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23 """The grace user function definitions for controlling the Grace data viewing software."""
24
25
26 import dep_check
27 if dep_check.wx_module:
28 from wx import FD_OPEN, FD_SAVE
29 else:
30 FD_OPEN = -1
31 FD_SAVE = -1
32
33
34 from graphics import WIZARD_IMAGE_PATH
35 from pipe_control import grace, minimise
36 from prompt.doc_string import regexp_doc
37 from specific_analyses.consistency_tests import Consistency_tests
38 from specific_analyses.jw_mapping import Jw_mapping
39 from specific_analyses.model_free import Model_free
40 from specific_analyses.noe import Noe
41 from specific_analyses.relax_fit import Relax_fit
42 from user_functions.data import Uf_info; uf_info = Uf_info()
43 from user_functions.objects import Desc_container
44
45
46
47 uf_class = uf_info.add_class('grace')
48 uf_class.title = "Class for interfacing with Grace."
49 uf_class.menu_text = "&grace"
50 uf_class.gui_icon = "relax.grace_icon"
51
52
53
54 uf = uf_info.add_uf('grace.view')
55 uf.title = "Visualise the file within Grace."
56 uf.title_short = "Grace execution."
57 uf.add_keyarg(
58 name = "file",
59 py_type = "str",
60 arg_type = "file sel",
61 desc_short = "file name",
62 desc = "The name of the file.",
63 wiz_filesel_wildcard = "Grace files (*.agr)|*.agr;*.AGR",
64 wiz_filesel_style = FD_OPEN
65 )
66 uf.add_keyarg(
67 name = "dir",
68 default = "grace",
69 py_type = "str",
70 arg_type = "dir",
71 desc_short = "directory name",
72 desc = "The directory name.",
73 can_be_none = True
74 )
75 uf.add_keyarg(
76 name = "grace_exe",
77 default = "xmgrace",
78 py_type = "str",
79 arg_type = "file sel",
80 desc_short = "Grace executable file",
81 desc = "The Grace executable file.",
82 wiz_filesel_style = FD_OPEN,
83 wiz_filesel_preview = False
84 )
85
86 uf.desc.append(Desc_container())
87 uf.desc[-1].add_paragraph("This can be used to view the specified Grace '*.agr' file by opening it with the Grace program.")
88
89 uf.desc.append(Desc_container("Prompt examples"))
90 uf.desc[-1].add_paragraph("To view the file 's2.agr' in the directory 'grace', type:")
91 uf.desc[-1].add_prompt("relax> grace.view(file='s2.agr')")
92 uf.desc[-1].add_prompt("relax> grace.view(file='s2.agr', dir='grace')")
93 uf.backend = grace.view
94 uf.menu_text = "&view"
95 uf.gui_icon = "relax.grace_icon"
96 uf.wizard_size = (900, 500)
97 uf.wizard_image = WIZARD_IMAGE_PATH + 'grace.png'
98
99
100
101 uf = uf_info.add_uf('grace.write')
102 uf.title = "Create a grace '.agr' file to visualise the 2D data."
103 uf.title_short = "Grace file creation."
104 uf.add_keyarg(
105 name = "x_data_type",
106 default = "res_num",
107 py_type = "str",
108 desc_short = "x data type",
109 desc = "The data type for the X-axis (no regular expression is allowed).",
110 wiz_element_type = 'combo',
111 wiz_combo_iter = grace.get_data_types
112 )
113 uf.add_keyarg(
114 name = "y_data_type",
115 py_type = "str",
116 desc_short = "y data type",
117 desc = "The data type for the Y-axis (no regular expression is allowed).",
118 wiz_element_type = 'combo',
119 wiz_combo_iter = grace.get_data_types
120 )
121 uf.add_keyarg(
122 name = "spin_id",
123 py_type = "str",
124 desc_short = "spin ID string",
125 desc = "The spin ID string.",
126 can_be_none = True
127 )
128 uf.add_keyarg(
129 name = "plot_data",
130 default = "value",
131 py_type = "str",
132 desc_short = "plot data",
133 desc = "The data to use for the plot.",
134 wiz_element_type = "combo",
135 wiz_combo_choices = [
136 "Values",
137 "Errors",
138 "Simulation values"
139 ],
140 wiz_combo_data = [
141 "value",
142 "error",
143 "sims"
144 ],
145 wiz_read_only = True
146 )
147 uf.add_keyarg(
148 name = "file",
149 py_type = "str",
150 arg_type = "file sel",
151 desc_short = "file name",
152 desc = "The name of the file.",
153 wiz_filesel_wildcard = "Grace files (*.agr)|*.agr;*.AGR",
154 wiz_filesel_style = FD_SAVE
155 )
156 uf.add_keyarg(
157 name = "dir",
158 default = "grace",
159 py_type = "str",
160 arg_type = "dir",
161 desc_short = "directory name",
162 desc = "The directory name.",
163 can_be_none = True
164 )
165 uf.add_keyarg(
166 name = "force",
167 default = False,
168 py_type = "bool",
169 desc_short = "force flag",
170 desc = "A flag which, if set to True, will cause the file to be overwritten."
171 )
172 uf.add_keyarg(
173 name = "norm",
174 default = False,
175 py_type = "bool",
176 desc_short = "normalisation flag",
177 desc = "A flag which, if set to True, will cause all graphs to be normalised to a starting value of 1. This is for the normalisation of series type data."
178 )
179
180 uf.desc.append(Desc_container())
181 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.")
182 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.")
183 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:")
184 uf.desc[-1].add_item_list_element("'res_num'", "The axis will consist of the residue numbering.")
185 uf.desc[-1].add_item_list_element("'spin_num'", "The axis will consist of the spin numbering.")
186 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.")
187 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:")
188 uf.desc[-1].add_item_list_element("'value'", "Plot values (with errors if they exist).")
189 uf.desc[-1].add_item_list_element("'error'", "Plot errors.")
190 uf.desc[-1].add_item_list_element("'sims'", "Plot the simulation values.")
191 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.")
192 uf.desc.append(regexp_doc)
193 uf.desc.append(minimise.return_data_name_doc)
194 uf.desc.append(Noe.return_data_name_doc)
195 uf.desc.append(Relax_fit.return_data_name_doc)
196 uf.desc.append(Jw_mapping.return_data_name_doc)
197 uf.desc.append(Consistency_tests.return_data_name_doc)
198 uf.desc.append(Model_free.return_data_name_doc)
199
200 uf.desc.append(Desc_container("Prompt examples"))
201 uf.desc[-1].add_paragraph("To write the NOE values for all spins to the Grace file 'noe.agr', type one of:")
202 uf.desc[-1].add_prompt("relax> grace.write('res_num', 'noe', file='noe.agr')")
203 uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe', file='noe.agr')")
204 uf.desc[-1].add_prompt("relax> grace.write(x_data_type='res_num', y_data_type='noe', file='noe.agr')")
205 uf.desc[-1].add_prompt("relax> grace.write(y_data_type='noe', file='noe.agr', force=True)")
206 uf.desc[-1].add_paragraph("To create a Grace file of 's2' vs. 'te' for all spins, type one of:")
207 uf.desc[-1].add_prompt("relax> grace.write('s2', 'te', file='s2_te.agr')")
208 uf.desc[-1].add_prompt("relax> grace.write(x_data_type='s2', y_data_type='te', file='s2_te.agr')")
209 uf.desc[-1].add_prompt("relax> grace.write(x_data_type='s2', y_data_type='te', file='s2_te.agr', force=True)")
210 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:")
211 uf.desc[-1].add_prompt("relax> grace.write('rex', 'te', spin_id=':123', plot_data='sims', file='s2_te.agr')")
212 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')")
213 uf.desc[-1].add_paragraph("By plotting the peak intensities, the integrity of exponential relaxation curves can be checked and anomalies searched for prior to model-free analysis or reduced spectral density mapping. For example the normalised average peak intensities can be plotted verses the relaxation time periods for the relaxation curves of all residues of a protein. The normalisation, whereby the initial peak intensity of each residue I(0) is set to 1, emphasises any problems. To produce this Grace file, type:")
214 uf.desc[-1].add_prompt("relax> grace.write(x_data_type='relax_times', y_data_type='ave_int', file='intensities_norm.agr', force=True, norm=True)")
215 uf.backend = grace.write
216 uf.menu_text = "&write"
217 uf.gui_icon = "oxygen.actions.document-save"
218 uf.wizard_size = (1000, 700)
219 uf.wizard_image = WIZARD_IMAGE_PATH + 'grace.png'
220