prompt.dx

33 - def __init__(self, relax):

34 # Help. 35 self.__relax_help__ = \ 36 """Class for interfacing with OpenDX.""" 37 38 # Add the generic help string. 39 self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 40 41 # Place relax in the class namespace. 42 self.__relax__ = relax

43 44

45 - def execute(self, file="map", dir="dx", dx_exe="dx", vp_exec=1):

46 """Function for running OpenDX. 47 48 Keyword Arguments 49 ~~~~~~~~~~~~~~~~~ 50 51 file: The file name prefix. For example if file is set to 'temp', then the OpenDX program 52 temp.net will be loaded. 53 54 dir: The directory to change to for running OpenDX. If this is set to 'None', OpenDX will 55 be run in the current directory. 56 57 dx_exe: The OpenDX executable file. 58 59 vp_exec: A flag specifying whether to execute the visual program automatically at 60 start-up. The default is 1 which turns execution on. Setting the value to zero turns 61 execution off. 62 """ 63 64 # Function intro text. 65 if self.__relax__.interpreter.intro: 66 text = sys.ps3 + "dx(" 67 text = text + "file=" + `file` 68 text = text + ", dir=" + `dir` 69 text = text + ", dx_exe=" + `dx_exe` 70 text = text + ", vp_exec=" + `vp_exec` + ")" 71 print text 72 73 # File name. 74 if type(file) != str: 75 raise RelaxStrError, ('file name', file) 76 77 # Directory name. 78 if dir == None: 79 pass 80 elif type(dir) != str: 81 raise RelaxNoneStrError, ('file name', file) 82 83 # The OpenDX executable file. 84 if type(dx_exe) != str: 85 raise RelaxStrError, ('OpenDX executable file name', dx_exe) 86 87 # Visual program execution flag. 88 if type(vp_exec) != int or (vp_exec != 0 and vp_exec != 1): 89 raise RelaxBinError, ('visual program execution flag', vp_exec) 90 91 # Execute the functional code. 92 self.__relax__.generic.opendx.run(file=file, dir=dir, dx_exe=dx_exe, vp_exec=vp_exec)

93 94

95 - def map(self, run=None, params=None, map_type="Iso3D", res_num=None, inc=20, lower=None, upper=None, axis_incs=10, file="map", dir="dx", point=None, point_file="point", remap=None):

96 """Function for creating a map of the given space in OpenDX format. 97 98 Keyword Arguments 99 ~~~~~~~~~~~~~~~~~ 100 101 run: The name of the run. 102 103 params: The parameters to be mapped. This argument should be an array of strings, values 104 of which are described below. 105 106 map_type: The type of map to create. For example the default, a 3D isosurface, the type is 107 'Iso3D'. See below for more details. 108 109 res_num: The residue number. 110 111 inc: The number of increments to map in each dimension. This value controls the resolution 112 of the map. 113 114 lower: The lower bounds of the space. If you wish to change the lower bounds of the map 115 then supply an array of length equal to the number of parameters in the model. A lower 116 bound for each parameter must be supplied. If nothing is supplied then the defaults will 117 be used. 118 119 upper: The upper bounds of the space. If you wish to change the upper bounds of the map 120 then supply an array of length equal to the number of parameters in the model. A upper 121 bound for each parameter must be supplied. If nothing is supplied then the defaults will 122 be used. 123 124 axis_incs: The number of increments or ticks displaying parameter values along the axes of 125 the OpenDX plot. 126 127 file: The file name. All the output files are prefixed with this name. The main file 128 containing the data points will be called the value of 'file'. The OpenDX program will be 129 called 'file.net' and the OpenDX import file will be called 'file.general'. 130 131 dir: The directory to output files to. Set this to 'None' if you do not want the files to 132 be placed in subdirectory. If the directory does not exist, it will be created. 133 134 point: An array of parameter values where a point in the map, shown as a red sphere, will 135 be placed. The length must be equal to the number of parameters. 136 137 point_file: The name of that the point output files will be prefixed with. 138 139 remap: A user supplied remapping function. This function will receive the parameter array 140 and must return an array of equal length. 141 142 143 Map type 144 ~~~~~~~~ 145 146 The map type can be changed by supplying the 'map_type' keyword argument. Here is a list of 147 currently supported map types: 148 _____________________________________________________________________________ 149 | | | 150 | Surface type | Pattern | 151 |___________________________________________|_______________________________| 152 | | | 153 | 3D isosurface | '^[Ii]so3[Dd]' | 154 |___________________________________________|_______________________________| 155 156 Pattern syntax is simply regular expression syntax where square brackets '[]' means any 157 character within the brackets, '^' means the start of the string, etc. 158 159 160 Examples 161 ~~~~~~~~ 162 163 The following commands will generate a map of the extended model-free space defined as run 164 'm5' which consists of the parameters {S2, S2f, ts}. Files will be output into the 165 directory 'dx' and will be prefixed by 'map'. The residue, in this case, is number 6. 166 167 relax> dx.map('m5', ['S2', 'S2f', 'ts'], 6) 168 relax> dx.map('m5', ['S2', 'S2f', 'ts'], 6, 20, 'map', 'dx') 169 relax> dx.map('m5', ['S2', 'S2f', 'ts'], res_num=6, file='map', dir='dx') 170 relax> dx.map(run='m5', params=['S2', 'S2f', 'ts'], res_num=6, inc=20, file='map', dir='dx') 171 relax> dx.map(run='m5', params=['S2', 'S2f', 'ts'], res_num=6, type='Iso3D', inc=20, 172 swap=[0, 1, 2], file='map', dir='dx') 173 174 175 To map the model-free space 'm4' defined by the parameters {S2, te, Rex}, name the results 176 'test', and not place the files in a subdirectory, use the following commands (assuming 177 residue 2). 178 179 relax> dx.map('m4', ['S2', 'te', 'Rex'], res_num=2, file='test', dir=None) 180 relax> dx.map(run='m4', params=['S2', 'te', 'Rex'], res_num=2, inc=100, file='test', 181 dir=None) 182 """ 183 184 # Function intro text. 185 if self.__relax__.interpreter.intro: 186 text = sys.ps3 + "map(" 187 text = text + "run=" + `run` 188 text = text + ", params=" + `params` 189 text = text + ", map_type=" + `map_type` 190 text = text + ", res_num=" + `res_num` 191 text = text + ", inc=" + `inc` 192 text = text + ", lower=" + `lower` 193 text = text + ", upper=" + `upper` 194 text = text + ", axis_incs=" + `axis_incs` 195 text = text + ", file=" + `file` 196 text = text + ", dir=" + `dir` 197 text = text + ", point=" + `point` 198 text = text + ", point_file=" + `point_file` 199 text = text + ", remap=" + `remap` + ")" 200 print text 201 202 # The run argument. 203 if type(run) != str: 204 raise RelaxStrError, ('run', run) 205 206 # The parameters to map. 207 if type(params) != list: 208 raise RelaxListError, ('parameters', params) 209 num_params = len(params) 210 for i in xrange(num_params): 211 if type(params[i]) != str: 212 raise RelaxListStrError, ('parameters', params) 213 214 # Space type. 215 if type(map_type) != str: 216 raise RelaxStrError, ('map type', map_type) 217 218 # The residue number. 219 if type(res_num) != int and res_num != None: 220 raise RelaxNoneIntError, ('residue number', res_num) 221 222 # Increment. 223 if type(inc) != int: 224 raise RelaxIntError, ('increment', inc) 225 elif inc <= 1: 226 raise RelaxError, "The increment value needs to be greater than 1." 227 228 # Lower bounds. 229 if lower != None: 230 if type(lower) != list: 231 raise RelaxListError, ('lower bounds', lower) 232 if len(lower) != num_params: 233 raise RelaxLenError, ('lower bounds', num_params) 234 for i in xrange(len(lower)): 235 if type(lower[i]) != int and type(lower[i]) != float: 236 raise RelaxListNumError, ('lower bounds', lower) 237 238 # Upper bounds. 239 if upper != None: 240 if type(upper) != list: 241 raise RelaxListError, ('upper bounds', upper) 242 if len(upper) != num_params: 243 raise RelaxLenError, ('upper bounds', num_params) 244 for i in xrange(len(upper)): 245 if type(upper[i]) != int and type(upper[i]) != float: 246 raise RelaxListNumError, ('upper bounds', upper) 247 248 # Axis increments. 249 if type(axis_incs) != int: 250 raise RelaxIntError, ('axis increments', axis_incs) 251 elif axis_incs <= 1: 252 raise RelaxError, "The axis increment value needs to be greater than 1." 253 254 # File name. 255 if type(file) != str: 256 raise RelaxStrError, ('file name', file) 257 258 # Directory name. 259 if dir != None and type(dir) != str: 260 raise RelaxNoneStrError, ('directory name', dir) 261 262 # Point. 263 if point != None: 264 if type(point) != list: 265 raise RelaxListError, ('point', point) 266 if len(point) != num_params: 267 raise RelaxLenError, ('point', point) 268 if type(point_file) != str: 269 raise RelaxStrError, ('point file name', point_file) 270 for i in xrange(len(point)): 271 if type(point[i]) != int and type(point[i]) != float: 272 raise RelaxListNumError, ('point', point) 273 274 # Remap function. 275 if remap != None and type(remap) is not FunctionType: 276 raise RelaxFunctionError, ('remap function', remap) 277 278 # Execute the functional code. 279 self.__relax__.generic.opendx.map(run=run, params=params, map_type=map_type, res_num=res_num, inc=inc, lower=lower, upper=upper, axis_incs=axis_incs, file=file, dir=dir, point=point, point_file=point_file, remap=remap)

280 281 282 # Docstring modification. 283 ######################### 284 285 # Write function. 286 map.__doc__ = map.__doc__ + "\n\n" + regexp_doc() + "\n" 287 map.__doc__ = map.__doc__ + Diffusion_tensor.return_data_name.__doc__ + "\n\n" 288 map.__doc__ = map.__doc__ + Model_free.return_data_name.__doc__ + "\n\n"

Source Code for Module prompt.dx