| 1 | <?xml version='1.0' encoding='ISO-8859-1' standalone='yes' ?>
|
|---|
| 2 | <tagfile>
|
|---|
| 3 | <compound kind="page">
|
|---|
| 4 | <name>index</name>
|
|---|
| 5 | <title>pySMMP: Python bindings to SMMP v. 1.1.</title>
|
|---|
| 6 | <filename>index</filename>
|
|---|
| 7 | <docanchor file="index">sec_tutorial</docanchor>
|
|---|
| 8 | </compound>
|
|---|
| 9 | <compound kind="file">
|
|---|
| 10 | <name>algorithms.py</name>
|
|---|
| 11 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 12 | <filename>algorithms_8py</filename>
|
|---|
| 13 | <namespace>algorithms</namespace>
|
|---|
| 14 | <namespace>math</namespace>
|
|---|
| 15 | <class kind="class">algorithms::CanonicalMonteCarlo</class>
|
|---|
| 16 | </compound>
|
|---|
| 17 | <compound kind="file">
|
|---|
| 18 | <name>main.py</name>
|
|---|
| 19 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 20 | <filename>main_8py</filename>
|
|---|
| 21 | <namespace>main</namespace>
|
|---|
| 22 | <member kind="variable" static="yes">
|
|---|
| 23 | <type>string</type>
|
|---|
| 24 | <name>usage</name>
|
|---|
| 25 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 26 | <anchor>d363bdabd6492750c79e74bb23e01005</anchor>
|
|---|
| 27 | <arglist></arglist>
|
|---|
| 28 | </member>
|
|---|
| 29 | <member kind="variable" static="yes">
|
|---|
| 30 | <type>tuple</type>
|
|---|
| 31 | <name>parser</name>
|
|---|
| 32 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 33 | <anchor>6596d20927a9196bbb33aef704e88297</anchor>
|
|---|
| 34 | <arglist></arglist>
|
|---|
| 35 | </member>
|
|---|
| 36 | <member kind="variable" static="yes">
|
|---|
| 37 | <type>string</type>
|
|---|
| 38 | <name>help</name>
|
|---|
| 39 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 40 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 41 | <arglist></arglist>
|
|---|
| 42 | </member>
|
|---|
| 43 | <member kind="variable" static="yes">
|
|---|
| 44 | <type>string</type>
|
|---|
| 45 | <name>help</name>
|
|---|
| 46 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 47 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 48 | <arglist></arglist>
|
|---|
| 49 | </member>
|
|---|
| 50 | <member kind="variable" static="yes">
|
|---|
| 51 | <type>string</type>
|
|---|
| 52 | <name>help</name>
|
|---|
| 53 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 54 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 55 | <arglist></arglist>
|
|---|
| 56 | </member>
|
|---|
| 57 | <member kind="variable" static="yes">
|
|---|
| 58 | <type>string</type>
|
|---|
| 59 | <name>help</name>
|
|---|
| 60 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 61 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 62 | <arglist></arglist>
|
|---|
| 63 | </member>
|
|---|
| 64 | <member kind="variable" static="yes">
|
|---|
| 65 | <type>string</type>
|
|---|
| 66 | <name>help</name>
|
|---|
| 67 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 68 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 69 | <arglist></arglist>
|
|---|
| 70 | </member>
|
|---|
| 71 | <member kind="variable" static="yes">
|
|---|
| 72 | <type>string</type>
|
|---|
| 73 | <name>help</name>
|
|---|
| 74 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 75 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 76 | <arglist></arglist>
|
|---|
| 77 | </member>
|
|---|
| 78 | <member kind="variable" static="yes">
|
|---|
| 79 | <type>list</type>
|
|---|
| 80 | <name>seqFileName</name>
|
|---|
| 81 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 82 | <anchor>2a4367ed60a67e069e0b5d9788a10801</anchor>
|
|---|
| 83 | <arglist></arglist>
|
|---|
| 84 | </member>
|
|---|
| 85 | <member kind="variable" static="yes">
|
|---|
| 86 | <type>tuple</type>
|
|---|
| 87 | <name>myUniv</name>
|
|---|
| 88 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 89 | <anchor>d7a3fa6b22dda1cbd41815dd2a5a6f76</anchor>
|
|---|
| 90 | <arglist></arglist>
|
|---|
| 91 | </member>
|
|---|
| 92 | <member kind="variable" static="yes">
|
|---|
| 93 | <type>tuple</type>
|
|---|
| 94 | <name>p1</name>
|
|---|
| 95 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 96 | <anchor>08bd12d1a3d5f6b17f7c12559b79e87c</anchor>
|
|---|
| 97 | <arglist></arglist>
|
|---|
| 98 | </member>
|
|---|
| 99 | <member kind="variable" static="yes">
|
|---|
| 100 | <type>float</type>
|
|---|
| 101 | <name>T</name>
|
|---|
| 102 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 103 | <anchor>98e836cf59f46c8f187e64eceb62bad9</anchor>
|
|---|
| 104 | <arglist></arglist>
|
|---|
| 105 | </member>
|
|---|
| 106 | <member kind="variable" static="yes">
|
|---|
| 107 | <type>tuple</type>
|
|---|
| 108 | <name>ts</name>
|
|---|
| 109 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 110 | <anchor>7c1ab8aaf906bf136a0aad2fc320c099</anchor>
|
|---|
| 111 | <arglist></arglist>
|
|---|
| 112 | </member>
|
|---|
| 113 | <member kind="variable" static="yes">
|
|---|
| 114 | <type>tuple</type>
|
|---|
| 115 | <name>t1</name>
|
|---|
| 116 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 117 | <anchor>1c35537490e5d4cc72ea798d80ee7578</anchor>
|
|---|
| 118 | <arglist></arglist>
|
|---|
| 119 | </member>
|
|---|
| 120 | <member kind="variable" static="yes">
|
|---|
| 121 | <type>tuple</type>
|
|---|
| 122 | <name>te</name>
|
|---|
| 123 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 124 | <anchor>208f1ab948fb0311a3199e58cc777d7c</anchor>
|
|---|
| 125 | <arglist></arglist>
|
|---|
| 126 | </member>
|
|---|
| 127 | </compound>
|
|---|
| 128 | <compound kind="file">
|
|---|
| 129 | <name>protein.py</name>
|
|---|
| 130 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 131 | <filename>protein_8py</filename>
|
|---|
| 132 | <namespace>protein</namespace>
|
|---|
| 133 | <class kind="class">protein::Atom</class>
|
|---|
| 134 | <class kind="class">protein::Residue</class>
|
|---|
| 135 | <class kind="class">protein::Protein</class>
|
|---|
| 136 | <member kind="function">
|
|---|
| 137 | <type>def</type>
|
|---|
| 138 | <name>nursvr</name>
|
|---|
| 139 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 140 | <anchor>6f178e1c980241ce2e8ec9ba807492e8</anchor>
|
|---|
| 141 | <arglist></arglist>
|
|---|
| 142 | </member>
|
|---|
| 143 | <member kind="variable" static="yes">
|
|---|
| 144 | <type>float</type>
|
|---|
| 145 | <name>crd</name>
|
|---|
| 146 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 147 | <anchor>ccf520a3c785c7e1da5a1f6c369c66a7</anchor>
|
|---|
| 148 | <arglist></arglist>
|
|---|
| 149 | </member>
|
|---|
| 150 | <member kind="variable" static="yes">
|
|---|
| 151 | <type>string</type>
|
|---|
| 152 | <name>libdir</name>
|
|---|
| 153 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 154 | <anchor>55146e5ace572b13bd76966bb56a4dba</anchor>
|
|---|
| 155 | <arglist></arglist>
|
|---|
| 156 | </member>
|
|---|
| 157 | <member kind="variable" static="yes">
|
|---|
| 158 | <type>tuple</type>
|
|---|
| 159 | <name>p1</name>
|
|---|
| 160 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 161 | <anchor>214ebeb5b08a560b5283cb08eeb21bc0</anchor>
|
|---|
| 162 | <arglist></arglist>
|
|---|
| 163 | </member>
|
|---|
| 164 | </compound>
|
|---|
| 165 | <compound kind="file">
|
|---|
| 166 | <name>restoreexclpoint.py</name>
|
|---|
| 167 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 168 | <filename>restoreexclpoint_8py</filename>
|
|---|
| 169 | <namespace>restoreexclpoint</namespace>
|
|---|
| 170 | </compound>
|
|---|
| 171 | <compound kind="file">
|
|---|
| 172 | <name>rmexclpoint.py</name>
|
|---|
| 173 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 174 | <filename>rmexclpoint_8py</filename>
|
|---|
| 175 | <namespace>rmexclpoint</namespace>
|
|---|
| 176 | <member kind="variable" static="yes">
|
|---|
| 177 | <type>string</type>
|
|---|
| 178 | <name>patternstring</name>
|
|---|
| 179 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 180 | <anchor>86242b4a75e4538ed51da15642c85e28</anchor>
|
|---|
| 181 | <arglist></arglist>
|
|---|
| 182 | </member>
|
|---|
| 183 | <member kind="variable" static="yes">
|
|---|
| 184 | <type>string</type>
|
|---|
| 185 | <name>patternstring2</name>
|
|---|
| 186 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 187 | <anchor>c3f5a790770fb7300f387adc8759f769</anchor>
|
|---|
| 188 | <arglist></arglist>
|
|---|
| 189 | </member>
|
|---|
| 190 | <member kind="variable" static="yes">
|
|---|
| 191 | <type>string</type>
|
|---|
| 192 | <name>patternstring3</name>
|
|---|
| 193 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 194 | <anchor>95065921525bd513903b35af66076eaf</anchor>
|
|---|
| 195 | <arglist></arglist>
|
|---|
| 196 | </member>
|
|---|
| 197 | <member kind="variable" static="yes">
|
|---|
| 198 | <type>tuple</type>
|
|---|
| 199 | <name>pattern</name>
|
|---|
| 200 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 201 | <anchor>7152c4b3e9458952f0f7e807a8fcc118</anchor>
|
|---|
| 202 | <arglist></arglist>
|
|---|
| 203 | </member>
|
|---|
| 204 | <member kind="variable" static="yes">
|
|---|
| 205 | <type>tuple</type>
|
|---|
| 206 | <name>pattern2</name>
|
|---|
| 207 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 208 | <anchor>1eefe42773502750ba26b29e9daaf12a</anchor>
|
|---|
| 209 | <arglist></arglist>
|
|---|
| 210 | </member>
|
|---|
| 211 | <member kind="variable" static="yes">
|
|---|
| 212 | <type>tuple</type>
|
|---|
| 213 | <name>pattern3</name>
|
|---|
| 214 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 215 | <anchor>c4bff9bcc3a56186ffc45bea0ed74fcb</anchor>
|
|---|
| 216 | <arglist></arglist>
|
|---|
| 217 | </member>
|
|---|
| 218 | <member kind="variable" static="yes">
|
|---|
| 219 | <type>tuple</type>
|
|---|
| 220 | <name>f</name>
|
|---|
| 221 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 222 | <anchor>30f86c4fa6e0250721c2e17d0a71e73a</anchor>
|
|---|
| 223 | <arglist></arglist>
|
|---|
| 224 | </member>
|
|---|
| 225 | <member kind="variable" static="yes">
|
|---|
| 226 | <type>tuple</type>
|
|---|
| 227 | <name>s</name>
|
|---|
| 228 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 229 | <anchor>9f0bd653bab192dad5ad9e71c198277f</anchor>
|
|---|
| 230 | <arglist></arglist>
|
|---|
| 231 | </member>
|
|---|
| 232 | <member kind="variable" static="yes">
|
|---|
| 233 | <type>tuple</type>
|
|---|
| 234 | <name>t</name>
|
|---|
| 235 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 236 | <anchor>5eea3706a180934d1eb7cf55b6cc8902</anchor>
|
|---|
| 237 | <arglist></arglist>
|
|---|
| 238 | </member>
|
|---|
| 239 | <member kind="variable" static="yes">
|
|---|
| 240 | <type>tuple</type>
|
|---|
| 241 | <name>t</name>
|
|---|
| 242 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 243 | <anchor>5eea3706a180934d1eb7cf55b6cc8902</anchor>
|
|---|
| 244 | <arglist></arglist>
|
|---|
| 245 | </member>
|
|---|
| 246 | <member kind="variable" static="yes">
|
|---|
| 247 | <type>tuple</type>
|
|---|
| 248 | <name>t</name>
|
|---|
| 249 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 250 | <anchor>5eea3706a180934d1eb7cf55b6cc8902</anchor>
|
|---|
| 251 | <arglist></arglist>
|
|---|
| 252 | </member>
|
|---|
| 253 | <member kind="variable" static="yes">
|
|---|
| 254 | <type>tuple</type>
|
|---|
| 255 | <name>f</name>
|
|---|
| 256 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 257 | <anchor>30f86c4fa6e0250721c2e17d0a71e73a</anchor>
|
|---|
| 258 | <arglist></arglist>
|
|---|
| 259 | </member>
|
|---|
| 260 | </compound>
|
|---|
| 261 | <compound kind="file">
|
|---|
| 262 | <name>test.py</name>
|
|---|
| 263 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 264 | <filename>test_8py</filename>
|
|---|
| 265 | <namespace>test</namespace>
|
|---|
| 266 | <namespace>smmp</namespace>
|
|---|
| 267 | <namespace>random</namespace>
|
|---|
| 268 | <namespace>time</namespace>
|
|---|
| 269 | <member kind="variable" static="yes">
|
|---|
| 270 | <type>string</type>
|
|---|
| 271 | <name>libdir</name>
|
|---|
| 272 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 273 | <anchor>6fa2049667bd4ad558f12fa937b0f371</anchor>
|
|---|
| 274 | <arglist></arglist>
|
|---|
| 275 | </member>
|
|---|
| 276 | <member kind="variable" static="yes">
|
|---|
| 277 | <type>string</type>
|
|---|
| 278 | <name>grpn</name>
|
|---|
| 279 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 280 | <anchor>45640d02312df311aa623e0e86f02b1a</anchor>
|
|---|
| 281 | <arglist></arglist>
|
|---|
| 282 | </member>
|
|---|
| 283 | <member kind="variable" static="yes">
|
|---|
| 284 | <type>string</type>
|
|---|
| 285 | <name>grpc</name>
|
|---|
| 286 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 287 | <anchor>fdce7a7b24d00b30a07ba3e65a00e5a0</anchor>
|
|---|
| 288 | <arglist></arglist>
|
|---|
| 289 | </member>
|
|---|
| 290 | <member kind="variable" static="yes">
|
|---|
| 291 | <type>int</type>
|
|---|
| 292 | <name>nequi</name>
|
|---|
| 293 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 294 | <anchor>df2298f8864993aebf9ba53f812ee595</anchor>
|
|---|
| 295 | <arglist></arglist>
|
|---|
| 296 | </member>
|
|---|
| 297 | <member kind="variable" static="yes">
|
|---|
| 298 | <type>int</type>
|
|---|
| 299 | <name>nswp</name>
|
|---|
| 300 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 301 | <anchor>155edc50375b57e5cdb2b81de24652a7</anchor>
|
|---|
| 302 | <arglist></arglist>
|
|---|
| 303 | </member>
|
|---|
| 304 | <member kind="variable" static="yes">
|
|---|
| 305 | <type>int</type>
|
|---|
| 306 | <name>nmes</name>
|
|---|
| 307 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 308 | <anchor>565f363ab69b2fcbb062da2ad67f3569</anchor>
|
|---|
| 309 | <arglist></arglist>
|
|---|
| 310 | </member>
|
|---|
| 311 | <member kind="variable" static="yes">
|
|---|
| 312 | <type>int</type>
|
|---|
| 313 | <name>Tmax</name>
|
|---|
| 314 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 315 | <anchor>b9451198b74ce8b65df7b61e93e27821</anchor>
|
|---|
| 316 | <arglist></arglist>
|
|---|
| 317 | </member>
|
|---|
| 318 | <member kind="variable" static="yes">
|
|---|
| 319 | <type>int</type>
|
|---|
| 320 | <name>Tmin</name>
|
|---|
| 321 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 322 | <anchor>4ffceb0284a3e2cadf27ed155dbd555b</anchor>
|
|---|
| 323 | <arglist></arglist>
|
|---|
| 324 | </member>
|
|---|
| 325 | <member kind="variable" static="yes">
|
|---|
| 326 | <type>int</type>
|
|---|
| 327 | <name>T</name>
|
|---|
| 328 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 329 | <anchor>021821f6c47ffff20b56e91dfb9ac63e</anchor>
|
|---|
| 330 | <arglist></arglist>
|
|---|
| 331 | </member>
|
|---|
| 332 | <member kind="variable" static="yes">
|
|---|
| 333 | <type>tuple</type>
|
|---|
| 334 | <name>timeseries</name>
|
|---|
| 335 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 336 | <anchor>df0b843e5561c2d2def0ecedc181b618</anchor>
|
|---|
| 337 | <arglist></arglist>
|
|---|
| 338 | </member>
|
|---|
| 339 | <member kind="variable" static="yes">
|
|---|
| 340 | <type>int</type>
|
|---|
| 341 | <name>iabin</name>
|
|---|
| 342 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 343 | <anchor>6ee3c009f0ac3ebaf75897d0d09f1c44</anchor>
|
|---|
| 344 | <arglist></arglist>
|
|---|
| 345 | </member>
|
|---|
| 346 | <member kind="variable" static="yes">
|
|---|
| 347 | <type>tuple</type>
|
|---|
| 348 | <name>eol</name>
|
|---|
| 349 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 350 | <anchor>5d5bdfad6a87904ae6efd9d69ef3b1a0</anchor>
|
|---|
| 351 | <arglist></arglist>
|
|---|
| 352 | </member>
|
|---|
| 353 | <member kind="variable" static="yes">
|
|---|
| 354 | <type>int</type>
|
|---|
| 355 | <name>acc</name>
|
|---|
| 356 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 357 | <anchor>ffde8edcabf285406c61e3823d023e39</anchor>
|
|---|
| 358 | <arglist></arglist>
|
|---|
| 359 | </member>
|
|---|
| 360 | </compound>
|
|---|
| 361 | <compound kind="file">
|
|---|
| 362 | <name>universe.py</name>
|
|---|
| 363 | <path>/home/meinke/research/software/SMMP/SMMP-3.0/</path>
|
|---|
| 364 | <filename>universe_8py</filename>
|
|---|
| 365 | <namespace>universe</namespace>
|
|---|
| 366 | <class kind="class">universe::Universe</class>
|
|---|
| 367 | </compound>
|
|---|
| 368 | <compound kind="namespace">
|
|---|
| 369 | <name>algorithms</name>
|
|---|
| 370 | <filename>namespacealgorithms.html</filename>
|
|---|
| 371 | <class kind="class">algorithms::CanonicalMonteCarlo</class>
|
|---|
| 372 | </compound>
|
|---|
| 373 | <compound kind="class">
|
|---|
| 374 | <name>algorithms::CanonicalMonteCarlo</name>
|
|---|
| 375 | <filename>classalgorithms_1_1CanonicalMonteCarlo.html</filename>
|
|---|
| 376 | <member kind="function">
|
|---|
| 377 | <type>def</type>
|
|---|
| 378 | <name>__init__</name>
|
|---|
| 379 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 380 | <anchor>6cd1b7245cc7023ff3c0e47535e6c28b</anchor>
|
|---|
| 381 | <arglist></arglist>
|
|---|
| 382 | </member>
|
|---|
| 383 | <member kind="function">
|
|---|
| 384 | <type>def</type>
|
|---|
| 385 | <name>acceptanceRate</name>
|
|---|
| 386 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 387 | <anchor>5882eb86466b36e7d3404002788905c3</anchor>
|
|---|
| 388 | <arglist></arglist>
|
|---|
| 389 | </member>
|
|---|
| 390 | <member kind="function">
|
|---|
| 391 | <type>def</type>
|
|---|
| 392 | <name>minimumEnergy</name>
|
|---|
| 393 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 394 | <anchor>b81e1a1687fa543342003c1f3d3ff86d</anchor>
|
|---|
| 395 | <arglist></arglist>
|
|---|
| 396 | </member>
|
|---|
| 397 | <member kind="function">
|
|---|
| 398 | <type>def</type>
|
|---|
| 399 | <name>performedSweeps</name>
|
|---|
| 400 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 401 | <anchor>feedd6c4800c4b8ca29f850683386e3e</anchor>
|
|---|
| 402 | <arglist></arglist>
|
|---|
| 403 | </member>
|
|---|
| 404 | <member kind="function">
|
|---|
| 405 | <type>def</type>
|
|---|
| 406 | <name>run</name>
|
|---|
| 407 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 408 | <anchor>70adf3a29b3526efd776aa804b216dbf</anchor>
|
|---|
| 409 | <arglist></arglist>
|
|---|
| 410 | </member>
|
|---|
| 411 | <member kind="function">
|
|---|
| 412 | <type>def</type>
|
|---|
| 413 | <name>equilibrate</name>
|
|---|
| 414 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 415 | <anchor>8f2bc300bdb70ea4bf5b62a0683bdec1</anchor>
|
|---|
| 416 | <arglist></arglist>
|
|---|
| 417 | </member>
|
|---|
| 418 | <member kind="function">
|
|---|
| 419 | <type>def</type>
|
|---|
| 420 | <name>sweeps</name>
|
|---|
| 421 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 422 | <anchor>753772a0e2426f82d70b45b2d5ae0ea2</anchor>
|
|---|
| 423 | <arglist></arglist>
|
|---|
| 424 | </member>
|
|---|
| 425 | <member kind="function">
|
|---|
| 426 | <type>def</type>
|
|---|
| 427 | <name>sweep</name>
|
|---|
| 428 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 429 | <anchor>e88249691d745084945476d4f7cb3f83</anchor>
|
|---|
| 430 | <arglist></arglist>
|
|---|
| 431 | </member>
|
|---|
| 432 | <member kind="function">
|
|---|
| 433 | <type>def</type>
|
|---|
| 434 | <name>metropolis</name>
|
|---|
| 435 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 436 | <anchor>6ca780076d74a74b4c330a4eab6552a8</anchor>
|
|---|
| 437 | <arglist></arglist>
|
|---|
| 438 | </member>
|
|---|
| 439 | <member kind="variable" protection="private">
|
|---|
| 440 | <type></type>
|
|---|
| 441 | <name>__defSweeps</name>
|
|---|
| 442 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 443 | <anchor>d933a732a652ab169b75ab60a865f4c9</anchor>
|
|---|
| 444 | <arglist></arglist>
|
|---|
| 445 | </member>
|
|---|
| 446 | <member kind="variable" protection="private">
|
|---|
| 447 | <type></type>
|
|---|
| 448 | <name>__defEqui</name>
|
|---|
| 449 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 450 | <anchor>4afff0a2e51ca1aec49663057c48d500</anchor>
|
|---|
| 451 | <arglist></arglist>
|
|---|
| 452 | </member>
|
|---|
| 453 | <member kind="variable" protection="private">
|
|---|
| 454 | <type></type>
|
|---|
| 455 | <name>__univ</name>
|
|---|
| 456 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 457 | <anchor>bbff71fb27fe659ffe1279e9fa4d3bdf</anchor>
|
|---|
| 458 | <arglist></arglist>
|
|---|
| 459 | </member>
|
|---|
| 460 | <member kind="variable" protection="private">
|
|---|
| 461 | <type></type>
|
|---|
| 462 | <name>__acc</name>
|
|---|
| 463 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 464 | <anchor>6b21bfb4832253022c98f27a735ca52b</anchor>
|
|---|
| 465 | <arglist></arglist>
|
|---|
| 466 | </member>
|
|---|
| 467 | <member kind="variable" protection="private">
|
|---|
| 468 | <type></type>
|
|---|
| 469 | <name>__performedSweeps</name>
|
|---|
| 470 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 471 | <anchor>a70d5dd3e5f92a503a5923d5d0c4a20f</anchor>
|
|---|
| 472 | <arglist></arglist>
|
|---|
| 473 | </member>
|
|---|
| 474 | <member kind="variable" protection="private">
|
|---|
| 475 | <type></type>
|
|---|
| 476 | <name>__minEnergy</name>
|
|---|
| 477 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 478 | <anchor>8dc79da4542d780787f3b74db02a4211</anchor>
|
|---|
| 479 | <arglist></arglist>
|
|---|
| 480 | </member>
|
|---|
| 481 | <member kind="variable" protection="private">
|
|---|
| 482 | <type></type>
|
|---|
| 483 | <name>__l</name>
|
|---|
| 484 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 485 | <anchor>554d655af2979d965c62e4f115e85ed6</anchor>
|
|---|
| 486 | <arglist></arglist>
|
|---|
| 487 | </member>
|
|---|
| 488 | <member kind="variable" protection="private">
|
|---|
| 489 | <type></type>
|
|---|
| 490 | <name>__minCounter</name>
|
|---|
| 491 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 492 | <anchor>d899e2fce6d27c863b6f5fefdab4ae5b</anchor>
|
|---|
| 493 | <arglist></arglist>
|
|---|
| 494 | </member>
|
|---|
| 495 | <member kind="variable" protection="private">
|
|---|
| 496 | <type></type>
|
|---|
| 497 | <name>__weight</name>
|
|---|
| 498 | <anchorfile>classalgorithms_1_1CanonicalMonteCarlo.html</anchorfile>
|
|---|
| 499 | <anchor>062adc9555c3fcf7104ff00c7560b6aa</anchor>
|
|---|
| 500 | <arglist></arglist>
|
|---|
| 501 | </member>
|
|---|
| 502 | </compound>
|
|---|
| 503 | <compound kind="namespace">
|
|---|
| 504 | <name>main</name>
|
|---|
| 505 | <filename>namespacemain.html</filename>
|
|---|
| 506 | <member kind="variable" static="yes">
|
|---|
| 507 | <type>string</type>
|
|---|
| 508 | <name>usage</name>
|
|---|
| 509 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 510 | <anchor>d363bdabd6492750c79e74bb23e01005</anchor>
|
|---|
| 511 | <arglist></arglist>
|
|---|
| 512 | </member>
|
|---|
| 513 | <member kind="variable" static="yes">
|
|---|
| 514 | <type>tuple</type>
|
|---|
| 515 | <name>parser</name>
|
|---|
| 516 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 517 | <anchor>6596d20927a9196bbb33aef704e88297</anchor>
|
|---|
| 518 | <arglist></arglist>
|
|---|
| 519 | </member>
|
|---|
| 520 | <member kind="variable" static="yes">
|
|---|
| 521 | <type>string</type>
|
|---|
| 522 | <name>help</name>
|
|---|
| 523 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 524 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 525 | <arglist></arglist>
|
|---|
| 526 | </member>
|
|---|
| 527 | <member kind="variable" static="yes">
|
|---|
| 528 | <type>string</type>
|
|---|
| 529 | <name>help</name>
|
|---|
| 530 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 531 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 532 | <arglist></arglist>
|
|---|
| 533 | </member>
|
|---|
| 534 | <member kind="variable" static="yes">
|
|---|
| 535 | <type>string</type>
|
|---|
| 536 | <name>help</name>
|
|---|
| 537 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 538 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 539 | <arglist></arglist>
|
|---|
| 540 | </member>
|
|---|
| 541 | <member kind="variable" static="yes">
|
|---|
| 542 | <type>string</type>
|
|---|
| 543 | <name>help</name>
|
|---|
| 544 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 545 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 546 | <arglist></arglist>
|
|---|
| 547 | </member>
|
|---|
| 548 | <member kind="variable" static="yes">
|
|---|
| 549 | <type>string</type>
|
|---|
| 550 | <name>help</name>
|
|---|
| 551 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 552 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 553 | <arglist></arglist>
|
|---|
| 554 | </member>
|
|---|
| 555 | <member kind="variable" static="yes">
|
|---|
| 556 | <type>string</type>
|
|---|
| 557 | <name>help</name>
|
|---|
| 558 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 559 | <anchor>c7d49462b57b1cc0d6a0b5c909e9e65e</anchor>
|
|---|
| 560 | <arglist></arglist>
|
|---|
| 561 | </member>
|
|---|
| 562 | <member kind="variable" static="yes">
|
|---|
| 563 | <type>list</type>
|
|---|
| 564 | <name>seqFileName</name>
|
|---|
| 565 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 566 | <anchor>2a4367ed60a67e069e0b5d9788a10801</anchor>
|
|---|
| 567 | <arglist></arglist>
|
|---|
| 568 | </member>
|
|---|
| 569 | <member kind="variable" static="yes">
|
|---|
| 570 | <type>tuple</type>
|
|---|
| 571 | <name>myUniv</name>
|
|---|
| 572 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 573 | <anchor>d7a3fa6b22dda1cbd41815dd2a5a6f76</anchor>
|
|---|
| 574 | <arglist></arglist>
|
|---|
| 575 | </member>
|
|---|
| 576 | <member kind="variable" static="yes">
|
|---|
| 577 | <type>tuple</type>
|
|---|
| 578 | <name>p1</name>
|
|---|
| 579 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 580 | <anchor>08bd12d1a3d5f6b17f7c12559b79e87c</anchor>
|
|---|
| 581 | <arglist></arglist>
|
|---|
| 582 | </member>
|
|---|
| 583 | <member kind="variable" static="yes">
|
|---|
| 584 | <type>float</type>
|
|---|
| 585 | <name>T</name>
|
|---|
| 586 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 587 | <anchor>98e836cf59f46c8f187e64eceb62bad9</anchor>
|
|---|
| 588 | <arglist></arglist>
|
|---|
| 589 | </member>
|
|---|
| 590 | <member kind="variable" static="yes">
|
|---|
| 591 | <type>tuple</type>
|
|---|
| 592 | <name>ts</name>
|
|---|
| 593 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 594 | <anchor>7c1ab8aaf906bf136a0aad2fc320c099</anchor>
|
|---|
| 595 | <arglist></arglist>
|
|---|
| 596 | </member>
|
|---|
| 597 | <member kind="variable" static="yes">
|
|---|
| 598 | <type>tuple</type>
|
|---|
| 599 | <name>t1</name>
|
|---|
| 600 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 601 | <anchor>1c35537490e5d4cc72ea798d80ee7578</anchor>
|
|---|
| 602 | <arglist></arglist>
|
|---|
| 603 | </member>
|
|---|
| 604 | <member kind="variable" static="yes">
|
|---|
| 605 | <type>tuple</type>
|
|---|
| 606 | <name>te</name>
|
|---|
| 607 | <anchorfile>namespacemain.html</anchorfile>
|
|---|
| 608 | <anchor>208f1ab948fb0311a3199e58cc777d7c</anchor>
|
|---|
| 609 | <arglist></arglist>
|
|---|
| 610 | </member>
|
|---|
| 611 | </compound>
|
|---|
| 612 | <compound kind="namespace">
|
|---|
| 613 | <name>math</name>
|
|---|
| 614 | <filename>namespacemath.html</filename>
|
|---|
| 615 | </compound>
|
|---|
| 616 | <compound kind="namespace">
|
|---|
| 617 | <name>protein</name>
|
|---|
| 618 | <filename>namespaceprotein.html</filename>
|
|---|
| 619 | <class kind="class">protein::Atom</class>
|
|---|
| 620 | <class kind="class">protein::Residue</class>
|
|---|
| 621 | <class kind="class">protein::Protein</class>
|
|---|
| 622 | <member kind="function">
|
|---|
| 623 | <type>def</type>
|
|---|
| 624 | <name>nursvr</name>
|
|---|
| 625 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 626 | <anchor>6f178e1c980241ce2e8ec9ba807492e8</anchor>
|
|---|
| 627 | <arglist></arglist>
|
|---|
| 628 | </member>
|
|---|
| 629 | <member kind="variable" static="yes">
|
|---|
| 630 | <type>float</type>
|
|---|
| 631 | <name>crd</name>
|
|---|
| 632 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 633 | <anchor>ccf520a3c785c7e1da5a1f6c369c66a7</anchor>
|
|---|
| 634 | <arglist></arglist>
|
|---|
| 635 | </member>
|
|---|
| 636 | <member kind="variable" static="yes">
|
|---|
| 637 | <type>string</type>
|
|---|
| 638 | <name>libdir</name>
|
|---|
| 639 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 640 | <anchor>55146e5ace572b13bd76966bb56a4dba</anchor>
|
|---|
| 641 | <arglist></arglist>
|
|---|
| 642 | </member>
|
|---|
| 643 | <member kind="variable" static="yes">
|
|---|
| 644 | <type>tuple</type>
|
|---|
| 645 | <name>p1</name>
|
|---|
| 646 | <anchorfile>namespaceprotein.html</anchorfile>
|
|---|
| 647 | <anchor>214ebeb5b08a560b5283cb08eeb21bc0</anchor>
|
|---|
| 648 | <arglist></arglist>
|
|---|
| 649 | </member>
|
|---|
| 650 | </compound>
|
|---|
| 651 | <compound kind="class">
|
|---|
| 652 | <name>protein::Atom</name>
|
|---|
| 653 | <filename>classprotein_1_1Atom.html</filename>
|
|---|
| 654 | <member kind="function">
|
|---|
| 655 | <type>def</type>
|
|---|
| 656 | <name>__init__</name>
|
|---|
| 657 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 658 | <anchor>7c5fceb449a6f6c1cb35a5589c980bff</anchor>
|
|---|
| 659 | <arglist></arglist>
|
|---|
| 660 | </member>
|
|---|
| 661 | <member kind="function">
|
|---|
| 662 | <type>def</type>
|
|---|
| 663 | <name>position</name>
|
|---|
| 664 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 665 | <anchor>b4f5fcb84786cd6f59d66632b93988dc</anchor>
|
|---|
| 666 | <arglist></arglist>
|
|---|
| 667 | </member>
|
|---|
| 668 | <member kind="function">
|
|---|
| 669 | <type>def</type>
|
|---|
| 670 | <name>charge</name>
|
|---|
| 671 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 672 | <anchor>0b5932fd6cec2d20a7286840aa689616</anchor>
|
|---|
| 673 | <arglist></arglist>
|
|---|
| 674 | </member>
|
|---|
| 675 | <member kind="function">
|
|---|
| 676 | <type>def</type>
|
|---|
| 677 | <name>radius</name>
|
|---|
| 678 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 679 | <anchor>c8b0c9371c3c1ba4888e056920d3354e</anchor>
|
|---|
| 680 | <arglist></arglist>
|
|---|
| 681 | </member>
|
|---|
| 682 | <member kind="function">
|
|---|
| 683 | <type>def</type>
|
|---|
| 684 | <name>name</name>
|
|---|
| 685 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 686 | <anchor>1dfdc07d0905af53b846e64069ffb751</anchor>
|
|---|
| 687 | <arglist></arglist>
|
|---|
| 688 | </member>
|
|---|
| 689 | <member kind="function">
|
|---|
| 690 | <type>def</type>
|
|---|
| 691 | <name>__str__</name>
|
|---|
| 692 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 693 | <anchor>db9fc39fd29a30aeb2a6bdf8bbc2bcc5</anchor>
|
|---|
| 694 | <arglist></arglist>
|
|---|
| 695 | </member>
|
|---|
| 696 | <member kind="variable" protection="private">
|
|---|
| 697 | <type></type>
|
|---|
| 698 | <name>__id</name>
|
|---|
| 699 | <anchorfile>classprotein_1_1Atom.html</anchorfile>
|
|---|
| 700 | <anchor>a6698d931f90d0d2cbf0dbd099b7ec3b</anchor>
|
|---|
| 701 | <arglist></arglist>
|
|---|
| 702 | </member>
|
|---|
| 703 | </compound>
|
|---|
| 704 | <compound kind="class">
|
|---|
| 705 | <name>protein::Residue</name>
|
|---|
| 706 | <filename>classprotein_1_1Residue.html</filename>
|
|---|
| 707 | <member kind="function">
|
|---|
| 708 | <type>def</type>
|
|---|
| 709 | <name>__init__</name>
|
|---|
| 710 | <anchorfile>classprotein_1_1Residue.html</anchorfile>
|
|---|
| 711 | <anchor>1dd8f41d52d51b6602dc1a9a6786b454</anchor>
|
|---|
| 712 | <arglist></arglist>
|
|---|
| 713 | </member>
|
|---|
| 714 | <member kind="function">
|
|---|
| 715 | <type>def</type>
|
|---|
| 716 | <name>atoms</name>
|
|---|
| 717 | <anchorfile>classprotein_1_1Residue.html</anchorfile>
|
|---|
| 718 | <anchor>d9e7013d19a24c4b81d07aa69a594c76</anchor>
|
|---|
| 719 | <arglist></arglist>
|
|---|
| 720 | </member>
|
|---|
| 721 | <member kind="variable" protection="private">
|
|---|
| 722 | <type></type>
|
|---|
| 723 | <name>__id</name>
|
|---|
| 724 | <anchorfile>classprotein_1_1Residue.html</anchorfile>
|
|---|
| 725 | <anchor>6d7fef994a951a3041e7803453ad28d2</anchor>
|
|---|
| 726 | <arglist></arglist>
|
|---|
| 727 | </member>
|
|---|
| 728 | </compound>
|
|---|
| 729 | <compound kind="class">
|
|---|
| 730 | <name>protein::Protein</name>
|
|---|
| 731 | <filename>classprotein_1_1Protein.html</filename>
|
|---|
| 732 | <member kind="function">
|
|---|
| 733 | <type>def</type>
|
|---|
| 734 | <name>__init__</name>
|
|---|
| 735 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 736 | <anchor>798e43c469433451a8f5b3b7a72020a2</anchor>
|
|---|
| 737 | <arglist></arglist>
|
|---|
| 738 | </member>
|
|---|
| 739 | <member kind="function">
|
|---|
| 740 | <type>def</type>
|
|---|
| 741 | <name>setOrigin</name>
|
|---|
| 742 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 743 | <anchor>0d35f51a5bd4fd9df4ef8f08754aad89</anchor>
|
|---|
| 744 | <arglist></arglist>
|
|---|
| 745 | </member>
|
|---|
| 746 | <member kind="function">
|
|---|
| 747 | <type>def</type>
|
|---|
| 748 | <name>origin</name>
|
|---|
| 749 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 750 | <anchor>74b49b343f637f7d438289c1c6666491</anchor>
|
|---|
| 751 | <arglist></arglist>
|
|---|
| 752 | </member>
|
|---|
| 753 | <member kind="function">
|
|---|
| 754 | <type>def</type>
|
|---|
| 755 | <name>getDihedral</name>
|
|---|
| 756 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 757 | <anchor>c6e1e49b82c1a1e7b712426282540f2c</anchor>
|
|---|
| 758 | <arglist></arglist>
|
|---|
| 759 | </member>
|
|---|
| 760 | <member kind="function">
|
|---|
| 761 | <type>def</type>
|
|---|
| 762 | <name>findResidue</name>
|
|---|
| 763 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 764 | <anchor>77f22c3c282dd759efca28fc668f3582</anchor>
|
|---|
| 765 | <arglist></arglist>
|
|---|
| 766 | </member>
|
|---|
| 767 | <member kind="function">
|
|---|
| 768 | <type>def</type>
|
|---|
| 769 | <name>atoms</name>
|
|---|
| 770 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 771 | <anchor>6fce2702a3863770fe2bdd0c63221421</anchor>
|
|---|
| 772 | <arglist></arglist>
|
|---|
| 773 | </member>
|
|---|
| 774 | <member kind="function">
|
|---|
| 775 | <type>def</type>
|
|---|
| 776 | <name>residues</name>
|
|---|
| 777 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 778 | <anchor>65f225dd68c0d3d9886d92db9d56560d</anchor>
|
|---|
| 779 | <arglist></arglist>
|
|---|
| 780 | </member>
|
|---|
| 781 | <member kind="function">
|
|---|
| 782 | <type>def</type>
|
|---|
| 783 | <name>id</name>
|
|---|
| 784 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 785 | <anchor>45aa03e958de4a7df51f3e210f0ab054</anchor>
|
|---|
| 786 | <arglist></arglist>
|
|---|
| 787 | </member>
|
|---|
| 788 | <member kind="function">
|
|---|
| 789 | <type>def</type>
|
|---|
| 790 | <name>strand</name>
|
|---|
| 791 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 792 | <anchor>51bedbc8c4a966019d93194f39f543ce</anchor>
|
|---|
| 793 | <arglist></arglist>
|
|---|
| 794 | </member>
|
|---|
| 795 | <member kind="function">
|
|---|
| 796 | <type>def</type>
|
|---|
| 797 | <name>directionVector</name>
|
|---|
| 798 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 799 | <anchor>c5cdd2d012357974ce7001e34f79fbd1</anchor>
|
|---|
| 800 | <arglist></arglist>
|
|---|
| 801 | </member>
|
|---|
| 802 | <member kind="function">
|
|---|
| 803 | <type>def</type>
|
|---|
| 804 | <name>contacts</name>
|
|---|
| 805 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 806 | <anchor>faf50658d2655b02c81bbb60fdbf1dc0</anchor>
|
|---|
| 807 | <arglist></arglist>
|
|---|
| 808 | </member>
|
|---|
| 809 | <member kind="function">
|
|---|
| 810 | <type>def</type>
|
|---|
| 811 | <name>hbond</name>
|
|---|
| 812 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 813 | <anchor>e17650e6aaa144f72ed7e37d341d8ba3</anchor>
|
|---|
| 814 | <arglist></arglist>
|
|---|
| 815 | </member>
|
|---|
| 816 | <member kind="function">
|
|---|
| 817 | <type>def</type>
|
|---|
| 818 | <name>energy</name>
|
|---|
| 819 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 820 | <anchor>e9883d7c14fffc8245e40d2e3ce5aa6a</anchor>
|
|---|
| 821 | <arglist></arglist>
|
|---|
| 822 | </member>
|
|---|
| 823 | <member kind="function">
|
|---|
| 824 | <type>def</type>
|
|---|
| 825 | <name>rgyr</name>
|
|---|
| 826 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 827 | <anchor>e8987b2d89b5df2e36e5360249270b32</anchor>
|
|---|
| 828 | <arglist></arglist>
|
|---|
| 829 | </member>
|
|---|
| 830 | <member kind="function">
|
|---|
| 831 | <type>def</type>
|
|---|
| 832 | <name>rmsdfun</name>
|
|---|
| 833 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 834 | <anchor>76af119bf485f72c5f19354fac09779e</anchor>
|
|---|
| 835 | <arglist></arglist>
|
|---|
| 836 | </member>
|
|---|
| 837 | <member kind="function">
|
|---|
| 838 | <type>def</type>
|
|---|
| 839 | <name>savePDB</name>
|
|---|
| 840 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 841 | <anchor>963fb2c8ec522527edd29835ea553dec</anchor>
|
|---|
| 842 | <arglist></arglist>
|
|---|
| 843 | </member>
|
|---|
| 844 | <member kind="function">
|
|---|
| 845 | <type>def</type>
|
|---|
| 846 | <name>saveVariables</name>
|
|---|
| 847 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 848 | <anchor>3f9645153f34d1d70ae4d37329f3b513</anchor>
|
|---|
| 849 | <arglist></arglist>
|
|---|
| 850 | </member>
|
|---|
| 851 | <member kind="function">
|
|---|
| 852 | <type>def</type>
|
|---|
| 853 | <name>zimmer</name>
|
|---|
| 854 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 855 | <anchor>31268dbb730b314a517891123332afb5</anchor>
|
|---|
| 856 | <arglist></arglist>
|
|---|
| 857 | </member>
|
|---|
| 858 | <member kind="function">
|
|---|
| 859 | <type>def</type>
|
|---|
| 860 | <name>__len__</name>
|
|---|
| 861 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 862 | <anchor>03e827404d96a6e924d2d72669f90edd</anchor>
|
|---|
| 863 | <arglist></arglist>
|
|---|
| 864 | </member>
|
|---|
| 865 | <member kind="variable" protection="private">
|
|---|
| 866 | <type></type>
|
|---|
| 867 | <name>__id</name>
|
|---|
| 868 | <anchorfile>classprotein_1_1Protein.html</anchorfile>
|
|---|
| 869 | <anchor>e5cd5a64e8114e82f1b1e0e3fa69348d</anchor>
|
|---|
| 870 | <arglist></arglist>
|
|---|
| 871 | </member>
|
|---|
| 872 | </compound>
|
|---|
| 873 | <compound kind="namespace">
|
|---|
| 874 | <name>random</name>
|
|---|
| 875 | <filename>namespacerandom.html</filename>
|
|---|
| 876 | </compound>
|
|---|
| 877 | <compound kind="namespace">
|
|---|
| 878 | <name>restoreexclpoint</name>
|
|---|
| 879 | <filename>namespacerestoreexclpoint.html</filename>
|
|---|
| 880 | </compound>
|
|---|
| 881 | <compound kind="namespace">
|
|---|
| 882 | <name>rmexclpoint</name>
|
|---|
| 883 | <filename>namespacermexclpoint.html</filename>
|
|---|
| 884 | <member kind="variable" static="yes">
|
|---|
| 885 | <type>string</type>
|
|---|
| 886 | <name>patternstring</name>
|
|---|
| 887 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 888 | <anchor>86242b4a75e4538ed51da15642c85e28</anchor>
|
|---|
| 889 | <arglist></arglist>
|
|---|
| 890 | </member>
|
|---|
| 891 | <member kind="variable" static="yes">
|
|---|
| 892 | <type>string</type>
|
|---|
| 893 | <name>patternstring2</name>
|
|---|
| 894 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 895 | <anchor>c3f5a790770fb7300f387adc8759f769</anchor>
|
|---|
| 896 | <arglist></arglist>
|
|---|
| 897 | </member>
|
|---|
| 898 | <member kind="variable" static="yes">
|
|---|
| 899 | <type>string</type>
|
|---|
| 900 | <name>patternstring3</name>
|
|---|
| 901 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 902 | <anchor>95065921525bd513903b35af66076eaf</anchor>
|
|---|
| 903 | <arglist></arglist>
|
|---|
| 904 | </member>
|
|---|
| 905 | <member kind="variable" static="yes">
|
|---|
| 906 | <type>tuple</type>
|
|---|
| 907 | <name>pattern</name>
|
|---|
| 908 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 909 | <anchor>7152c4b3e9458952f0f7e807a8fcc118</anchor>
|
|---|
| 910 | <arglist></arglist>
|
|---|
| 911 | </member>
|
|---|
| 912 | <member kind="variable" static="yes">
|
|---|
| 913 | <type>tuple</type>
|
|---|
| 914 | <name>pattern2</name>
|
|---|
| 915 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 916 | <anchor>1eefe42773502750ba26b29e9daaf12a</anchor>
|
|---|
| 917 | <arglist></arglist>
|
|---|
| 918 | </member>
|
|---|
| 919 | <member kind="variable" static="yes">
|
|---|
| 920 | <type>tuple</type>
|
|---|
| 921 | <name>pattern3</name>
|
|---|
| 922 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 923 | <anchor>c4bff9bcc3a56186ffc45bea0ed74fcb</anchor>
|
|---|
| 924 | <arglist></arglist>
|
|---|
| 925 | </member>
|
|---|
| 926 | <member kind="variable" static="yes">
|
|---|
| 927 | <type>tuple</type>
|
|---|
| 928 | <name>f</name>
|
|---|
| 929 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 930 | <anchor>30f86c4fa6e0250721c2e17d0a71e73a</anchor>
|
|---|
| 931 | <arglist></arglist>
|
|---|
| 932 | </member>
|
|---|
| 933 | <member kind="variable" static="yes">
|
|---|
| 934 | <type>tuple</type>
|
|---|
| 935 | <name>s</name>
|
|---|
| 936 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 937 | <anchor>9f0bd653bab192dad5ad9e71c198277f</anchor>
|
|---|
| 938 | <arglist></arglist>
|
|---|
| 939 | </member>
|
|---|
| 940 | <member kind="variable" static="yes">
|
|---|
| 941 | <type>tuple</type>
|
|---|
| 942 | <name>t</name>
|
|---|
| 943 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 944 | <anchor>5eea3706a180934d1eb7cf55b6cc8902</anchor>
|
|---|
| 945 | <arglist></arglist>
|
|---|
| 946 | </member>
|
|---|
| 947 | <member kind="variable" static="yes">
|
|---|
| 948 | <type>tuple</type>
|
|---|
| 949 | <name>t</name>
|
|---|
| 950 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 951 | <anchor>5eea3706a180934d1eb7cf55b6cc8902</anchor>
|
|---|
| 952 | <arglist></arglist>
|
|---|
| 953 | </member>
|
|---|
| 954 | <member kind="variable" static="yes">
|
|---|
| 955 | <type>tuple</type>
|
|---|
| 956 | <name>t</name>
|
|---|
| 957 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 958 | <anchor>5eea3706a180934d1eb7cf55b6cc8902</anchor>
|
|---|
| 959 | <arglist></arglist>
|
|---|
| 960 | </member>
|
|---|
| 961 | <member kind="variable" static="yes">
|
|---|
| 962 | <type>tuple</type>
|
|---|
| 963 | <name>f</name>
|
|---|
| 964 | <anchorfile>namespacermexclpoint.html</anchorfile>
|
|---|
| 965 | <anchor>30f86c4fa6e0250721c2e17d0a71e73a</anchor>
|
|---|
| 966 | <arglist></arglist>
|
|---|
| 967 | </member>
|
|---|
| 968 | </compound>
|
|---|
| 969 | <compound kind="namespace">
|
|---|
| 970 | <name>smmp</name>
|
|---|
| 971 | <filename>namespacesmmp.html</filename>
|
|---|
| 972 | </compound>
|
|---|
| 973 | <compound kind="namespace">
|
|---|
| 974 | <name>test</name>
|
|---|
| 975 | <filename>namespacetest.html</filename>
|
|---|
| 976 | <member kind="variable" static="yes">
|
|---|
| 977 | <type>string</type>
|
|---|
| 978 | <name>libdir</name>
|
|---|
| 979 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 980 | <anchor>6fa2049667bd4ad558f12fa937b0f371</anchor>
|
|---|
| 981 | <arglist></arglist>
|
|---|
| 982 | </member>
|
|---|
| 983 | <member kind="variable" static="yes">
|
|---|
| 984 | <type>string</type>
|
|---|
| 985 | <name>grpn</name>
|
|---|
| 986 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 987 | <anchor>45640d02312df311aa623e0e86f02b1a</anchor>
|
|---|
| 988 | <arglist></arglist>
|
|---|
| 989 | </member>
|
|---|
| 990 | <member kind="variable" static="yes">
|
|---|
| 991 | <type>string</type>
|
|---|
| 992 | <name>grpc</name>
|
|---|
| 993 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 994 | <anchor>fdce7a7b24d00b30a07ba3e65a00e5a0</anchor>
|
|---|
| 995 | <arglist></arglist>
|
|---|
| 996 | </member>
|
|---|
| 997 | <member kind="variable" static="yes">
|
|---|
| 998 | <type>int</type>
|
|---|
| 999 | <name>nequi</name>
|
|---|
| 1000 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1001 | <anchor>df2298f8864993aebf9ba53f812ee595</anchor>
|
|---|
| 1002 | <arglist></arglist>
|
|---|
| 1003 | </member>
|
|---|
| 1004 | <member kind="variable" static="yes">
|
|---|
| 1005 | <type>int</type>
|
|---|
| 1006 | <name>nswp</name>
|
|---|
| 1007 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1008 | <anchor>155edc50375b57e5cdb2b81de24652a7</anchor>
|
|---|
| 1009 | <arglist></arglist>
|
|---|
| 1010 | </member>
|
|---|
| 1011 | <member kind="variable" static="yes">
|
|---|
| 1012 | <type>int</type>
|
|---|
| 1013 | <name>nmes</name>
|
|---|
| 1014 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1015 | <anchor>565f363ab69b2fcbb062da2ad67f3569</anchor>
|
|---|
| 1016 | <arglist></arglist>
|
|---|
| 1017 | </member>
|
|---|
| 1018 | <member kind="variable" static="yes">
|
|---|
| 1019 | <type>int</type>
|
|---|
| 1020 | <name>Tmax</name>
|
|---|
| 1021 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1022 | <anchor>b9451198b74ce8b65df7b61e93e27821</anchor>
|
|---|
| 1023 | <arglist></arglist>
|
|---|
| 1024 | </member>
|
|---|
| 1025 | <member kind="variable" static="yes">
|
|---|
| 1026 | <type>int</type>
|
|---|
| 1027 | <name>Tmin</name>
|
|---|
| 1028 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1029 | <anchor>4ffceb0284a3e2cadf27ed155dbd555b</anchor>
|
|---|
| 1030 | <arglist></arglist>
|
|---|
| 1031 | </member>
|
|---|
| 1032 | <member kind="variable" static="yes">
|
|---|
| 1033 | <type>int</type>
|
|---|
| 1034 | <name>T</name>
|
|---|
| 1035 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1036 | <anchor>021821f6c47ffff20b56e91dfb9ac63e</anchor>
|
|---|
| 1037 | <arglist></arglist>
|
|---|
| 1038 | </member>
|
|---|
| 1039 | <member kind="variable" static="yes">
|
|---|
| 1040 | <type>tuple</type>
|
|---|
| 1041 | <name>timeseries</name>
|
|---|
| 1042 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1043 | <anchor>df0b843e5561c2d2def0ecedc181b618</anchor>
|
|---|
| 1044 | <arglist></arglist>
|
|---|
| 1045 | </member>
|
|---|
| 1046 | <member kind="variable" static="yes">
|
|---|
| 1047 | <type>int</type>
|
|---|
| 1048 | <name>iabin</name>
|
|---|
| 1049 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1050 | <anchor>6ee3c009f0ac3ebaf75897d0d09f1c44</anchor>
|
|---|
| 1051 | <arglist></arglist>
|
|---|
| 1052 | </member>
|
|---|
| 1053 | <member kind="variable" static="yes">
|
|---|
| 1054 | <type>tuple</type>
|
|---|
| 1055 | <name>eol</name>
|
|---|
| 1056 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1057 | <anchor>5d5bdfad6a87904ae6efd9d69ef3b1a0</anchor>
|
|---|
| 1058 | <arglist></arglist>
|
|---|
| 1059 | </member>
|
|---|
| 1060 | <member kind="variable" static="yes">
|
|---|
| 1061 | <type>int</type>
|
|---|
| 1062 | <name>acc</name>
|
|---|
| 1063 | <anchorfile>namespacetest.html</anchorfile>
|
|---|
| 1064 | <anchor>ffde8edcabf285406c61e3823d023e39</anchor>
|
|---|
| 1065 | <arglist></arglist>
|
|---|
| 1066 | </member>
|
|---|
| 1067 | </compound>
|
|---|
| 1068 | <compound kind="namespace">
|
|---|
| 1069 | <name>time</name>
|
|---|
| 1070 | <filename>namespacetime.html</filename>
|
|---|
| 1071 | </compound>
|
|---|
| 1072 | <compound kind="namespace">
|
|---|
| 1073 | <name>universe</name>
|
|---|
| 1074 | <filename>namespaceuniverse.html</filename>
|
|---|
| 1075 | <class kind="class">universe::Universe</class>
|
|---|
| 1076 | </compound>
|
|---|
| 1077 | <compound kind="class">
|
|---|
| 1078 | <name>universe::Universe</name>
|
|---|
| 1079 | <filename>classuniverse_1_1Universe.html</filename>
|
|---|
| 1080 | <member kind="function">
|
|---|
| 1081 | <type>def</type>
|
|---|
| 1082 | <name>__init__</name>
|
|---|
| 1083 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1084 | <anchor>53c2f2d66f53ee3d9905a5776f1d9e2b</anchor>
|
|---|
| 1085 | <arglist></arglist>
|
|---|
| 1086 | </member>
|
|---|
| 1087 | <member kind="function">
|
|---|
| 1088 | <type>def</type>
|
|---|
| 1089 | <name>add</name>
|
|---|
| 1090 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1091 | <anchor>075b5c85b807aca5e55fc1ec96f6dfba</anchor>
|
|---|
| 1092 | <arglist></arglist>
|
|---|
| 1093 | </member>
|
|---|
| 1094 | <member kind="function">
|
|---|
| 1095 | <type>def</type>
|
|---|
| 1096 | <name>energy</name>
|
|---|
| 1097 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1098 | <anchor>a74332af5046d995242a8aad7a83adee</anchor>
|
|---|
| 1099 | <arglist></arglist>
|
|---|
| 1100 | </member>
|
|---|
| 1101 | <member kind="function">
|
|---|
| 1102 | <type>def</type>
|
|---|
| 1103 | <name>rgyr</name>
|
|---|
| 1104 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1105 | <anchor>8abb97f3b1d9725c17a46df7442608cf</anchor>
|
|---|
| 1106 | <arglist></arglist>
|
|---|
| 1107 | </member>
|
|---|
| 1108 | <member kind="function">
|
|---|
| 1109 | <type>def</type>
|
|---|
| 1110 | <name>endToEnd</name>
|
|---|
| 1111 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1112 | <anchor>2dc096f407d0ee8a37e51b981848138c</anchor>
|
|---|
| 1113 | <arglist></arglist>
|
|---|
| 1114 | </member>
|
|---|
| 1115 | <member kind="function">
|
|---|
| 1116 | <type>def</type>
|
|---|
| 1117 | <name>hbond</name>
|
|---|
| 1118 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1119 | <anchor>fe3e07ca52b9db28c9655f5a2655e80b</anchor>
|
|---|
| 1120 | <arglist></arglist>
|
|---|
| 1121 | </member>
|
|---|
| 1122 | <member kind="function">
|
|---|
| 1123 | <type>def</type>
|
|---|
| 1124 | <name>helix</name>
|
|---|
| 1125 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1126 | <anchor>1ce2036eade748e536b868f3d8b6bdab</anchor>
|
|---|
| 1127 | <arglist></arglist>
|
|---|
| 1128 | </member>
|
|---|
| 1129 | <member kind="function">
|
|---|
| 1130 | <type>def</type>
|
|---|
| 1131 | <name>sheet</name>
|
|---|
| 1132 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1133 | <anchor>a5a47ce0c1c2680fb02dc02dcdebbc1d</anchor>
|
|---|
| 1134 | <arglist></arglist>
|
|---|
| 1135 | </member>
|
|---|
| 1136 | <member kind="function">
|
|---|
| 1137 | <type>def</type>
|
|---|
| 1138 | <name>temperature</name>
|
|---|
| 1139 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1140 | <anchor>b6ed4a93fd925168d951cb80f8a2380a</anchor>
|
|---|
| 1141 | <arglist></arglist>
|
|---|
| 1142 | </member>
|
|---|
| 1143 | <member kind="function">
|
|---|
| 1144 | <type>def</type>
|
|---|
| 1145 | <name>setTemperature</name>
|
|---|
| 1146 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1147 | <anchor>44d41532870041010153bdeda7379b8b</anchor>
|
|---|
| 1148 | <arglist></arglist>
|
|---|
| 1149 | </member>
|
|---|
| 1150 | <member kind="function">
|
|---|
| 1151 | <type>def</type>
|
|---|
| 1152 | <name>boxSize</name>
|
|---|
| 1153 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1154 | <anchor>2285c4856a474d62e034a69a559d7d25</anchor>
|
|---|
| 1155 | <arglist></arglist>
|
|---|
| 1156 | </member>
|
|---|
| 1157 | <member kind="function">
|
|---|
| 1158 | <type>def</type>
|
|---|
| 1159 | <name>objects</name>
|
|---|
| 1160 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1161 | <anchor>624a6a72491cdba03e0c6e3d80c659db</anchor>
|
|---|
| 1162 | <arglist></arglist>
|
|---|
| 1163 | </member>
|
|---|
| 1164 | <member kind="function">
|
|---|
| 1165 | <type>def</type>
|
|---|
| 1166 | <name>save</name>
|
|---|
| 1167 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1168 | <anchor>3bdf145a14c780e7ef9e7b781c71ae63</anchor>
|
|---|
| 1169 | <arglist></arglist>
|
|---|
| 1170 | </member>
|
|---|
| 1171 | <member kind="variable" protection="private">
|
|---|
| 1172 | <type></type>
|
|---|
| 1173 | <name>__objects</name>
|
|---|
| 1174 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1175 | <anchor>6645c79f63c0e175396d3f2e588d4fd8</anchor>
|
|---|
| 1176 | <arglist></arglist>
|
|---|
| 1177 | </member>
|
|---|
| 1178 | <member kind="variable" protection="private">
|
|---|
| 1179 | <type></type>
|
|---|
| 1180 | <name>__boxSize</name>
|
|---|
| 1181 | <anchorfile>classuniverse_1_1Universe.html</anchorfile>
|
|---|
| 1182 | <anchor>ed96934b4bd68016eb75e92bdbec893e</anchor>
|
|---|
| 1183 | <arglist></arglist>
|
|---|
| 1184 | </member>
|
|---|
| 1185 | </compound>
|
|---|
| 1186 | </tagfile>
|
|---|
