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