to_gui(ds.tmpdir))

        # Create the sequence data.
        self._execute_uf(uf_name='spin.create', res_name='Trp', res_num=1, spin_name='N')
        interpreter.flush()
        self._execute_uf(uf_name='spin.create', res_name='Trp', res_num=2, spin_name='N')
        interpreter.flush()
        self._execute_uf(uf_name='sequence.display')
        interpreter.flush()

        # Set up the nuclear isotopes.
        analysis.spin_isotope()
        uf_store['spin.isotope'].page.SetValue('spin_id', '')
        uf_store['spin.isotope'].wizard._go_next()
        interpreter.flush()    # Required because of the asynchronous uf call.

        # Load the chemical shift data.
        self._execute_uf(uf_name='chemical_shift.read', file='ref_500MHz.list', dir=data_path)
        interpreter.flush()

        # The spectral data.
        frq = [500, 800]
        frq_label = ['500MHz', '800MHz']
        error = 200000.0
        data = []
        spin_lock = [None, 1000.0, 1500.0, 2000.0, 2500.0, 3000.0, 3500.0, 4000.0, 4500.0, 5000.0, 5500.0, 6000.0]
        for frq_index in range(len(frq)):
            for spin_lock_index in range(len(spin_lock)):
                # The reference.
                if spin_lock[spin_lock_index] == None:
                    id = 'ref_%s' % frq_label[frq_index]
                    file = "ref_%s.list" % frq_label[frq_index]

                # Normal data.
                else:
                    id = "nu_%s_%s" % (spin_lock[spin_lock_index], frq_label[frq_index])
                    file = "nu_%s_%s.list" % (spin_lock[spin_lock_index], frq_label[frq_index])

                # Append the data.
                data.append([id, file, spin_lock[spin_lock_index], frq[frq_index]])

        # Load the R1 data.
        for frq_index in range(len(frq)):
            label = 'R1_%s' % frq_label[frq_index]
            self._execute_uf(uf_name='relax_data.read', ri_id=label, ri_type='R1', frq=frq[frq_index]*1e6, file='%s.out'%label, dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
            interpreter.flush()

        # Set up the peak intensity wizard.
        analysis.peak_wizard_launch(None)
        wizard = analysis.peak_wizard

        # The spectra.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='read', file=data_path+file, spectrum_id=id, int_method='height', dim=1)
            wizard._apply(None)
        wizard._skip(None)

        # The error type.
        page = wizard.get_page(wizard.page_indices['err_type'])
        page.selection = 'rmsd'
        wizard._go_next(None)

        # Baseplane RMSD.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='rmsd', spectrum_id=id, error=error)
            wizard._apply(None)
        wizard._skip(None)

        # The experiment type.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='exp_type', spectrum_id=id, exp_type='R1rho')
            wizard._apply(None)
        wizard._skip(None)

        # Set the spectrometer frequency.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='spectrometer_frequency', id=id, frq=H_frq, units='MHz')
            wizard._apply(None)
        wizard._skip(None)

        # Set the relaxation times.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='relax_time', spectrum_id=id, time=0.1)
            wizard._apply(None)
        wizard._skip(None)

        # Set the relaxation dispersion spin-lock field strength (nu1).
        for id, file, field, H_frq in data:
            wizard.setup_page(page='spin_lock_field', spectrum_id=id, field=field)
            wizard._apply(None)
        wizard._skip(None)

        # Set the spin-lock offset.
        for id, file, field, H_frq in data:
            wizard.setup_page(page='spin_lock_offset', spectrum_id=id, offset=110.0)
            wizard._apply(None)
        wizard._skip(None)

        # Flush all wx events (to allow the spectrum list GUI element to populate all its rows).
        wx.Yield()

        # Simulate right clicking in the spectrum list element to test the popup menu.
        analysis.peak_intensity.on_right_click(Fake_right_click())

        # Simulate the popup menu entries to catch bugs there (just apply the user functions with the currently set values).
        # FIXME: skipping the checks for certain wxPython bugs.
        if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)':
            analysis.peak_intensity.action_relax_disp_spin_lock_field(item=4)
            uf_store['relax_disp.spin_lock_field'].wizard._go_next()
            interpreter.flush()
            analysis.peak_intensity.action_relax_disp_exp_type(item=5)
            uf_store['relax_disp.exp_type'].wizard._go_next()
            interpreter.flush()
            analysis.peak_intensity.action_relax_disp_relax_time(item=0)
            uf_store['relax_disp.relax_time'].wizard._go_next()
            interpreter.flush()
            analysis.peak_intensity.action_spectrometer_frq(item=10)
            uf_store['spectrometer.frequency'].wizard._go_next()
            interpreter.flush()

        # Deselect all but the 'TP02' model.
        models = [MODEL_R2EFF, MODEL_NOREX, MODEL_TP02]
        for i in range(len(analysis.model_field.models_stripped)):
            if analysis.model_field.models_stripped[i] in models:
                analysis.model_field.select[i] = True
            else:
                analysis.model_field.select[i] = False
        analysis.model_field.modify()

        # Set the grid search size and number of MC sims.
        analysis.grid_inc.SetValue(4)
        analysis.mc_sim_num.SetValue(3)

        # Optimisation speedups.
        analysis.opt_func_tol = 1e-10
        analysis.opt_max_iterations = 10000

        # Execute relax.
        analysis.execute(wx.CommandEvent(wx.wxEVT_COMMAND_BUTTON_CLICKED, analysis.button_exec_relax.GetId()))

        # Wait for execution to complete.
        analysis.thread.join()

        # Flush all wx events.
        wx.Yield()

        # Exceptions in the thread.
        self.check_exceptions()

        # Check the relax controller.
        # FIXME: skipping the checks for certain wxPython bugs.
        if status.relax_mode != 'gui' and wx.version() != '2.9.4.1 gtk2 (classic)':
            self.assertEqual(self.app.gui.controller.mc_gauge_rx.GetValue(), 100)
            self.assertEqual(self.app.gui.controller.main_gauge.GetValue(), 100)

        # The original parameters.
        r1rho_prime = [[10.0, 15.0], [12.0, 18.0]]
        pA = 0.7654321
        kex = 1234.56789
        delta_omega = [7.0, 9.0]

        # The R20 keys.
        r20_key1 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=500e6)
        r20_key2 = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)

        # Switch to the 'TP02' model data pipe, then check for each spin.
        switch("%s - %s" % ('TP02', get_bundle()))
        spin_index = 0
        for spin, spin_id in spin_loop(return_id=True):
            # Printout.
            print("\nSpin %s." % spin_id)

            # Check the fitted parameters.
            self.assertAlmostEqual(spin.r2[r20_key1]/10, r1rho_prime[spin_index][0]/10, 4)
            self.assertAlmostEqual(spin.r2[r20_key2]/10, r1rho_prime[spin_index][1]/10, 4)
            self.assertAlmostEqual(spin.dw, delta_omega[spin_index], 3)
            self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 3)

            # Increment the spin index.
            spin_index += 1
Exemplo n.º 16
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        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id,
                               file=file,
                               dir=DATA_PATH,
                               spin_id=spin_id,
                               disp_point_col=7,
                               data_col=10,
                               error_col=9)

# Change the model.
relax_disp.select_model('NS MMQ 3-site linear')

# The R20 keys.
r20_1h_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
                                     frq=400e6)
r20_1h_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
                                     frq=600e6)
r20_1h_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
                                     frq=800e6)
r20_1h_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
                                      frq=1000e6)
r20_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=400e6)
r20_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=1000e6)
r20_zq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=400e6)
r20_zq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_zq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_zq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=1000e6)
r20_dq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=400e6)
Exemplo n.º 17
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        relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)

        # Relaxation dispersion CPMG constant time delay T (in s).
        relax_disp.relax_time(spectrum_id=new_id, time=relax_time)

        # Set the CPMG frequency.
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir='../..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)

# Change the model.
relax_disp.select_model('NS MMQ 2-site')

# The R20 keys.
r20_key_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key_1h_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key_1h_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key_1h_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key_zq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key_zq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key_zq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key_dq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key_dq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key_dq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
r20_key_mq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
r20_key_mq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
r20_key_1h_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
Exemplo n.º 18
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                frq=800e6,
                file='R1_800MHz.out',
                dir='..',
                mol_name_col=1,
                res_num_col=2,
                res_name_col=3,
                spin_num_col=4,
                spin_name_col=5,
                data_col=6,
                error_col=7)

# Change the model.
relax_disp.select_model('TP02')

# The R20 keys.
r20_600_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=600e6)
r20_800_key = generate_r20_key(exp_type=EXP_TYPE_R1RHO, frq=800e6)

# Manually set the parameter values.
spin_N = cdp.mol[0].res[0].spin[0]
spin_N.r2 = {
    r20_600_key: 9.108060397660111,
    r20_800_key: 13.793213528551924,
}
spin_N.pA = 0.945912353996981
spin_N.pB = 0.054087646003019
spin_N.kex = 367.981715073974556
spin_N.dw = 4.305697497613982
spin_N.ri_data['600MHz'] = 3.179051390898238
spin_N.ri_data['800MHz'] = 4.452840879991469
Exemplo n.º 19
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                                                             return_id=True,
                                                             skip_desel=True):
        # Generate spin string.
        spin_string = generate_spin_string(spin=cur_spin,
                                           mol_name=mol_name,
                                           res_num=resi,
                                           res_name=resn)

        # Loop over the parameters.
        print("\nOptimised parameters for spin: %s" % (spin_string))
        for param in cur_spin.params + ['chi2']:
            # Get the value.
            if param in ['r1', 'r2']:
                for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
                    # Generate the R20 key.
                    r20_key = generate_r20_key(exp_type=exp_type, frq=frq)

                    # Get the value.
                    value = getattr(cur_spin, param)[r20_key]

                    # Print value.
                    print("%-10s %-6s %-6s %3.8f" %
                          ("Parameter:", param, "Value:", value))

            # For all other parameters.
            else:
                # Get the value.
                value = getattr(cur_spin, param)

                # Print value.
                print("%-10s %-6s %-6s %3.8f" %
Exemplo n.º 20
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        relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)

        # Relaxation dispersion CPMG constant time delay T (in s).
        relax_disp.relax_time(spectrum_id=new_id, time=relax_time)

        # Set the CPMG frequency.
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir='../..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)

# Change the model.
relax_disp.select_model('NS MMQ 2-site')

# The R20 keys.
r20_key_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key_1h_sq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key_1h_sq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key_1h_sq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)
r20_key_zq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
r20_key_zq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
r20_key_zq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
r20_key_dq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
r20_key_dq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
r20_key_dq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
r20_key_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
r20_key_mq_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
r20_key_mq_800 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
r20_key_1h_mq_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, frq=500e6)
Exemplo n.º 21
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        relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)

        # Relaxation dispersion CPMG constant time delay T (in s).
        relax_disp.relax_time(spectrum_id=new_id, time=relax_time)

        # Set the CPMG frequency.
        relax_disp.cpmg_setup(spectrum_id=new_id, cpmg_frq=cpmg_frq)

    # Read the R2eff data.
    relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)

# Change the model.
relax_disp.select_model('NS MMQ 2-site')

# The R20 keys.
r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
r20_key3 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
r20_key4 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=500e6)
r20_key5 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=600e6)
r20_key6 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, frq=800e6)

# Manually set the parameter values.
spin_N = cdp.mol[0].res[0].spin[1]
spin_N.r2 = {r20_key1: 8.412998, r20_key2: 8.847946, r20_key3: 10.329567, r20_key4: 6.779626, r20_key5: 7.089813, r20_key6: 5.610770}
spin_N.pA = 0.947960
spin_N.kex = 408.394
spin_N.dw = 4.369907
spin_N.dwH = -0.267240

# Optimisation.