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24 """The n_state_model user function definitions."""
25
26
27 import wx
28
29
30 from graphics import WIZARD_IMAGE_PATH
31 from specific_fns.setup import n_state_model_obj
32 from user_functions.data import Uf_info; uf_info = Uf_info()
33 from user_functions.objects import Desc_container
34
35
36
37 uf_class = uf_info.add_class('n_state_model')
38 uf_class.title = "Class for the N-state models."
39 uf_class.menu_text = "&n_state_model"
40 uf_class.gui_icon = "relax.n_state_model"
41
42
43
44 uf = uf_info.add_uf('n_state_model.CoM')
45 uf.title = "The defunct centre of mass (CoM) analysis."
46 uf.title_short = "CoM analysis."
47 uf.add_keyarg(
48 name = "pivot_point",
49 default = [0.0, 0.0, 0.0],
50 py_type = "num_list",
51 dim = 3,
52 desc_short = "pivot point",
53 desc = "The pivot point of the motions between the two domains."
54 )
55 uf.add_keyarg(
56 name = "centre",
57 py_type = "num_list",
58 dim = 3,
59 desc_short = "centre of mass",
60 desc = "Manually specify the CoM of the initial position prior to the N rotations to the positions of the N states. This is optional.",
61 can_be_none = True
62 )
63
64 uf.desc.append(Desc_container())
65 uf.desc[-1].add_paragraph("WARNING: This analysis is now defunct!")
66 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.")
67 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.")
68
69 uf.desc.append(Desc_container("Prompt examples"))
70 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:")
71 uf.desc[-1].add_prompt("relax> n_state_model.CoM()")
72 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:")
73 uf.desc[-1].add_prompt("relax> n_state_model.CoM(centre=[0, 0, 1])")
74 uf.desc[-1].add_prompt("relax> n_state_model.CoM(centre=[0.0, 0.0, 1.0])")
75 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])")
76 uf.backend = n_state_model_obj._CoM
77 uf.menu_text = "Co&M"
78 uf.wizard_height_desc = 350
79 uf.wizard_size = (800, 600)
80 uf.wizard_apply_button = False
81 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
82
83
84
85 uf = uf_info.add_uf('n_state_model.cone_pdb')
86 uf.title = "Create a PDB file representing the cone models from the centre of mass (CoM) analysis."
87 uf.title_short = "Cone PDB creation."
88 uf.add_keyarg(
89 name = "cone_type",
90 py_type = "str",
91 desc_short = "cone type",
92 desc = "The type of cone model to represent.",
93 wiz_element_type = "combo",
94 wiz_combo_choices = [
95 'diff in cone',
96 'diff on cone'
97 ],
98 wiz_read_only = True
99 )
100
101 uf.add_keyarg(
102 name = "scale",
103 default = 1.0,
104 py_type = "num",
105 desc_short = "scaling factor",
106 desc = "Value for scaling the pivot-CoM distance which the size of the cone defaults to."
107 )
108
109 uf.add_keyarg(
110 name = "file",
111 default = "cone.pdb",
112 py_type = "str",
113 arg_type = "file sel",
114 desc_short = "file name",
115 desc = "The name of the PDB file.",
116 wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
117 wiz_filesel_style = wx.FD_SAVE
118 )
119
120 uf.add_keyarg(
121 name = "dir",
122 py_type = "str",
123 arg_type = "dir",
124 desc_short = "directory name",
125 desc = "The directory where the file is located.",
126 can_be_none = True
127 )
128
129 uf.add_keyarg(
130 name = "force",
131 default = False,
132 py_type = "bool",
133 desc_short = "force flag",
134 desc = "A flag which, if set to True, will overwrite the any pre-existing file."
135 )
136
137 uf.desc.append(Desc_container())
138 uf.desc[-1].add_paragraph("WARNING: This analysis is now defunct!")
139 uf.desc[-1].add_paragraph("This creates a PDB file containing an artificial geometric structure to represent the various cone models. These models include:")
140 uf.desc[-1].add_list_element("'diff in cone'")
141 uf.desc[-1].add_list_element("'diff on cone'")
142 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.")
143 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.")
144 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.")
145 uf.backend = n_state_model_obj._cone_pdb
146 uf.menu_text = "&cone_pdb"
147 uf.wizard_height_desc = 480
148 uf.wizard_size = (1000, 750)
149 uf.wizard_apply_button = False
150 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
151
152
153
154 uf = uf_info.add_uf('n_state_model.elim_no_prob')
155 uf.title = "Eliminate the structures or states with no probability."
156 uf.title_short = "Insignificant state elimination."
157
158 uf.desc.append(Desc_container())
159 uf.desc[-1].add_paragraph("This will simply remove the structures from the N-state analysis which have an optimised probability of zero.")
160
161 uf.desc.append(Desc_container("Prompt examples"))
162 uf.desc[-1].add_paragraph("Simply type:")
163 uf.desc[-1].add_prompt("relax> n_state_model.elim_no_prob(N=8)")
164 uf.backend = n_state_model_obj._elim_no_prob
165 uf.menu_text = "&elim_no_prob"
166 uf.gui_icon = "oxygen.actions.list-remove"
167 uf.wizard_size = (700, 400)
168 uf.wizard_apply_button = False
169 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
170
171
172
173 uf = uf_info.add_uf('n_state_model.number_of_states')
174 uf.title = "Set the number of states in the N-state model."
175 uf.title_short = "Number of states."
176 uf.add_keyarg(
177 name = "N",
178 default = 1,
179 py_type = "int",
180 desc_short = "number of states N",
181 desc = "The number of states."
182 )
183
184 uf.desc.append(Desc_container())
185 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.")
186
187 uf.desc.append(Desc_container("Prompt examples"))
188 uf.desc[-1].add_paragraph("To set up an 8-state model, type:")
189 uf.desc[-1].add_prompt("relax> n_state_model.number_of_states(N=8)")
190 uf.backend = n_state_model_obj._number_of_states
191 uf.menu_text = "&number_of_states"
192 uf.gui_icon = "oxygen.actions.edit-rename"
193 uf.wizard_apply_button = False
194 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
195
196
197
198 uf = uf_info.add_uf('n_state_model.ref_domain')
199 uf.title = "Set the reference domain for the '2-domain' N-state model."
200 uf.title_short = "Reference domain identification."
201 uf.add_keyarg(
202 name = "ref",
203 py_type = "str",
204 desc_short = "reference frame",
205 desc = "The domain which will act as the frame of reference. This is only valid for the '2-domain' N-state model."
206 )
207
208 uf.desc.append(Desc_container())
209 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.")
210
211 uf.desc.append(Desc_container("Prompt examples"))
212 uf.desc[-1].add_paragraph("To set up a 5-state model with 'C' domain being the frame of reference, type:")
213 uf.desc[-1].add_prompt("relax> n_state_model.ref_domain(ref='C')")
214 uf.backend = n_state_model_obj._ref_domain
215 uf.menu_text = "&ref_domain"
216 uf.gui_icon = "oxygen.actions.edit-rename"
217 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
218
219
220
221 uf = uf_info.add_uf('n_state_model.select_model')
222 uf.title = "Select the N-state model type and set up the model."
223 uf.title_short = "N-state model choice."
224 uf.add_keyarg(
225 name = "model",
226 default = "population",
227 py_type = "str",
228 desc_short = "model",
229 desc = "The name of the preset N-state model.",
230 wiz_element_type = "combo",
231 wiz_combo_choices = ["population", "fixed", "2-domain"],
232 wiz_read_only = True
233 )
234
235 uf.desc.append(Desc_container())
236 uf.desc[-1].add_paragraph("Prior to optimisation, the N-state model type should be selected. The preset models are:")
237 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, ...}.")
238 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, ...}.")
239 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.")
240
241 uf.desc.append(Desc_container("Prompt examples"))
242 uf.desc[-1].add_paragraph("To analyse populations of states, type:")
243 uf.desc[-1].add_prompt("relax> n_state_model.select_model(model='populations')")
244 uf.backend = n_state_model_obj._select_model
245 uf.menu_text = "&select_model"
246 uf.gui_icon = "oxygen.actions.list-add"
247 uf.wizard_height_desc = 400
248 uf.wizard_size = (800, 600)
249 uf.wizard_image = WIZARD_IMAGE_PATH + 'n_state_model.png'
250