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23 """The pcs user function definitions."""
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 generic_fns import align_tensor, pcs, pipes
35 from graphics import WIZARD_IMAGE_PATH
36 from user_functions.data import Uf_info; uf_info = Uf_info()
37 from user_functions.objects import Desc_container
38
39
40
41 uf_class = uf_info.add_class('pcs')
42 uf_class.title = "Class for handling pseudo-contact shifts."
43 uf_class.menu_text = "&pcs"
44 uf_class.gui_icon = "relax.align_tensor"
45
46
47
48 uf = uf_info.add_uf('pcs.back_calc')
49 uf.title = "Back calculate the pseudo-contact shifts."
50 uf.title_short = "PCS back calculation."
51 uf.display = True
52 uf.add_keyarg(
53 name = "align_id",
54 py_type = "str",
55 desc_short = "alignment ID string",
56 desc = "The alignment ID string.",
57 wiz_element_type = 'combo',
58 wiz_combo_iter = align_tensor.get_ids,
59 wiz_read_only = True,
60 can_be_none = True
61 )
62
63 uf.desc.append(Desc_container())
64 uf.desc[-1].add_paragraph("This will back calculate the pseudo-contact shifts if the paramagnetic centre, temperature and magnetic field strength has been specified, an alignment tensor is present, and atomic positions have been loaded into the relax data store.")
65 uf.backend = pcs.back_calc
66 uf.menu_text = "&back_calc"
67 uf.gui_icon = "oxygen.categories.applications-education"
68 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
69 uf.wizard_apply_button = False
70
71
72
73 uf = uf_info.add_uf('pcs.calc_q_factors')
74 uf.title = "Calculate the PCS Q factor for the selected spins."
75 uf.title_short = "PCS Q factor calculation."
76 uf.display = True
77 uf.add_keyarg(
78 name = "spin_id",
79 py_type = "str",
80 desc_short = "spin ID string",
81 desc = "The spin ID string for restricting to subset of all selected spins.",
82 can_be_none = True
83 )
84
85 uf.desc.append(Desc_container())
86 uf.desc[-1].add_paragraph("For this to work, the back-calculated PCS data must first be generated by the analysis specific code. Otherwise a warning will be given.")
87
88 uf.desc.append(Desc_container("Prompt examples"))
89 uf.desc[-1].add_paragraph("To calculate the PCS Q factor for only the spins '@H26', '@H27', and '@H28', type one of:")
90 uf.desc[-1].add_prompt("relax> pcs.calc_q_factors('@H26 & @H27 & @H28')")
91 uf.desc[-1].add_prompt("relax> pcs.calc_q_factors(spin_id='@H26 & @H27 & @H28')")
92 uf.backend = pcs.q_factors
93 uf.menu_text = "&calc_q_factors"
94 uf.gui_icon = "oxygen.categories.applications-education"
95 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
96 uf.wizard_apply_button = False
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152 uf = uf_info.add_uf('pcs.corr_plot')
153 uf.title = "Generate a correlation plot of the measured vs. the back-calculated PCSs."
154 uf.title_short = "Correlation plot generation."
155 uf.add_keyarg(
156 name = "format",
157 default = "grace",
158 py_type = "str",
159 desc_short = "format",
160 desc = "The format of the plot data.",
161 wiz_element_type = "combo",
162 wiz_combo_choices = ["grace"],
163 wiz_read_only = True,
164 can_be_none = True
165 )
166 uf.add_keyarg(
167 name = "file",
168 default = "pcs_corr_plot.agr",
169 py_type = "str",
170 arg_type = "file sel",
171 desc_short = "Grace file name",
172 desc = "The name of the Grace file to create.",
173 wiz_filesel_wildcard = "Grace files (*.agr)|*.agr;*.AGR",
174 wiz_filesel_style = FD_SAVE
175 )
176 uf.add_keyarg(
177 name = "dir",
178 py_type = "str",
179 arg_type = "dir",
180 desc_short = "directory name",
181 desc = "The directory name.",
182 can_be_none = True
183 )
184 uf.add_keyarg(
185 name = "force",
186 default = False,
187 py_type = "bool",
188 desc_short = "force flag",
189 desc = "A flag which if True will cause the file to be overwritten."
190 )
191
192 uf.desc.append(Desc_container())
193 uf.desc[-1].add_paragraph("Two formats are currently supported. If format is set to 'grace', then a Grace plot file will be created. If the format is not set then a plain text list of the measured and back-calculated data will be created.")
194
195 uf.desc.append(Desc_container("Prompt examples"))
196 uf.desc[-1].add_paragraph("To create a Grace plot of the data, type:")
197 uf.desc[-1].add_prompt("relax> pcs.corr_plot()")
198 uf.desc[-1].add_paragraph("To create a plain text list of the measured and back-calculated data, type one of:")
199 uf.desc[-1].add_prompt("relax> pcs.corr_plot(None)")
200 uf.desc[-1].add_prompt("relax> pcs.corr_plot(format=None)")
201 uf.backend = pcs.corr_plot
202 uf.menu_text = "corr_&plot"
203 uf.wizard_size = (800, 500)
204 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
205 uf.wizard_apply_button = False
206
207
208
209 uf = uf_info.add_uf('pcs.delete')
210 uf.title = "Delete the PCS data corresponding to the alignment ID."
211 uf.title_short = "PCS deletion."
212 uf.add_keyarg(
213 name = "align_id",
214 py_type = "str",
215 desc_short = "alignment ID string",
216 desc = "The alignment ID string of the data to delete.",
217 wiz_element_type = 'combo',
218 wiz_combo_iter = align_tensor.get_ids,
219 wiz_read_only = True,
220 can_be_none = True
221 )
222
223 uf.desc.append(Desc_container())
224 uf.desc[-1].add_paragraph("This will delete all PCS data associated with the alignment ID in the current data pipe.")
225
226 uf.desc.append(Desc_container("Prompt examples"))
227 uf.desc[-1].add_paragraph("To delete the PCS data corresponding to align_id='PH_gel', type:")
228 uf.desc[-1].add_prompt("relax> pcs.delete('PH_gel')")
229 uf.backend = pcs.delete
230 uf.menu_text = "&delete"
231 uf.gui_icon = "oxygen.actions.list-remove"
232 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
233
234
235
236 uf = uf_info.add_uf('pcs.display')
237 uf.title = "Display the PCS data corresponding to the alignment ID."
238 uf.title_short = "PCS data display."
239 uf.display = True
240 uf.add_keyarg(
241 name = "align_id",
242 py_type = "str",
243 desc_short = "alignment ID string",
244 desc = "The alignment ID string.",
245 wiz_element_type = 'combo',
246 wiz_combo_iter = align_tensor.get_ids,
247 wiz_read_only = True
248 )
249 uf.add_keyarg(
250 name = "bc",
251 default = False,
252 py_type = "bool",
253 desc_short = "back-calculation flag",
254 desc = "A flag which if set will display the back-calculated rather than measured RDCs."
255 )
256
257 uf.desc.append(Desc_container())
258 uf.desc[-1].add_paragraph("This will display all of the PCS data associated with the alignment ID in the current data pipe.")
259
260 uf.desc.append(Desc_container("Prompt examples"))
261 uf.desc[-1].add_paragraph("To display the 'phage' PCS data, type:")
262 uf.desc[-1].add_prompt("relax> pcs.display('phage')")
263 uf.backend = pcs.display
264 uf.menu_text = "di&splay"
265 uf.gui_icon = "oxygen.actions.document-preview"
266 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
267
268
269
270 uf = uf_info.add_uf('pcs.read')
271 uf.title = "Read the PCS data from file."
272 uf.title_short = "PCS data reading."
273 uf.add_keyarg(
274 name = "align_id",
275 py_type = "str",
276 desc_short = "alignment ID string",
277 desc = "The alignment ID string.",
278 wiz_element_type = 'combo',
279 wiz_combo_iter = align_tensor.get_ids
280 )
281 uf.add_keyarg(
282 name = "file",
283 py_type = "str",
284 arg_type = "file sel",
285 desc_short = "file name",
286 desc = "The name of the file containing the PCS data.",
287 wiz_filesel_style = FD_OPEN
288 )
289 uf.add_keyarg(
290 name = "dir",
291 py_type = "str",
292 arg_type = "dir",
293 desc_short = "directory name",
294 desc = "The directory where the file is located.",
295 can_be_none = True
296 )
297 uf.add_keyarg(
298 name = "spin_id_col",
299 py_type = "int",
300 arg_type = "free format",
301 desc_short = "spin ID column",
302 desc = "The spin ID string column (an alternative to the mol, res, and spin name and number columns).",
303 can_be_none = True
304 )
305 uf.add_keyarg(
306 name = "mol_name_col",
307 py_type = "int",
308 arg_type = "free format",
309 desc_short = "molecule name column",
310 desc = "The molecule name column (alternative to the spin_id_col).",
311 can_be_none = True
312 )
313 uf.add_keyarg(
314 name = "res_num_col",
315 py_type = "int",
316 arg_type = "free format",
317 desc_short = "residue number column",
318 desc = "The residue number column (alternative to the spin_id_col).",
319 can_be_none = True
320 )
321 uf.add_keyarg(
322 name = "res_name_col",
323 py_type = "int",
324 arg_type = "free format",
325 desc_short = "residue name column",
326 desc = "The residue name column (alternative to the spin_id_col).",
327 can_be_none = True
328 )
329 uf.add_keyarg(
330 name = "spin_num_col",
331 py_type = "int",
332 arg_type = "free format",
333 desc_short = "spin number column",
334 desc = "The spin number column (alternative to the spin_id_col).",
335 can_be_none = True
336 )
337 uf.add_keyarg(
338 name = "spin_name_col",
339 py_type = "int",
340 arg_type = "free format",
341 desc_short = "spin name column",
342 desc = "The spin name column (alternative to the spin_id_col).",
343 can_be_none = True
344 )
345 uf.add_keyarg(
346 name = "data_col",
347 py_type = "int",
348 arg_type = "free format",
349 desc_short = "data column",
350 desc = "The PCS data column.",
351 can_be_none = True
352 )
353 uf.add_keyarg(
354 name = "error_col",
355 py_type = "int",
356 arg_type = "free format",
357 desc_short = "error column",
358 desc = "The experimental error column.",
359 can_be_none = True
360 )
361 uf.add_keyarg(
362 name = "sep",
363 py_type = "str",
364 arg_type = "free format",
365 desc_short = "column separator",
366 desc = "The column separator (the default is white space).",
367 can_be_none = True
368 )
369 uf.add_keyarg(
370 name = "spin_id",
371 py_type = "str",
372 desc_short = "spin ID string",
373 desc = "The spin ID string to restrict the loading of data to certain spin subsets.",
374 can_be_none = True
375 )
376
377 uf.desc.append(Desc_container())
378 uf.desc[-1].add_paragraph("This will read PCS data from a file and associate it with an alignment ID, either a new ID or a preexisting one with no PCS data.")
379 uf.desc[-1].add_paragraph("The spin system can be identified in the file using two different formats. The first is the spin ID string column which can include the molecule name, the residue name and number, and the spin name and number. Alternatively the molecule name, residue number and name, and spin number and name columns can be supplied allowing this information to be in separate columns. Note that the numbering of columns starts at one. The spin ID can be used to restrict the reading to certain spin types, for example only 15N spins when only residue information is in the file.")
380
381 uf.desc.append(Desc_container("Prompt examples"))
382 uf.desc[-1].add_paragraph("The following commands will read the PCS data out of the file 'Tb.txt' where the columns are separated by the symbol ',', and store the PCSs under the ID 'Tb'.")
383 uf.desc[-1].add_prompt("relax> pcs.read('Tb', 'Tb.txt', sep=',')")
384 uf.desc[-1].add_paragraph("To read the 15N and 1H PCSs from the file 'Eu.txt', where the 15N values are in the 4th column and the 1H in the 9th, type both the following:")
385 uf.desc[-1].add_prompt("relax> pcs.read('Tb', 'Tb.txt', spin_id='@N', res_num_col=1, data_col=4)")
386 uf.desc[-1].add_prompt("relax> pcs.read('Tb', 'Tb.txt', spin_id='@H', res_num_col=1, data_col=9)")
387 uf.backend = pcs.read
388 uf.menu_text = "&read"
389 uf.gui_icon = "oxygen.actions.document-open"
390 uf.wizard_height_desc = 250
391 uf.wizard_size = (1000, 750)
392 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
393
394
395
396 uf = uf_info.add_uf('pcs.weight')
397 uf.title = "Set optimisation weights on the PCS data."
398 uf.title_short = "PCS weighting."
399 uf.add_keyarg(
400 name = "align_id",
401 py_type = "str",
402 desc_short = "alignment ID string",
403 desc = "The alignment ID string.",
404 wiz_element_type = 'combo',
405 wiz_combo_iter = align_tensor.get_ids,
406 wiz_read_only = True
407 )
408 uf.add_keyarg(
409 name = "spin_id",
410 py_type = "str",
411 desc_short = "spin ID string",
412 desc = "The spin ID string."
413 )
414 uf.add_keyarg(
415 name = "weight",
416 default = 1.0,
417 py_type = "num",
418 desc_short = "weight",
419 desc = "The weighting value."
420 )
421
422 uf.desc.append(Desc_container())
423 uf.desc[-1].add_paragraph("This can be used to force the PCS to contribute more or less to the chi-squared optimisation statistic. The higher the value, the more importance the PCS will have.")
424 uf.backend = pcs.weight
425 uf.menu_text = "wei&ght"
426 uf.wizard_size = (700, 500)
427 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
428
429
430
431 uf = uf_info.add_uf('pcs.write')
432 uf.title = "Write the PCS data to file."
433 uf.title_short = "PCS data writing."
434 uf.add_keyarg(
435 name = "align_id",
436 py_type = "str",
437 desc_short = "alignment ID string",
438 desc = "The alignment ID string.",
439 wiz_element_type = 'combo',
440 wiz_combo_iter = align_tensor.get_ids,
441 wiz_read_only = True
442 )
443 uf.add_keyarg(
444 name = "file",
445 py_type = "str",
446 arg_type = "file sel",
447 desc_short = "file name",
448 desc = "The name of the file.",
449 wiz_filesel_style = FD_SAVE
450 )
451 uf.add_keyarg(
452 name = "dir",
453 py_type = "str",
454 arg_type = "dir",
455 desc_short = "directory name",
456 desc = "The directory name.",
457 can_be_none = True
458 )
459 uf.add_keyarg(
460 name = "bc",
461 default = False,
462 py_type = "bool",
463 desc_short = "back-calculation flag",
464 desc = "A flag which if set will write out the back-calculated rather than measured RDCs."
465 )
466 uf.add_keyarg(
467 name = "force",
468 default = False,
469 py_type = "bool",
470 desc_short = "force flag",
471 desc = "A flag which if True will cause the file to be overwritten."
472 )
473
474 uf.desc.append(Desc_container())
475 uf.desc[-1].add_paragraph("If no directory name is given, the file will be placed in the current working directory. The alignment ID is required for selecting which PCS data set will be written to file.")
476 uf.backend = pcs.write
477 uf.menu_text = "&write"
478 uf.gui_icon = "oxygen.actions.document-save"
479 uf.wizard_size = (800, 600)
480 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
481