)
uf.add_keyarg(
name = "force",
default = False,
basic_types = ["bool"],
desc_short = "force flag",
desc = "A flag which, if set to True, will cause the destination parameter to be overwritten."
)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("If this is used to change values of previously minimised parameters, then the minimisation statistics (chi-squared value, iteration count, function count, gradient count, and Hessian count) will be reset.")
# Prompt examples.
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter value setting"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter value setting"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value setting"))
uf.desc.append(consistency_test_params.uf_doc(label="table: consistency testing parameter value setting"))
uf.desc.append(n_state_params.uf_doc(label="table: N-state parameter value setting"))
uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameter value setting"))
uf.desc.append(frame_order_params.uf_doc(label="table: frame order parameters"))
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To copy the CSA values from the data pipe 'm1' to 'm2', type:")
uf.desc[-1].add_prompt("relax> value.copy('m1', 'm2', 'csa')")
uf.backend = value.copy
uf.menu_text = "©"
uf.gui_icon = "oxygen.actions.list-add"
uf.wizard_height_desc = 500
uf.wizard_size = (1000, 750)
uf.wizard_image = WIZARD_IMAGE_PATH + 'value' + sep + 'value.png'
# The value.display user function.
name="force",
default=False,
py_type="bool",
desc_short="force flag",
desc="A flag which, if set to True, will cause the destination parameter to be overwritten.",
)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph(
"If this is used to change values of previously minimised parameters, then the minimisation statistics (chi-squared value, iteration count, function count, gradient count, and Hessian count) will be reset."
)
# Prompt examples.
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter value setting"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter value setting"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value setting"))
uf.desc.append(consistency_test_params.uf_doc(label="table: consistency testing parameter value setting"))
uf.desc.append(n_state_params.uf_doc(label="table: N-state parameter value setting"))
uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameter value setting"))
uf.desc.append(frame_order_params.uf_doc(label="table: frame order parameters"))
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To copy the CSA values from the data pipe 'm1' to 'm2', type:")
uf.desc[-1].add_prompt("relax> value.copy('m1', 'm2', 'csa')")
uf.backend = value.copy
uf.menu_text = "©"
uf.gui_icon = "oxygen.actions.list-add"
uf.wizard_height_desc = 500
uf.wizard_size = (1000, 750)
uf.wizard_image = WIZARD_IMAGE_PATH + "value" + sep + "value.png"
# The value.display user function.
uf.desc[-1].add_item_list_element("'value'",
"Plot values (with errors if they exist).")
uf.desc[-1].add_item_list_element("'error'", "Plot errors.")
uf.desc[-1].add_item_list_element("'sims'", "Plot the simulation values.")
uf.desc[-1].add_paragraph(
"Normalisation is only allowed for series type data, for example the R2 exponential curves, and will be ignored for all other data types. If the norm flag is set to True then the y-value of the first point of the series will be set to 1. This normalisation is useful for highlighting errors in the data sets."
)
uf.desc.append(
relax_fit_params.uf_doc(label="table: curve-fit parameters and min stats"))
uf.desc.append(noe_params.uf_doc(label="table: NOE parameters"))
uf.desc.append(
model_free_params.uf_doc(
label="table: model-free parameters and min stats"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
uf.desc.append(
consistency_test_params.uf_doc(
label="table: consistency testing parameters"))
uf.desc.append(
relax_disp_params.uf_doc(
label="table: dispersion parameters and min stats"))
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph(
"To write the NOE values for all spins to the Grace file 'noe.agr', type one of:"
)
uf.desc[-1].add_prompt("relax> grace.write('res_num', 'noe', file='noe.agr')")
uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe', file='noe.agr')")
uf.desc[-1].add_prompt(
"relax> grace.write(x_data_type='res_num', y_data_type='noe', file='noe.agr')"
)
uf.desc[-1].add_prompt(
"relax> grace.write(y_data_type='noe', file='noe.agr', force=True)")
uf.desc[-1].add_paragraph("This is designed to be as flexible as possible so that any combination of data can be plotted. The output is in the format of a Grace plot (also known as ACE/gr, Xmgr, and xmgrace) which only supports two dimensional plots. Three types of information can be used to create various types of plot. These include the x-axis and y-axis data types, the spin ID string, and the type of data plot.")
uf.desc[-1].add_paragraph("The x-axis and y-axis data types should be plain strings, regular expression is not allowed. The two axes of the Grace plot can be any of the data types listed in the tables below. The only limitation is that the data must belong to the same data pipe.")
uf.desc[-1].add_paragraph("If the x-axis data type is not given, the plot will default to having the residue numbering along the x-axis.Two special data types for the axes are:")
uf.desc[-1].add_item_list_element("'res_num'", "The axis will consist of the residue numbering.")
uf.desc[-1].add_item_list_element("'spin_num'", "The axis will consist of the spin numbering.")
uf.desc[-1].add_paragraph("The spin ID string can be used to limit which spins are used in the plot. The default is that all spins will be used, however, the ID string can be used to select a subset of all spins, or a single spin for plots of Monte Carlo simulations, etc.")
uf.desc[-1].add_paragraph("The property which is actually plotted can be controlled by the plot data setting. This can be one of the following:")
uf.desc[-1].add_item_list_element("'value'", "Plot values (with errors if they exist).")
uf.desc[-1].add_item_list_element("'error'", "Plot errors.")
uf.desc[-1].add_item_list_element("'sims'", "Plot the simulation values.")
uf.desc[-1].add_paragraph("Normalisation is only allowed for series type data, for example the R2 exponential curves, and will be ignored for all other data types. If the norm flag is set to True then the y-value of the first point of the series will be set to 1. This normalisation is useful for highlighting errors in the data sets.")
uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters and min stats"))
uf.desc.append(noe_params.uf_doc(label="table: NOE parameters"))
uf.desc.append(model_free_params.uf_doc(label="table: model-free parameters and min stats"))
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
uf.desc.append(consistency_test_params.uf_doc(label="table: consistency testing parameters"))
uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameters and min stats"))
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To write the NOE values for all spins to the Grace file 'noe.agr', type one of:")
uf.desc[-1].add_prompt("relax> grace.write('res_num', 'noe', file='noe.agr')")
uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe', file='noe.agr')")
uf.desc[-1].add_prompt("relax> grace.write(x_data_type='res_num', y_data_type='noe', file='noe.agr')")
uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe', file='noe.agr', force=True)")
uf.desc[-1].add_paragraph("To create a Grace file of 's2' vs. 'te' for all spins, type one of:")
uf.desc[-1].add_prompt("relax> grace.write('s2', 'te', file='s2_te.agr')")
uf.desc[-1].add_prompt("relax> grace.write(x_data_type='s2', y_data_type='te', file='s2_te.agr')")
uf.desc[-1].add_prompt("relax> grace.write(x_data_type='s2', y_data_type='te', file='s2_te.agr', force=True)")
uf.desc[-1].add_paragraph("To create a Grace file of the Monte Carlo simulation values of 'rex' vs. 'te' for residue 123, type one of:")
uf.desc[-1].add_prompt("relax> grace.write('rex', 'te', spin_id=':123', plot_data='sims', file='s2_te.agr')")
uf.desc[-1].add_prompt("relax> grace.write(x_data_type='rex', y_data_type='te', spin_id=':123', plot_data='sims', file='s2_te.agr')")
