prompt.select

29 __boolean_doc = """ 30 Boolean operators 31 ~~~~~~~~~~~~~~~~~ 32 33 The 'boolean' keyword argument can be used to change how spin systems are selected. The 34 allowed values are: 'OR', 'NOR', 'AND', 'NAND', 'XOR', 'XNOR'. The following table details 35 how the selections will occur for the different boolean operators. 36 __________________________________________________________ 37 | | | | | | | | | | | 38 | Spin system | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 39 |____________________|___|___|___|___|___|___|___|___|___| 40 | | | | | | | | | | | 41 | Original selection | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 42 | | | | | | | | | | | 43 | New selection | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 44 |____________________|___|___|___|___|___|___|___|___|___| 45 | | | | | | | | | | | 46 | OR | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 47 | | | | | | | | | | | 48 | NOR | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 49 | | | | | | | | | | | 50 | AND | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 51 | | | | | | | | | | | 52 | NAND | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 53 | | | | | | | | | | | 54 | XOR | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 55 | | | | | | | | | | | 56 | XNOR | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 57 |____________________|___|___|___|___|___|___|___|___|___| 58 """ 59 60

61 - def __init__(self, relax):

62 # Help. 63 self.__relax_help__ = \ 64 """Class for selecting residues.""" 65 66 # Add the generic help string. 67 self.__relax_help__ = self.__relax_help__ + "\n" + help.relax_class_help 68 69 # Place relax in the class namespace. 70 self.__relax__ = relax

71 72

73 - def all(self, run=None):

74 """Function for selecting all residues. 75 76 Keyword Arguments 77 ~~~~~~~~~~~~~~~~~ 78 79 run: The name of the run(s). By supplying a single string, array of strings, or None, a 80 single run, multiple runs, or all runs will be selected respectively. 81 82 83 Examples 84 ~~~~~~~~ 85 86 To select all residues for all runs type: 87 88 relax> select.all() 89 90 91 To select all residues for the run 'srls_m1', type: 92 93 relax> select.all('srls_m1') 94 relax> select.all(run='srls_m1') 95 """ 96 97 # Function intro test. 98 if self.__relax__.interpreter.intro: 99 text = sys.ps3 + "select.all(" 100 text = text + "run=" + `run` + ")" 101 print text 102 103 # The run argument. 104 if run != None and type(run) != str and type(run) != list: 105 raise RelaxNoneStrListError, ('run', run) 106 if type(run) == list: 107 for i in xrange(len(run)): 108 if type(run[i]) != str: 109 raise RelaxListStrError, ('run', run) 110 111 # Execute the functional code. 112 self.__relax__.generic.selection.sel_all(run=run)

113 114

115 - def read(self, run=None, file=None, dir=None, boolean='OR', change_all=0, column=0):

116 """Function for selecting the residues contained in a file. 117 118 Keyword Arguments 119 ~~~~~~~~~~~~~~~~~ 120 121 run: The name of the run(s). By supplying a single string, array of strings, or None, a 122 single run, multiple runs, or all runs will be selected respectively. 123 124 file: The name of the file containing the list of residues to select. 125 126 dir: The directory where the file is located. 127 128 boolean: The boolean operator specifying how residues should be selected. 129 130 change_all: A flag specifying if all other residues should be changed. 131 132 column: The column containing the residue numbers (defaulting to 0, the first column). 133 134 135 Description 136 ~~~~~~~~~~~ 137 138 Empty lines and lines beginning with a hash are ignored. 139 140 The 'change_all' flag argument default is zero meaning that all residues currently either 141 selected or unselected will remain that way. Setting the argument to 1 will cause all 142 residues not specified in the file to be unselected. 143 144 145 Examples 146 ~~~~~~~~ 147 148 To select all residues in the file 'isolated_peaks', type one of: 149 150 relax> select.read('noe', 'isolated_peaks') 151 relax> select.read(run='noe', file='isolated_peaks') 152 153 To select the residues in the second column of the relaxation data file 'r1.600' while 154 deselecting all other residues, type one of: 155 156 relax> select.read('test', 'r1.600', change_all=1, column=1) 157 relax> select.read(run='test', file='r1.600', change_all=1, column=1) 158 """ 159 160 # Function intro test. 161 if self.__relax__.interpreter.intro: 162 text = sys.ps3 + "select.read(" 163 text = text + "run=" + `run` 164 text = text + ", file=" + `file` 165 text = text + ", dir=" + `dir` 166 text = text + ", boolean=" + `boolean` 167 text = text + ", change_all=" + `change_all` 168 text = text + ", column=" + `column` + ")" 169 print text 170 171 # The run argument. 172 if run != None and type(run) != str and type(run) != list: 173 raise RelaxNoneStrListError, ('run', run) 174 if type(run) == list: 175 for i in xrange(len(run)): 176 if type(run[i]) != str: 177 raise RelaxListStrError, ('run', run) 178 179 # File name. 180 if type(file) != str: 181 raise RelaxStrError, ('file name', file) 182 183 # Directory. 184 if dir != None and type(dir) != str: 185 raise RelaxNoneStrError, ('directory name', dir) 186 187 # Boolean operator. 188 if type(boolean) != str: 189 raise RelaxStrError, ('boolean operator', boolean) 190 191 # Change all flag. 192 if type(change_all) != int or (change_all != 0 and change_all != 1): 193 raise RelaxBinError, ('change_all', change_all) 194 195 # The residue column. 196 if type(column) != int: 197 raise RelaxIntError, ('residue number column', column) 198 199 # Execute the functional code. 200 self.__relax__.generic.selection.sel_read(run=run, file=file, dir=dir, boolean=boolean, change_all=change_all, column=column)

201 202

203 - def res(self, run=None, num=None, name=None, boolean='OR', change_all=0):

204 """Function for selecting specific residues. 205 206 Keyword Arguments 207 ~~~~~~~~~~~~~~~~~ 208 209 run: The name of the run(s). By supplying a single string, array of strings, or None, a 210 single run, multiple runs, or all runs will be selected respectively. 211 212 num: The residue number. 213 214 name: The residue name. 215 216 boolean: The boolean operator specifying how residues should be selected. 217 218 change_all: A flag specifying if all other residues should be changed. 219 220 221 Description 222 ~~~~~~~~~~~ 223 224 The residue number can be either an integer for selecting a single residue or a python 225 regular expression, in string form, for selecting multiple residues. For details about 226 using regular expression, see the python documentation for the module 're'. 227 228 The residue name argument must be a string. Regular expression is also allowed. 229 230 The 'change_all' flag argument default is zero meaning that all residues currently either 231 selected or unselected will remain that way. Setting the argument to 1 will cause all 232 residues not specified by 'num' or 'name' to become unselected. 233 234 235 Examples 236 ~~~~~~~~ 237 238 To select only glycines and alanines for the run 'm3', assuming they have been loaded with 239 the names GLY and ALA, type: 240 241 relax> select.res(run='m3', name='GLY|ALA', change_all=1) 242 relax> select.res(run='m3', name='[GA]L[YA]', change_all=1) 243 244 To select residue 5 CYS in addition to the currently selected residues, type: 245 246 relax> select.res('m3', 5) 247 relax> select.res('m3', 5, 'CYS') 248 relax> select.res('m3', '5') 249 relax> select.res('m3', '5', 'CYS') 250 relax> select.res(run='m3', num='5', name='CYS') 251 """ 252 253 # Function intro test. 254 if self.__relax__.interpreter.intro: 255 text = sys.ps3 + "select.res(" 256 text = text + "run=" + `run` 257 text = text + ", num=" + `num` 258 text = text + ", name=" + `name` 259 text = text + ", boolean=" + `boolean` 260 text = text + ", change_all=" + `change_all` + ")" 261 print text 262 263 # The run argument. 264 if run != None and type(run) != str and type(run) != list: 265 raise RelaxNoneStrListError, ('run', run) 266 if type(run) == list: 267 for i in xrange(len(run)): 268 if type(run[i]) != str: 269 raise RelaxListStrError, ('run', run) 270 271 # Residue number. 272 if num != None and type(num) != int and type(num) != str: 273 raise RelaxNoneIntStrError, ('residue number', num) 274 275 # Residue name. 276 if name != None and type(name) != str: 277 raise RelaxNoneStrError, ('residue name', name) 278 279 # Neither are given. 280 if num == None and name == None: 281 raise RelaxError, "At least one of the number or name arguments is required." 282 283 # Boolean operator. 284 if type(boolean) != str: 285 raise RelaxStrError, ('boolean operator', boolean) 286 287 # Change all flag. 288 if type(change_all) != int or (change_all != 0 and change_all != 1): 289 raise RelaxBinError, ('change_all', change_all) 290 291 # Execute the functional code. 292 self.__relax__.generic.selection.sel_res(run=run, num=num, name=name, boolean=boolean, change_all=change_all)

293 294

295 - def reverse(self, run=None):

296 """Function for the reversal of the residue selection. 297 298 Keyword Arguments 299 ~~~~~~~~~~~~~~~~~ 300 301 run: The name of the run(s). By supplying a single string, array of strings, or None, a 302 single run, multiple runs, or all runs will be selected respectively. 303 304 305 Examples 306 ~~~~~~~~ 307 308 To unselect all currently selected residues and select those which are unselected type: 309 310 relax> select.reverse() 311 """ 312 313 # Function intro test. 314 if self.__relax__.interpreter.intro: 315 text = sys.ps3 + "select.reverse(" 316 text = text + "run=" + `run` + ")" 317 print text 318 319 # The run argument. 320 if run != None and type(run) != str and type(run) != list: 321 raise RelaxNoneStrListError, ('run', run) 322 if type(run) == list: 323 for i in xrange(len(run)): 324 if type(run[i]) != str: 325 raise RelaxListStrError, ('run', run) 326 327 # Execute the functional code. 328 self.__relax__.generic.selection.reverse(run=run)

329 330 331 332 # Docstring modification. 333 ######################### 334 335 # Read function. 336 read.__doc__ = read.__doc__ + "\n\n" + __boolean_doc + "\n"

Source Code for Module prompt.select