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23 """The n_state_model user function definitions."""
24
25
26 import dep_check
27 if dep_check.wx_module:
28 from wx import FD_SAVE
29 else:
30 FD_SAVE = -1
31
32
33 from graphics import WIZARD_IMAGE_PATH
34 from specific_fns.setup import n_state_model_obj
35 from user_functions.data import Uf_info; uf_info = Uf_info()
36 from user_functions.objects import Desc_container
37
38
39
40 uf_class = uf_info.add_class('n_state_model')
41 uf_class.title = "Class for the N-state models."
42 uf_class.menu_text = "&n_state_model"
43 uf_class.gui_icon = "relax.n_state_model"
44
45
46
47 uf = uf_info.add_uf('n_state_model.CoM')
48 uf.title = "The defunct centre of mass (CoM) analysis."
49 uf.title_short = "CoM analysis."
50 uf.add_keyarg(
51 name = "pivot_point",
52 default = [0.0, 0.0, 0.0],
53 py_type = "num_list",
54 dim = 3,
55 desc_short = "pivot point",
56 desc = "The pivot point of the motions between the two domains."
57 )
58 uf.add_keyarg(
59 name = "centre",
60 py_type = "num_list",
61 dim = 3,
62 desc_short = "centre of mass",
63 desc = "Manually specify the CoM of the initial position prior to the N rotations to the positions of the N states. This is optional.",
64 can_be_none = True
65 )
66
67 uf.desc.append(Desc_container())
68 uf.desc[-1].add_paragraph("WARNING: This analysis is now defunct!")
69 uf.desc[-1].add_paragraph("This is used for analysing the domain motion information content of the N states from the N-state model. The states do not correspond to physical states, hence nothing can be extracted from the individual states. This analysis involves the calculation of the pivot to centre of mass (pivot-CoM) order parameter and subsequent cone of motions.")
70 uf.desc[-1].add_paragraph("For the analysis, both the pivot point and centre of mass must be specified. The supplied pivot point must be a vector of floating point numbers of length 3. If the centre of mass is supplied, it must also be a vector of floating point numbers (of length 3). If the centre of mass is not supplied, then the CoM will be calculated from the selected parts of a previously loaded structure.")
71
72 uf.desc.append(Desc_container("Prompt examples"))
73 uf.desc[-1].add_paragraph("To perform an analysis where the pivot is at the origin and the CoM is set to the N-terminal domain of a previously loaded PDB file (the C-terminal domain has been deselected), type:")
74 uf.desc[-1].add_prompt("relax> n_state_model.CoM()")
75 uf.desc[-1].add_paragraph("To perform an analysis where the pivot is at the origin (because the real pivot has been shifted to this position) and the CoM is at the position [0, 0, 1], type one of:")
76 uf.desc[-1].add_prompt("relax> n_state_model.CoM(centre=[0, 0, 1])")
77 uf.desc[-1].add_prompt("relax> n_state_model.CoM(centre=[0.0, 0.0, 1.0])")
78 uf.desc[-1].add_prompt("relax> n_state_model.CoM(pivot_point=[0.0, 0.0, 0.0], centre=[0.0, 0.0, 1.0])")
79 uf.backend = n_state_model_obj._CoM
80 uf.menu_text = "Co&M"
81 uf.wizard_height_desc = 350
82 uf.wizard_size = (800, 600)
83 uf.wizard_apply_button = False
84 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
85
86
87
88 uf = uf_info.add_uf('n_state_model.cone_pdb')
89 uf.title = "Create a PDB file representing the cone models from the centre of mass (CoM) analysis."
90 uf.title_short = "Cone PDB creation."
91 uf.add_keyarg(
92 name = "cone_type",
93 py_type = "str",
94 desc_short = "cone type",
95 desc = "The type of cone model to represent.",
96 wiz_element_type = "combo",
97 wiz_combo_choices = [
98 'diff in cone',
99 'diff on cone'
100 ],
101 wiz_read_only = True
102 )
103
104 uf.add_keyarg(
105 name = "scale",
106 default = 1.0,
107 py_type = "num",
108 desc_short = "scaling factor",
109 desc = "Value for scaling the pivot-CoM distance which the size of the cone defaults to."
110 )
111
112 uf.add_keyarg(
113 name = "file",
114 default = "cone.pdb",
115 py_type = "str",
116 arg_type = "file sel",
117 desc_short = "file name",
118 desc = "The name of the PDB file.",
119 wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
120 wiz_filesel_style = FD_SAVE
121 )
122
123 uf.add_keyarg(
124 name = "dir",
125 py_type = "str",
126 arg_type = "dir",
127 desc_short = "directory name",
128 desc = "The directory where the file is located.",
129 can_be_none = True
130 )
131
132 uf.add_keyarg(
133 name = "force",
134 default = False,
135 py_type = "bool",
136 desc_short = "force flag",
137 desc = "A flag which, if set to True, will overwrite the any pre-existing file."
138 )
139
140 uf.desc.append(Desc_container())
141 uf.desc[-1].add_paragraph("WARNING: This analysis is now defunct!")
142 uf.desc[-1].add_paragraph("This creates a PDB file containing an artificial geometric structure to represent the various cone models. These models include:")
143 uf.desc[-1].add_list_element("'diff in cone'")
144 uf.desc[-1].add_list_element("'diff on cone'")
145 uf.desc[-1].add_paragraph("The model can be selected by setting the cone type to one of these values. The cone is represented as an isotropic cone with its axis parallel to the average pivot-CoM vector, the vertex placed at the pivot point of the domain motions, and the length of the edge of the cone equal to the pivot-CoM distance multiplied by the scaling factor. The resultant PDB file can subsequently read into any molecular viewer.")
146 uf.desc[-1].add_paragraph("There are four different types of residue within the PDB. The pivot point is represented as as a single carbon atom of the residue 'PIV'. The cone consists of numerous H atoms of the residue 'CON'. The average pivot-CoM vector is presented as the residue 'AVE' with one carbon atom positioned at the pivot and the other at the head of the vector (after scaling by the scaling factor). Finally, if Monte Carlo have been performed, there will be multiple 'MCC' residues representing the cone for each simulation, and multiple 'MCA' residues representing the varying average pivot-CoM vector for each simulation.")
147 uf.desc[-1].add_paragraph("To create the diffusion in a cone PDB representation, a uniform distribution of vectors on a sphere is generated using spherical coordinates with the polar angle defined from the average pivot-CoM vector. By incrementing the polar angle using an arccos distribution, a radial array of vectors representing latitude are created while incrementing the azimuthal angle evenly creates the longitudinal vectors. These are all placed into the PDB file as H atoms and are all connected using PDB CONECT records. Each H atom is connected to its two neighbours on the both the longitude and latitude. This creates a geometric PDB object with longitudinal and latitudinal lines representing the filled cone.")
148 uf.backend = n_state_model_obj._cone_pdb
149 uf.menu_text = "&cone_pdb"
150 uf.wizard_height_desc = 480
151 uf.wizard_size = (1000, 750)
152 uf.wizard_apply_button = False
153 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
154
155
156
157 uf = uf_info.add_uf('n_state_model.elim_no_prob')
158 uf.title = "Eliminate the structures or states with no probability."
159 uf.title_short = "Insignificant state elimination."
160
161 uf.desc.append(Desc_container())
162 uf.desc[-1].add_paragraph("This will simply remove the structures from the N-state analysis which have an optimised probability of zero.")
163
164 uf.desc.append(Desc_container("Prompt examples"))
165 uf.desc[-1].add_paragraph("Simply type:")
166 uf.desc[-1].add_prompt("relax> n_state_model.elim_no_prob(N=8)")
167 uf.backend = n_state_model_obj._elim_no_prob
168 uf.menu_text = "&elim_no_prob"
169 uf.gui_icon = "oxygen.actions.list-remove"
170 uf.wizard_size = (700, 400)
171 uf.wizard_apply_button = False
172 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
173
174
175
176 uf = uf_info.add_uf('n_state_model.number_of_states')
177 uf.title = "Set the number of states in the N-state model."
178 uf.title_short = "Number of states."
179 uf.add_keyarg(
180 name = "N",
181 default = 1,
182 py_type = "int",
183 desc_short = "number of states N",
184 desc = "The number of states."
185 )
186
187 uf.desc.append(Desc_container())
188 uf.desc[-1].add_paragraph("Prior to optimisation, the number of states in the N-state model can be specified. If the number of states is not set, then this parameter will be equal to the number of loaded structures - the ensemble size.")
189
190 uf.desc.append(Desc_container("Prompt examples"))
191 uf.desc[-1].add_paragraph("To set up an 8-state model, type:")
192 uf.desc[-1].add_prompt("relax> n_state_model.number_of_states(N=8)")
193 uf.backend = n_state_model_obj._number_of_states
194 uf.menu_text = "&number_of_states"
195 uf.gui_icon = "oxygen.actions.edit-rename"
196 uf.wizard_apply_button = False
197 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
198
199
200
201 uf = uf_info.add_uf('n_state_model.ref_domain')
202 uf.title = "Set the reference domain for the '2-domain' N-state model."
203 uf.title_short = "Reference domain identification."
204 uf.add_keyarg(
205 name = "ref",
206 py_type = "str",
207 desc_short = "reference frame",
208 desc = "The domain which will act as the frame of reference. This is only valid for the '2-domain' N-state model."
209 )
210
211 uf.desc.append(Desc_container())
212 uf.desc[-1].add_paragraph("Prior to optimisation of the '2-domain' N-state model, which of the two domains will act as the frame of reference must be specified. The N-states will be rotations of the other domain, so to switch the frame of reference to the other domain simply transpose the rotation matrices.")
213
214 uf.desc.append(Desc_container("Prompt examples"))
215 uf.desc[-1].add_paragraph("To set up a 5-state model with 'C' domain being the frame of reference, type:")
216 uf.desc[-1].add_prompt("relax> n_state_model.ref_domain(ref='C')")
217 uf.backend = n_state_model_obj._ref_domain
218 uf.menu_text = "&ref_domain"
219 uf.gui_icon = "oxygen.actions.edit-rename"
220 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
221
222
223
224 uf = uf_info.add_uf('n_state_model.select_model')
225 uf.title = "Select the N-state model type and set up the model."
226 uf.title_short = "N-state model choice."
227 uf.add_keyarg(
228 name = "model",
229 default = "population",
230 py_type = "str",
231 desc_short = "model",
232 desc = "The name of the preset N-state model.",
233 wiz_element_type = "combo",
234 wiz_combo_choices = ["population", "fixed", "2-domain"],
235 wiz_read_only = True
236 )
237
238 uf.desc.append(Desc_container())
239 uf.desc[-1].add_paragraph("Prior to optimisation, the N-state model type should be selected. The preset models are:")
240 uf.desc[-1].add_item_list_element("'population'", "The N-state model whereby only populations are optimised. The structures loaded into relax are assumed to be fixed, i.e. the orientations are not optimised, or if two domains are present the Euler angles for each state are fixed. The parameters of the model include the weight or probability for each state and the alignment tensors - {p0, p1, ..., pN, Axx, Ayy, Axy, Axz, Ayz, ...}.")
241 uf.desc[-1].add_item_list_element("'fixed'", "The N-state model whereby all motions are fixed and all populations are fixed to the set probabilities. The parameters of the model are simply the parameters of each alignment tensor {Axx, Ayy, Axy, Axz, Ayz, ...}.")
242 uf.desc[-1].add_item_list_element("'2-domain'", "The N-state model for a system of two domains, where one domain experiences a reduced tensor.")
243
244 uf.desc.append(Desc_container("Prompt examples"))
245 uf.desc[-1].add_paragraph("To analyse populations of states, type:")
246 uf.desc[-1].add_prompt("relax> n_state_model.select_model(model='populations')")
247 uf.backend = n_state_model_obj._select_model
248 uf.menu_text = "&select_model"
249 uf.gui_icon = "oxygen.actions.list-add"
250 uf.wizard_height_desc = 400
251 uf.wizard_size = (800, 600)
252 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
253