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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_analyses.n_state_model.parameters import elim_no_prob, number_of_states, ref_domain, select_model
35 from specific_analyses.setup import n_state_model_obj
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('n_state_model')
42 uf_class.title = "Class for the N-state models."
43 uf_class.menu_text = "&n_state_model"
44 uf_class.gui_icon = "relax.n_state_model"
45
46
47
48 uf = uf_info.add_uf('n_state_model.CoM')
49 uf.title = "The defunct centre of mass (CoM) analysis."
50 uf.title_short = "CoM analysis."
51 uf.add_keyarg(
52 name = "pivot_point",
53 default = [0.0, 0.0, 0.0],
54 py_type = "num_list",
55 dim = 3,
56 desc_short = "pivot point",
57 desc = "The pivot point of the motions between the two domains."
58 )
59 uf.add_keyarg(
60 name = "centre",
61 py_type = "num_list",
62 dim = 3,
63 desc_short = "centre of mass",
64 desc = "Manually specify the CoM of the initial position prior to the N rotations to the positions of the N states. This is optional.",
65 can_be_none = True
66 )
67
68 uf.desc.append(Desc_container())
69 uf.desc[-1].add_paragraph("WARNING: This analysis is now defunct!")
70 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.")
71 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.")
72
73 uf.desc.append(Desc_container("Prompt examples"))
74 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:")
75 uf.desc[-1].add_prompt("relax> n_state_model.CoM()")
76 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:")
77 uf.desc[-1].add_prompt("relax> n_state_model.CoM(centre=[0, 0, 1])")
78 uf.desc[-1].add_prompt("relax> n_state_model.CoM(centre=[0.0, 0.0, 1.0])")
79 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])")
80 uf.backend = n_state_model_obj._CoM
81 uf.menu_text = "Co&M"
82 uf.wizard_height_desc = 350
83 uf.wizard_size = (800, 600)
84 uf.wizard_apply_button = False
85 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
86
87
88
89 uf = uf_info.add_uf('n_state_model.cone_pdb')
90 uf.title = "Create a PDB file representing the cone models from the centre of mass (CoM) analysis."
91 uf.title_short = "Cone PDB creation."
92 uf.add_keyarg(
93 name = "cone_type",
94 py_type = "str",
95 desc_short = "cone type",
96 desc = "The type of cone model to represent.",
97 wiz_element_type = "combo",
98 wiz_combo_choices = [
99 'diff in cone',
100 'diff on cone'
101 ],
102 wiz_read_only = True
103 )
104
105 uf.add_keyarg(
106 name = "scale",
107 default = 1.0,
108 py_type = "num",
109 desc_short = "scaling factor",
110 desc = "Value for scaling the pivot-CoM distance which the size of the cone defaults to."
111 )
112
113 uf.add_keyarg(
114 name = "file",
115 default = "cone.pdb",
116 py_type = "str",
117 arg_type = "file sel",
118 desc_short = "file name",
119 desc = "The name of the PDB file.",
120 wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
121 wiz_filesel_style = FD_SAVE
122 )
123
124 uf.add_keyarg(
125 name = "dir",
126 py_type = "str",
127 arg_type = "dir",
128 desc_short = "directory name",
129 desc = "The directory where the file is located.",
130 can_be_none = True
131 )
132
133 uf.add_keyarg(
134 name = "force",
135 default = False,
136 py_type = "bool",
137 desc_short = "force flag",
138 desc = "A flag which, if set to True, will overwrite the any pre-existing file."
139 )
140
141 uf.desc.append(Desc_container())
142 uf.desc[-1].add_paragraph("WARNING: This analysis is now defunct!")
143 uf.desc[-1].add_paragraph("This creates a PDB file containing an artificial geometric structure to represent the various cone models. These models include:")
144 uf.desc[-1].add_list_element("'diff in cone'")
145 uf.desc[-1].add_list_element("'diff on cone'")
146 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.")
147 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.")
148 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.")
149 uf.backend = n_state_model_obj._cone_pdb
150 uf.menu_text = "&cone_pdb"
151 uf.wizard_height_desc = 480
152 uf.wizard_size = (1000, 750)
153 uf.wizard_apply_button = False
154 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
155
156
157
158 uf = uf_info.add_uf('n_state_model.elim_no_prob')
159 uf.title = "Eliminate the structures or states with no probability."
160 uf.title_short = "Insignificant state elimination."
161
162 uf.desc.append(Desc_container())
163 uf.desc[-1].add_paragraph("This will simply remove the structures from the N-state analysis which have an optimised probability of zero.")
164
165 uf.desc.append(Desc_container("Prompt examples"))
166 uf.desc[-1].add_paragraph("Simply type:")
167 uf.desc[-1].add_prompt("relax> n_state_model.elim_no_prob(N=8)")
168 uf.backend = elim_no_prob
169 uf.menu_text = "&elim_no_prob"
170 uf.gui_icon = "oxygen.actions.list-remove"
171 uf.wizard_size = (700, 400)
172 uf.wizard_apply_button = False
173 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
174
175
176
177 uf = uf_info.add_uf('n_state_model.number_of_states')
178 uf.title = "Set the number of states in the N-state model."
179 uf.title_short = "Number of states."
180 uf.add_keyarg(
181 name = "N",
182 default = 1,
183 py_type = "int",
184 desc_short = "number of states N",
185 desc = "The number of states."
186 )
187
188 uf.desc.append(Desc_container())
189 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.")
190
191 uf.desc.append(Desc_container("Prompt examples"))
192 uf.desc[-1].add_paragraph("To set up an 8-state model, type:")
193 uf.desc[-1].add_prompt("relax> n_state_model.number_of_states(N=8)")
194 uf.backend = number_of_states
195 uf.menu_text = "&number_of_states"
196 uf.gui_icon = "oxygen.actions.edit-rename"
197 uf.wizard_apply_button = False
198 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
199
200
201
202 uf = uf_info.add_uf('n_state_model.ref_domain')
203 uf.title = "Set the reference domain for the '2-domain' N-state model."
204 uf.title_short = "Reference domain identification."
205 uf.add_keyarg(
206 name = "ref",
207 py_type = "str",
208 desc_short = "reference frame",
209 desc = "The domain which will act as the frame of reference. This is only valid for the '2-domain' N-state model."
210 )
211
212 uf.desc.append(Desc_container())
213 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.")
214
215 uf.desc.append(Desc_container("Prompt examples"))
216 uf.desc[-1].add_paragraph("To set up a 5-state model with 'C' domain being the frame of reference, type:")
217 uf.desc[-1].add_prompt("relax> n_state_model.ref_domain(ref='C')")
218 uf.backend = ref_domain
219 uf.menu_text = "&ref_domain"
220 uf.gui_icon = "oxygen.actions.edit-rename"
221 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
222
223
224
225 uf = uf_info.add_uf('n_state_model.select_model')
226 uf.title = "Select the N-state model type and set up the model."
227 uf.title_short = "N-state model choice."
228 uf.add_keyarg(
229 name = "model",
230 default = "population",
231 py_type = "str",
232 desc_short = "model",
233 desc = "The name of the preset N-state model.",
234 wiz_element_type = "combo",
235 wiz_combo_choices = ["population", "fixed", "2-domain"],
236 wiz_read_only = True
237 )
238
239 uf.desc.append(Desc_container())
240 uf.desc[-1].add_paragraph("Prior to optimisation, the N-state model type should be selected. The preset models are:")
241 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, ...}.")
242 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, ...}.")
243 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.")
244
245 uf.desc.append(Desc_container("Prompt examples"))
246 uf.desc[-1].add_paragraph("To analyse populations of states, type:")
247 uf.desc[-1].add_prompt("relax> n_state_model.select_model(model='populations')")
248 uf.backend = select_model
249 uf.menu_text = "&select_model"
250 uf.gui_icon = "oxygen.actions.list-add"
251 uf.wizard_height_desc = 400
252 uf.wizard_size = (800, 600)
253 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
254