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.
uf = uf_info.add_uf('value.display')
uf.title = "Display spin specific parameter values."
default = False,
py_type = "bool",
desc_short = "creation of file with parameter and calculated chi2",
desc = "A flag specifying whether to create a file with parameters and associated chi2 value. The default of False causes the file not to be created."
)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will map the space corresponding to the spin identifier and create the OpenDX files. The map type can be changed to one of the following supported map types:")
table = uf_tables.add_table(label="table: opendx map", caption="OpenDx mapping types.")
table.add_headings(["Surface type", "Name"])
table.add_row(["3D isosurface", "'Iso3D'"])
uf.desc[-1].add_table(table.label)
# Additional.
uf.desc.append(model_free_params.uf_doc(label="table: all model-free parameters"))
uf.desc.append(n_state_params.uf_doc(label="table: N-state parameters"))
uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameters"))
uf.desc.append(frame_order_params.uf_doc(label="table: frame order parameters"))
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("The following commands will generate a map of the extended model-free space for model 'm5' consisting of the parameters {S2, S2f, ts}. Files will be output into the directory 'dx' and will be prefixed by 'map'. In this case, the system is a protein and residue number 6 will be mapped.")
uf.desc[-1].add_prompt("relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6')")
uf.desc[-1].add_prompt("relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6', file_prefix='map', dir='dx')")
uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 's2f', 'ts'], spin_id=':6', inc=20, file_prefix='map', dir='dx')")
uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 's2f', 'ts'], spin_id=':6', map_type='Iso3D', inc=20, file_prefix='map', dir='dx')")
uf.desc[-1].add_paragraph("To map the model-free space 'm4' for residue 2, spin N6 defined by the parameters {S2, te, Rex}, name the results 'test', and to place the files in the current directory, use one of the following commands:")
uf.desc[-1].add_prompt("relax> dx.map(['s2', 'te', 'rex'], spin_id=':2@N6', file_prefix='test', dir=None)")
uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 'te', 'rex'], spin_id=':2@N6', inc=100, file_prefix='test', dir=None)")
uf.backend = map
uf.menu_text = "&map"
uf.gui_icon = "relax.grid_search"
uf.wizard_height_desc = 260
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')")
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 = uf_info.add_uf("value.display")
uf.title = "Display spin specific parameter values."
