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24 """Module containing the 'dx' user function class for controlling the OpenDX visualisation software."""
25 __docformat__ = 'plaintext'
26
27
28 from base_class import User_fn_class, _build_doc
29 import arg_check
30 from doc_string import docs
31 from generic_fns import diffusion_tensor
32 import opendx.main
33 from relax_errors import RelaxError
34 from specific_fns.model_free import Model_free
35
36
38 """Class for interfacing with OpenDX."""
39
40 - def execute(self, file="map", dir="dx", dx_exe="dx", vp_exec=True):
41
42 if self._exec_info.intro:
43 text = self._exec_info.ps3 + "dx("
44 text = text + "file=" + repr(file)
45 text = text + ", dir=" + repr(dir)
46 text = text + ", dx_exe=" + repr(dx_exe)
47 text = text + ", vp_exec=" + repr(vp_exec) + ")"
48 print(text)
49
50
51 arg_check.is_str(file, 'file name')
52 arg_check.is_str(dir, 'directory name', can_be_none=True)
53 arg_check.is_str(dx_exe, 'OpenDX executable file name')
54 arg_check.is_bool(vp_exec, 'visual program execution flag')
55
56
57 opendx.main.run(file_prefix=file, dir=dir, dx_exe=dx_exe, vp_exec=vp_exec)
58
59
60 execute._doc_title = "Execution of OpenDX."
61 execute._doc_title_short = "OpenDX execution."
62 execute._doc_args = [
63 ["file", "The file name prefix. For example if file is set to 'temp', then the OpenDX program temp.net will be loaded."],
64 ["dir", "The directory to change to for running OpenDX. If this is set to None, OpenDX will be run in the current directory."],
65 ["dx_exe", "The OpenDX executable file."],
66 ["vp_exec", "A flag specifying whether to execute the visual program automatically at start-up. The default of True causes the program to be executed."]
67 ]
68 _build_doc(execute)
69
70
71 - def map(self, params=None, map_type="Iso3D", spin_id=None, inc=20, lower=None, upper=None, axis_incs=5, file_prefix="map", dir="dx", point=None, point_file="point", remap=None):
72
73 if self._exec_info.intro:
74 text = self._exec_info.ps3 + "map("
75 text = text + "params=" + repr(params)
76 text = text + ", map_type=" + repr(map_type)
77 text = text + ", spin_id=" + repr(spin_id)
78 text = text + ", inc=" + repr(inc)
79 text = text + ", lower=" + repr(lower)
80 text = text + ", upper=" + repr(upper)
81 text = text + ", axis_incs=" + repr(axis_incs)
82 text = text + ", file_prefix=" + repr(file_prefix)
83 text = text + ", dir=" + repr(dir)
84 text = text + ", point=" + repr(point)
85 text = text + ", point_file=" + repr(point_file)
86 text = text + ", remap=" + repr(remap) + ")"
87 print(text)
88
89
90 arg_check.is_str_list(params, 'parameters')
91 arg_check.is_str(map_type, 'map type')
92 arg_check.is_str(spin_id, 'spin identification string', can_be_none=True)
93 arg_check.is_int(inc, 'increment')
94 if inc <= 1:
95 raise RelaxError("The increment value needs to be greater than 1.")
96 arg_check.is_num_list(lower, 'lower bounds', size=len(params), can_be_none=True)
97 arg_check.is_num_list(upper, 'upper bounds', size=len(params), can_be_none=True)
98 arg_check.is_int(axis_incs, 'axis increments')
99 if axis_incs <= 1:
100 raise RelaxError("The axis increment value needs to be greater than 1.")
101 arg_check.is_str(file_prefix, 'file prefix')
102 arg_check.is_str(dir, 'directory name', can_be_none=True)
103 arg_check.is_num_list(point, 'point', size=len(params), can_be_none=True)
104 if point != None:
105 arg_check.is_str(point_file, 'point file name')
106 arg_check.is_func(remap, 'remap function', can_be_none=True)
107
108
109 opendx.main.map(params=params, map_type=map_type, spin_id=spin_id, inc=inc, lower=lower, upper=upper, axis_incs=axis_incs, file_prefix=file_prefix, dir=dir, point=point, point_file=point_file, remap=remap)
110
111
112 map._doc_title = "Create a map of the given space in OpenDX format."
113 map._doc_title_short = "OpenDX map creation."
114 map._doc_args = [
115 ["params", "The parameters to be mapped. This argument should be an array of strings, the meanings of which are described below."],
116 ["map_type", "The type of map to create. For example the default, a 3D isosurface, the type is 'Iso3D'. See below for more details."],
117 ["spin_id", "The spin identification numbe."],
118 ["inc", "The number of increments to map in each dimension. This value controls the resolution of the map."],
119 ["lower", "The lower bounds of the space. If you wish to change the lower bounds of the map then supply an array of length equal to the number of parameters in the model. A lower bound for each parameter must be supplied. If nothing is supplied then the defaults will be used."],
120 ["upper", "The upper bounds of the space. If you wish to change the upper bounds of the map then supply an array of length equal to the number of parameters in the model. A upper bound for each parameter must be supplied. If nothing is supplied then the defaults will be used."],
121 ["axis_incs", "The number of increments or ticks displaying parameter values along the axes of the OpenDX plot."],
122 ["file_prefix", "The file name. All the output files are prefixed with this name. The main file containing the data points will be called the value of 'file'. The OpenDX program will be called 'file.net' and the OpenDX import file will be called 'file.general'."],
123 ["dir", "The directory to output files to. Set this to 'None' if you do not want the files to be placed in subdirectory. If the directory does not exist, it will be created."],
124 ["point", "An array of parameter values where a point in the map, shown as a red sphere, will be placed. The length must be equal to the number of parameters."],
125 ["point_file", "The name of that the point output files will be prefixed with."],
126 ["remap", "A user supplied remapping function. This function will receive the parameter array and must return an array of equal length."]
127 ]
128 map._doc_desc = """
129 The map type can be changed to one of the following supported map types:
130 _____________________________________________________________________________
131 | | |
132 | Surface type | Name |
133 |___________________________________________|_______________________________|
134 | | |
135 | 3D isosurface | 'Iso3D' |
136 |___________________________________________|_______________________________|
137 """
138 map._doc_examples = """
139 The following commands will generate a map of the extended model-free space for model 'm5'
140 consisting of the parameters {S2, S2f, ts}. Files will be output into the
141 directory 'dx' and will be prefixed by 'map'. In this case, the system is a protein and
142 residue number 6 will be mapped.
143
144 relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6')
145 relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6', file_prefix='map', dir='dx')
146 relax> dx.map(params=['s2', 's2f', 'ts'], spin_id=':6', inc=20, file_prefix='map', dir='dx')
147 relax> dx.map(params=['s2', 's2f', 'ts'], spin_id=':6', map_type='Iso3D', inc=20,
148 file_prefix='map', dir='dx')
149
150
151 To map the model-free space 'm4' for residue 2, spin N6 defined by the parameters {S2, te,
152 Rex}, name the results 'test', and to place the files in the current directory, use one of
153 the following commands:
154
155 relax> dx.map(['s2', 'te', 'rex'], spin_id=':2@N6', file_prefix='test', dir=None)
156 relax> dx.map(params=['s2', 'te', 'rex'], spin_id=':2@N6', inc=100, file_prefix='test', dir=None)
157 """
158 map._doc_additional = [
159 docs.regexp.doc,
160 diffusion_tensor.__return_data_name_prompt_doc__,
161 Model_free.return_data_name_doc
162 ]
163 _build_doc(map)
164