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23 """The interatom user function definitions."""
24
25
26 import dep_check
27 from os import sep
28 if dep_check.wx_module:
29 from wx import FD_OPEN
30 else:
31 FD_OPEN = -1
32
33
34 from graphics import WIZARD_IMAGE_PATH
35 from lib.physical_constants import NH_BOND_LENGTH
36 from pipe_control.mol_res_spin import get_spin_ids
37 from pipe_control import pipes, interatomic
38 from user_functions.data import Uf_info; uf_info = Uf_info()
39 from user_functions.objects import Desc_container
40
41
42
43 uf_class = uf_info.add_class('interatom')
44 uf_class.title = "Class for manipulating magnetic dipole-dipole interactions."
45 uf_class.menu_text = "&interatom"
46 uf_class.gui_icon = "relax.dipole_pair"
47
48
49
50 uf = uf_info.add_uf('interatom.copy')
51 uf.title = "Copy all data associated with a interatomic data container."
52 uf.title_short = "Interatomic interaction copying."
53 uf.display = True
54 uf.add_keyarg(
55 name = "pipe_from",
56 py_type = "str",
57 desc_short = "source data pipe",
58 desc = "The data pipe containing the interatomic data container from which the data will be copied. This defaults to the current data pipe.",
59 wiz_element_type = 'combo',
60 wiz_combo_iter = pipes.pipe_names,
61 wiz_read_only = True,
62 can_be_none = True
63 )
64 uf.add_keyarg(
65 name = "pipe_to",
66 py_type = "str",
67 desc_short = "destination data pipe",
68 desc = "The data pipe to copy the interatomic data container to. This defaults to the current data pipe.",
69 wiz_element_type = 'combo',
70 wiz_combo_iter = pipes.pipe_names,
71 wiz_read_only = True,
72 can_be_none = True
73 )
74 uf.add_keyarg(
75 name = "spin_id1",
76 py_type = "str",
77 arg_type = "spin ID",
78 desc_short = "first spin ID",
79 desc = "The spin ID of the first spin.",
80 wiz_combo_iter = get_spin_ids,
81 can_be_none = True
82 )
83 uf.add_keyarg(
84 name = "spin_id2",
85 py_type = "str",
86 arg_type = "spin ID",
87 desc_short = "second spin ID",
88 desc = "The spin ID of the first spin.",
89 wiz_combo_iter = get_spin_ids,
90 can_be_none = True
91 )
92
93 uf.desc.append(Desc_container())
94 uf.desc[-1].add_paragraph("This will copy all the data associated with the identified interatomic data container to a different data pipe. The new interatomic data container must not already exist.")
95
96 uf.desc.append(Desc_container("Prompt examples"))
97 uf.desc[-1].add_paragraph("To copy the interatomic data container between ':2@C' and ':2@H', from the 'orig' data pipe to the current data pipe, type one of:")
98 uf.desc[-1].add_prompt("relax> interatom.copy('orig', spin_id1=':2@C', spin_id2=':2@H')")
99 uf.desc[-1].add_prompt("relax> interatom.copy(pipe_from='orig', spin_id1=':2@C', spin_id2=':2@H')")
100 uf.backend = interatomic.copy
101 uf.menu_text = "©"
102 uf.gui_icon = "oxygen.actions.list-add"
103 uf.wizard_size = (700, 600)
104 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 'NH_dipole_pair.png'
105
106
107
108 uf = uf_info.add_uf('interatom.define')
109 uf.title = "Define interatomic interactions between pairs of spins."
110 uf.title_short = "Interatomic interaction setup."
111 uf.add_keyarg(
112 name = "spin_id1",
113 default = "@N",
114 py_type = "str",
115 arg_type = "spin ID",
116 desc_short = "first spin ID string",
117 desc = "The spin ID string for the first spin of the interatomic interaction.",
118 can_be_none = True
119 )
120 uf.add_keyarg(
121 name = "spin_id2",
122 default = "@H",
123 py_type = "str",
124 arg_type = "spin ID",
125 desc_short = "second spin ID string",
126 desc = "The spin ID string for the second spin of the interatomic interaction.",
127 can_be_none = True
128 )
129 uf.add_keyarg(
130 name = "direct_bond",
131 default = True,
132 py_type = "bool",
133 desc_short = "directly bonded atoms flag",
134 desc = "This is a flag which if True means that the two spins are directly bonded. This flag is useful to simplify the set up of the main heteronuclear relaxation mechanism or one-bond residual dipolar couplings."
135 )
136 uf.add_keyarg(
137 name = "pipe",
138 py_type = "str",
139 desc_short = "alternative data pipe",
140 desc = "The data pipe to create the interatomic data container for. This defaults to the current data pipe if not supplied.",
141 wiz_element_type = 'combo',
142 wiz_combo_iter = pipes.pipe_names,
143 wiz_read_only = True,
144 can_be_none = True
145 )
146
147 uf.desc.append(Desc_container())
148 uf.desc[-1].add_paragraph("To analyse relaxation or residual dipolar coupling (RDC) data, for example, pairs of spins which are coupled need to be defined. This can be via the magnetic dipole-dipole interaction or scalar coupling interaction. This function will create an interatomic data object connecting two existing spins. This data container will be used to store all information about the interactomic interaction including interatomic vectors and distances.")
149 uf.desc[-1].add_paragraph("For analyses which use relaxation data, simply defining the interatomic interaction will indicate that there is a dipolar relaxation mechanism operating between the two spins. Note that for model-free analyses or reduced spectral density mapping, only a single relaxation mechanism can be handled. For RDC dependent analyses, the presence of the interatomic interaction indicates that dipolar coupling is expected between the two spins.")
150
151 uf.desc.append(Desc_container("Prompt examples"))
152 uf.desc[-1].add_paragraph("To connect the spins ':1@N' to ':1@H', type one of:")
153 uf.desc[-1].add_prompt("relax> interatom.define(':1@N', ':1@H')")
154 uf.desc[-1].add_prompt("relax> interatom.define(spin_id1=':1@N', spin_id2=':1@H')")
155 uf.desc[-1].add_paragraph("To define the protein 15N heteronuclear relaxation mechanism for a model-free analysis, type one of the following:")
156 uf.desc[-1].add_prompt("relax> interatom.define('@N', '@H', True)")
157 uf.desc[-1].add_prompt("relax> interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)")
158 uf.backend = interatomic.define
159 uf.menu_text = "&define"
160 uf.gui_icon = "oxygen.actions.list-add-relax-blue"
161 uf.wizard_height_desc = 350
162 uf.wizard_size = (900, 700)
163 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 'NH_dipole_pair.png'
164
165
166
167 uf = uf_info.add_uf('interatom.read_dist')
168 uf.title = "Read inter-spin distances from a file."
169 uf.title_short = "Interatomic distance reading."
170 uf.add_keyarg(
171 name = "file",
172 py_type = "str",
173 arg_type = "file sel",
174 desc_short = "file name",
175 desc = "The name of the file containing the averaged distance data.",
176 wiz_filesel_style = FD_OPEN
177 )
178 uf.add_keyarg(
179 name = "dir",
180 py_type = "str",
181 arg_type = "dir",
182 desc_short = "directory name",
183 desc = "The directory where the file is located.",
184 can_be_none = True
185 )
186 uf.add_keyarg(
187 name = "unit",
188 default = "meter",
189 py_type = "str",
190 desc_short = "distance unit",
191 desc = "The unit of distance. The default is meter, but Angstrom can also be specified.",
192 wiz_element_type = "combo",
193 wiz_combo_choices = ["meter", "Angstrom"],
194 wiz_read_only = True
195 )
196 uf.add_keyarg(
197 name = "spin_id1_col",
198 default = 1,
199 py_type = "int",
200 min = 1,
201 desc_short = "first spin ID column",
202 desc = "The spin ID string column for the first spin."
203 )
204 uf.add_keyarg(
205 name = "spin_id2_col",
206 default = 2,
207 py_type = "int",
208 min = 1,
209 desc_short = "second spin ID column",
210 desc = "The spin ID string column for the second spin."
211 )
212 uf.add_keyarg(
213 name = "data_col",
214 default = 3,
215 py_type = "int",
216 min = 1,
217 desc_short = "data column",
218 desc = "The distance data column."
219 )
220 uf.add_keyarg(
221 name = "sep",
222 py_type = "str",
223 desc_short = "column separator",
224 desc = "The column separator (the default is white space).",
225 wiz_element_type = "combo",
226 wiz_combo_choices = ["white space", ",", ";", ":"],
227 wiz_combo_data = [None, ",", ";", ":"],
228 wiz_read_only = False,
229 can_be_none = True
230 )
231
232 uf.desc.append(Desc_container())
233 uf.desc[-1].add_paragraph("This allows interatomic distances to be read from a file. This is useful in the case when the distances vary, avoiding having to tediously use the interatom.set_dist user function for each spin-pair separately. The format of the file should be columnar, with the two spin ID strings in two separate columns and the distances in any other. The default measurement unit is meter but this can be changed to Angstrom.")
234 uf.desc[-1].add_paragraph("For RDC and relaxation based analyses, as the magnetic dipole-dipole interaction is averaged in NMR over the interatomic distance to the inverse third power, the interatomic distances within a 3D structural file are of no use for defining the interaction. Therefore these r^-3 average distances must be explicitly defined.")
235
236 uf.desc.append(Desc_container("Prompt examples"))
237 uf.desc[-1].add_paragraph("To load the distances in meters from the fifth column of the 'distances' file, and where the spin IDs are in the first and second columns, type one of the following:")
238 uf.desc[-1].add_prompt("relax> interatom.read_dist('distances', 1, 2, 5)")
239 uf.desc[-1].add_prompt("relax> interatom.read_dist(file='distances', unit='meter', spin_id1_col=1, spin_id2_col=2, data_col=5)")
240 uf.backend = interatomic.read_dist
241 uf.menu_text = "&read_dist"
242 uf.gui_icon = "oxygen.actions.document-open"
243 uf.wizard_height_desc = 350
244 uf.wizard_size = (900, 700)
245 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 'NH_dipole_pair.png'
246
247
248
249 uf = uf_info.add_uf('interatom.set_dist')
250 uf.title = "Set the inter-spin distances."
251 uf.title_short = "Interatomic distance setup."
252 uf.add_keyarg(
253 name = "spin_id1",
254 default = "@N",
255 py_type = "str",
256 arg_type = "spin ID",
257 desc_short = "first spin ID string",
258 desc = "The spin identification string for the first spin of the dipole pair."
259 )
260 uf.add_keyarg(
261 name = "spin_id2",
262 default = "@H",
263 py_type = "str",
264 arg_type = "spin ID",
265 desc_short = "second spin ID string",
266 desc = "The spin identification string for the second spin of the dipole pair."
267 )
268 uf.add_keyarg(
269 name = "ave_dist",
270 default = NH_BOND_LENGTH,
271 py_type = "float",
272 desc_short = "averaged interatomic distance",
273 desc = "The r^-3 averaged distance between the two spins to be used in the magnetic dipole constant, defaulting to meters."
274 )
275 uf.add_keyarg(
276 name = "unit",
277 default = "meter",
278 py_type = "str",
279 desc_short = "distance unit",
280 desc = "The unit of distance (the default is 'meter').",
281 wiz_element_type = "combo",
282 wiz_combo_choices = ["meter", "Angstrom"],
283 wiz_read_only = True
284 )
285
286 uf.desc.append(Desc_container())
287 uf.desc[-1].add_paragraph("For many NMR interactions, the distance between the spin of interest and another spin or atom must be defined. This information can be extracted from a 3D structure but, in many cases, these distances are not of interest. For example the empirical or fixed distance calculation of proton positions in X-ray crystallographic structures will often not correspond to the real interatomic distances.")
288 uf.desc[-1].add_paragraph("Another example is the magnetic dipole-dipole interaction which is averaged over the interatomic distance to the inverse third power. In this case, the interatomic distances from any 3D structural file can be of no use for defining the interaction. The average distances must be explicitly supplied. This user function allows these distances to be set up. The default measurement unit is meter but this can be changed to Angstrom. Alternatively the distances can be read from a file using other user functions in this class.")
289
290 uf.desc.append(Desc_container("Prompt examples"))
291 uf.desc[-1].add_paragraph("To set the N-H distance for protein the 15N heteronuclear relaxation mechanism to 1.02 Angstrom, type one of the following:")
292 uf.desc[-1].add_prompt("relax> interatom.set_dist('@N', '@H', 1.02 * 1e-10)")
293 uf.desc[-1].add_prompt("relax> interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10, unit='meter')")
294 uf.desc[-1].add_prompt("relax> interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02, unit='Angstrom')")
295 uf.backend = interatomic.set_dist
296 uf.menu_text = "&set_dist"
297 uf.gui_icon = "oxygen.actions.edit-rename"
298 uf.wizard_height_desc = 350
299 uf.wizard_size = (900, 700)
300 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 'NH_dipole_pair.png'
301
302
303
304 uf = uf_info.add_uf('interatom.unit_vectors')
305 uf.title = "Calculate the unit vectors for all interatomic interactions."
306 uf.title_short = "Interatomic unit vector calculation."
307 uf.add_keyarg(
308 name = "ave",
309 default = True,
310 py_type = "bool",
311 desc_short = "average vector flag",
312 desc = "A flag which if True will cause the bond vectors from all models to be averaged. If vectors from only one model is extracted, this will have no effect."
313 )
314
315 uf.desc.append(Desc_container())
316 uf.desc[-1].add_paragraph("For an orientational dependent analysis, such as model-free analysis with the spheroidal and ellipsoidal global diffusion tensors or any analysis using RDCs, the unit vectors between the two dipoles must be calculated prior to starting the analysis. For the unit vector extraction, the two interacting spins should already possess positional information and the dipole-dipole interaction should already be defined via the interatom.define user function. This information will be used to calculate unit vectors between the two spins. Without positional information from a 3D structure, no vectors can be calculated and an orientational dependent analysis will not be possible.")
317 uf.desc[-1].add_paragraph("The number of unit vectors per interaction will be defined by the number of positions each spin possesses together with the averaging flag. If both spins have N and M positions loaded, the number of positions for both must match (N=M). In this case, as well as when one spin has N positions and the other a single position, then N unit vectors will be calculated. This is unless the averaging flag is set in which case an averaged vector of unit length will be calculated.")
318
319 uf.desc.append(Desc_container("Prompt examples"))
320 uf.desc[-1].add_paragraph("To calculate the unit vectors prior to a model-free analysis, type one of the following:")
321 uf.desc[-1].add_prompt("relax> interatom.unit_vectors(True)")
322 uf.desc[-1].add_prompt("relax> interatom.unit_vectors(ave=True)")
323 uf.backend = interatomic.unit_vectors
324 uf.menu_text = "&unit_vectors"
325 uf.wizard_height_desc = 400
326 uf.wizard_size = (900, 600)
327 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 'NH_dipole_pair.png'
328