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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 generic_fns.mol_res_spin import get_spin_ids
36 from graphics import WIZARD_IMAGE_PATH
37 from user_functions.data import Uf_info; uf_info = Uf_info()
38 from user_functions.objects import Desc_container
39
40
41
42 uf_class = uf_info.add_class('pcs')
43 uf_class.title = "Class for handling pseudo-contact shifts."
44 uf_class.menu_text = "&pcs"
45 uf_class.gui_icon = "relax.align_tensor"
46
47
48
49 uf = uf_info.add_uf('pcs.back_calc')
50 uf.title = "Back calculate the pseudo-contact shifts."
51 uf.title_short = "PCS back calculation."
52 uf.display = True
53 uf.add_keyarg(
54 name = "align_id",
55 py_type = "str",
56 desc_short = "alignment ID string",
57 desc = "The alignment ID string.",
58 wiz_element_type = 'combo',
59 wiz_combo_iter = align_tensor.get_ids,
60 wiz_read_only = True,
61 can_be_none = True
62 )
63
64 uf.desc.append(Desc_container())
65 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.")
66 uf.backend = pcs.back_calc
67 uf.menu_text = "&back_calc"
68 uf.gui_icon = "oxygen.categories.applications-education"
69 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
70 uf.wizard_apply_button = False
71
72
73
74 uf = uf_info.add_uf('pcs.calc_q_factors')
75 uf.title = "Calculate the PCS Q factor for the selected spins."
76 uf.title_short = "PCS Q factor calculation."
77 uf.display = True
78 uf.add_keyarg(
79 name = "spin_id",
80 py_type = "str",
81 desc_short = "spin ID string",
82 desc = "The spin ID string for restricting to subset of all selected spins.",
83 can_be_none = True
84 )
85
86 uf.desc.append(Desc_container())
87 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.")
88
89 uf.desc.append(Desc_container("Prompt examples"))
90 uf.desc[-1].add_paragraph("To calculate the PCS Q factor for only the spins '@H26', '@H27', and '@H28', type one of:")
91 uf.desc[-1].add_prompt("relax> pcs.calc_q_factors('@H26 & @H27 & @H28')")
92 uf.desc[-1].add_prompt("relax> pcs.calc_q_factors(spin_id='@H26 & @H27 & @H28')")
93 uf.backend = pcs.q_factors
94 uf.menu_text = "&calc_q_factors"
95 uf.gui_icon = "oxygen.categories.applications-education"
96 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
97 uf.wizard_apply_button = False
98
99
100
101 uf = uf_info.add_uf('pcs.copy')
102 uf.title = "Copy PCS data from one data pipe to another."
103 uf.title_short = "PCS copying."
104 uf.add_keyarg(
105 name = "pipe_from",
106 py_type = "str",
107 desc_short = "source pipe",
108 desc = "The name of the pipe to copy the PCS data from.",
109 wiz_element_type = 'combo',
110 wiz_combo_iter = pipes.pipe_names,
111 can_be_none = True
112 )
113 uf.add_keyarg(
114 name = "pipe_to",
115 py_type = "str",
116 desc_short = "destination pipe",
117 desc = "The name of the pipe to copy the PCS data to.",
118 wiz_element_type = 'combo',
119 wiz_combo_iter = pipes.pipe_names,
120 can_be_none = True
121 )
122 uf.add_keyarg(
123 name = "align_id",
124 py_type = "str",
125 desc_short = "alignment ID string",
126 desc = "The alignment ID string.",
127 wiz_element_type = 'combo',
128 wiz_combo_iter = align_tensor.get_ids,
129 wiz_read_only = True,
130 can_be_none = True
131 )
132
133 uf.desc.append(Desc_container())
134 uf.desc[-1].add_paragraph("This function will copy PCS data from 'pipe_from' to 'pipe_to'. If align_id is not given then all PCS data will be copied, otherwise only a specific data set will be.")
135
136 uf.desc.append(Desc_container("Prompt examples"))
137 uf.desc[-1].add_paragraph("To copy all PCS data from pipe 'm1' to pipe 'm9', type one of:")
138 uf.desc[-1].add_prompt("relax> pcs.copy('m1', 'm9')")
139 uf.desc[-1].add_prompt("relax> pcs.copy(pipe_from='m1', pipe_to='m9')")
140 uf.desc[-1].add_prompt("relax> pcs.copy('m1', 'm9', None)")
141 uf.desc[-1].add_prompt("relax> pcs.copy(pipe_from='m1', pipe_to='m9', align_id=None)")
142 uf.desc[-1].add_paragraph("To copy only the 'Th' PCS data from 'm3' to 'm6', type one of:")
143 uf.desc[-1].add_prompt("relax> pcs.copy('m3', 'm6', 'Th')")
144 uf.desc[-1].add_prompt("relax> pcs.copy(pipe_from='m3', pipe_to='m6', align_id='Th')")
145 uf.backend = pcs.copy
146 uf.menu_text = "cop&y"
147 uf.gui_icon = "oxygen.actions.list-add"
148 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
149
150
151
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.set_errors')
397 uf.title = "Set the errors for the PCSs."
398 uf.title_short = "PCS error setting."
399 uf.add_keyarg(
400 name = "align_id",
401 py_type = "str",
402 desc_short = "alignment ID string",
403 desc = "The optional alignment ID string.",
404 wiz_element_type = 'combo',
405 wiz_combo_iter = align_tensor.get_ids,
406 wiz_read_only = True,
407 can_be_none = True
408 )
409 uf.add_keyarg(
410 name = "spin_id",
411 py_type = "str",
412 arg_type = "spin ID",
413 desc_short = "spin ID string",
414 desc = "The optional spin ID string.",
415 wiz_combo_iter = get_spin_ids,
416 can_be_none = True
417 )
418 uf.add_keyarg(
419 name = "sd",
420 default = 0.1,
421 py_type = "num",
422 desc_short = "PCS error (ppm)",
423 desc = "The PCS standard deviation value in ppm."
424 )
425
426 uf.desc.append(Desc_container())
427 uf.desc[-1].add_paragraph("If the PCS errors have not already been read from a PCS data file or if they need to be changed, then the errors can be set via this user function.")
428 uf.backend = pcs.set_errors
429 uf.menu_text = "&set_errors"
430 uf.gui_icon = "oxygen.actions.edit-rename"
431 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
432
433
434
435 uf = uf_info.add_uf('pcs.structural_noise')
436 uf.title = "Determine the PCS error due to structural noise via simulation."
437 uf.title_short = "PCS structural noise simulation."
438 uf.display = True
439 uf.add_keyarg(
440 name = "align_id",
441 py_type = "str",
442 desc_short = "alignment ID string",
443 desc = "The optional alignment ID string.",
444 wiz_element_type = 'combo',
445 wiz_combo_iter = align_tensor.get_ids,
446 wiz_read_only = True,
447 can_be_none = True
448 )
449 uf.add_keyarg(
450 name = "rmsd",
451 default = 0.2,
452 py_type = "float",
453 desc_short = "structural RMSD",
454 desc = "The atomic position RMSD, in Angstrom, to randomise the spin positions with for the simulations."
455 )
456 uf.add_keyarg(
457 name = "sim_num",
458 default = 1000,
459 min = 3,
460 max = 10000000,
461 py_type = "int",
462 desc_short = "simulation number N",
463 desc = "The number of simulations, N, to perform to determine the structural noise component of the PCS errors."
464 )
465 uf.add_keyarg(
466 name = "file",
467 py_type = "str",
468 arg_type = "file sel",
469 desc_short = "Grace file name",
470 desc = "The optional name of the Grace file to plot the structural errors verses the paramagnetic centre to spin distances.",
471 wiz_filesel_wildcard = "Grace files (*.agr)|*.agr;*.AGR",
472 wiz_filesel_style = FD_SAVE,
473 can_be_none = True
474 )
475 uf.add_keyarg(
476 name = "dir",
477 py_type = "str",
478 arg_type = "dir",
479 desc_short = "directory name",
480 desc = "The directory name to place the Grace file into.",
481 can_be_none = True
482 )
483 uf.add_keyarg(
484 name = "force",
485 default = False,
486 py_type = "bool",
487 desc_short = "force flag",
488 desc = "A flag which if True will cause the file to be overwritten."
489 )
490
491 uf.desc.append(Desc_container())
492 uf.desc[-1].add_paragraph("The analysis of the pseudo-contact shift is influenced by two significant sources of noise - that of the NMR experiment and structural noise from the 3D molecular structure used. The closer the spin to the paramagnetic centre, the greater the influence of structural noise. This distance dependence is governed by the equation:")
493 uf.desc[-1].add_verbatim("""
494 sqrt(3) * abs(delta) * RMSD
495 sigma_dist = --------------------------- ,
496 r
497 """)
498 uf.desc[-1].add_paragraph("where sigma_dist is the distance component of the structural noise as a standard deviation, delta is the PCS value, RMSD is the atomic position root-mean-square deviation, and r is the paramagnetic centre to spin distance. When close to the paramagnetic centre, this error source can exceed that of the NMR experiment. The equation for the angular component of the structural noise is more complicated. The PCS error is influenced by distance, angle in the alignment frame, and the magnetic susceptibility tensor.")
499 uf.desc[-1].add_paragraph("For the simulation the following must already be set up in the current data pipe:")
500 uf.desc[-1].add_list_element("The position of the paramagnetic centre.")
501 uf.desc[-1].add_list_element("The alignment and magnetic susceptibility tensor.")
502 uf.desc[-1].add_paragraph("The protocol for the simulation is as follows:")
503 uf.desc[-1].add_list_element("The lanthanide or paramagnetic centre position will be fixed. Its motion is assumed to be on the femto- to pico- and nanosecond timescales. Hence the motion is averaged over the evolution of the PCS and can be ignored.")
504 uf.desc[-1].add_list_element("The positions of the nuclear spins will be randomised N times. For each simulation a random unit vector will be generated. Then a random distance along the unit vector will be generated by sampling from a Gaussian distribution centered at zero, the original spin position, with a standard deviation set to the given RMSD. Both positive and negative displacements will be used.")
505 uf.desc[-1].add_list_element("The PCS for the randomised position will be back calculated.")
506 uf.desc[-1].add_list_element("The PCS standard deviation will be calculated from the N randomised PCS values.")
507 uf.desc[-1].add_paragraph("The standard deviation will both be stored in the spin container data structure in the relax data store as well as being added to the already present PCS error (using variance addition). This will then be used in any optimisations involving the PCS.")
508 uf.desc[-1].add_paragraph("If the alignment ID string is not supplied, the procedure will be applied to the PCS data from all alignments.")
509 uf.backend = pcs.structural_noise
510 uf.menu_text = "&structural_noise"
511 uf.wizard_size = (1000, 700)
512 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
513 uf.wizard_apply_button = False
514
515
516
517 uf = uf_info.add_uf('pcs.weight')
518 uf.title = "Set optimisation weights on the PCS data."
519 uf.title_short = "PCS weighting."
520 uf.add_keyarg(
521 name = "align_id",
522 py_type = "str",
523 desc_short = "alignment ID string",
524 desc = "The alignment ID string.",
525 wiz_element_type = 'combo',
526 wiz_combo_iter = align_tensor.get_ids,
527 wiz_read_only = True
528 )
529 uf.add_keyarg(
530 name = "spin_id",
531 py_type = "str",
532 desc_short = "spin ID string",
533 desc = "The spin ID string."
534 )
535 uf.add_keyarg(
536 name = "weight",
537 default = 1.0,
538 py_type = "num",
539 desc_short = "weight",
540 desc = "The weighting value."
541 )
542
543 uf.desc.append(Desc_container())
544 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.")
545 uf.backend = pcs.weight
546 uf.menu_text = "wei&ght"
547 uf.wizard_size = (700, 500)
548 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
549
550
551
552 uf = uf_info.add_uf('pcs.write')
553 uf.title = "Write the PCS data to file."
554 uf.title_short = "PCS data writing."
555 uf.add_keyarg(
556 name = "align_id",
557 py_type = "str",
558 desc_short = "alignment ID string",
559 desc = "The alignment ID string.",
560 wiz_element_type = 'combo',
561 wiz_combo_iter = align_tensor.get_ids,
562 wiz_read_only = True
563 )
564 uf.add_keyarg(
565 name = "file",
566 py_type = "str",
567 arg_type = "file sel",
568 desc_short = "file name",
569 desc = "The name of the file.",
570 wiz_filesel_style = FD_SAVE
571 )
572 uf.add_keyarg(
573 name = "dir",
574 py_type = "str",
575 arg_type = "dir",
576 desc_short = "directory name",
577 desc = "The directory name.",
578 can_be_none = True
579 )
580 uf.add_keyarg(
581 name = "bc",
582 default = False,
583 py_type = "bool",
584 desc_short = "back-calculation flag",
585 desc = "A flag which if set will write out the back-calculated rather than measured RDCs."
586 )
587 uf.add_keyarg(
588 name = "force",
589 default = False,
590 py_type = "bool",
591 desc_short = "force flag",
592 desc = "A flag which if True will cause the file to be overwritten."
593 )
594
595 uf.desc.append(Desc_container())
596 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.")
597 uf.backend = pcs.write
598 uf.menu_text = "&write"
599 uf.gui_icon = "oxygen.actions.document-save"
600 uf.wizard_size = (800, 600)
601 uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
602