binaries/src/ViennaRNA/doc/html/globals_func.html

   1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
   2 <html xmlns="http://www.w3.org/1999/xhtml">
   3 <head>
   4 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
   5 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
   6 <title>RNAlib-2.1.2: Globals</title>
   7 <link href="tabs.css" rel="stylesheet" type="text/css"/>
   8 <script type="text/javascript" src="jquery.js"></script>
   9 <script type="text/javascript" src="dynsections.js"></script>
  10 <link href="navtree.css" rel="stylesheet" type="text/css"/>
  11 <script type="text/javascript" src="resize.js"></script>
  12 <script type="text/javascript" src="navtree.js"></script>
  13 <script type="text/javascript">
  14   $(document).ready(initResizable);
  15 </script>
  16 <link href="doxygen.css" rel="stylesheet" type="text/css" />
  17 </head>
  18 <body>
  19 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
  20 <div id="titlearea">
  21 <table cellspacing="0" cellpadding="0">
  22  <tbody>
  23  <tr style="height: 56px;">
  24   <td style="padding-left: 0.5em;">
  25    <div id="projectname">RNAlib-2.1.2
  26    </div>
  27   </td>
  28  </tr>
  29  </tbody>
  30 </table>
  31 </div>
  32 <!-- end header part -->
  33 <!-- Generated by Doxygen 1.8.1.1 -->
  34   <div id="navrow1" class="tabs">
  35     <ul class="tablist">
  36       <li><a href="index.html"><span>Main&#160;Page</span></a></li>
  37       <li><a href="pages.html"><span>Related&#160;Pages</span></a></li>
  38       <li><a href="modules.html"><span>Modules</span></a></li>
  39       <li><a href="annotated.html"><span>Data&#160;Structures</span></a></li>
  40       <li class="current"><a href="files.html"><span>Files</span></a></li>
  41     </ul>
  42   </div>
  43   <div id="navrow2" class="tabs2">
  44     <ul class="tablist">
  45       <li><a href="files.html"><span>File&#160;List</span></a></li>
  46       <li class="current"><a href="globals.html"><span>Globals</span></a></li>
  47     </ul>
  48   </div>
  49   <div id="navrow3" class="tabs2">
  50     <ul class="tablist">
  51       <li><a href="globals.html"><span>All</span></a></li>
  52       <li class="current"><a href="globals_func.html"><span>Functions</span></a></li>
  53       <li><a href="globals_vars.html"><span>Variables</span></a></li>
  54       <li><a href="globals_defs.html"><span>Macros</span></a></li>
  55     </ul>
  56   </div>
  57   <div id="navrow4" class="tabs3">
  58     <ul class="tablist">
  59       <li><a href="#index_a"><span>a</span></a></li>
  60       <li><a href="#index_b"><span>b</span></a></li>
  61       <li><a href="#index_c"><span>c</span></a></li>
  62       <li><a href="#index_d"><span>d</span></a></li>
  63       <li><a href="#index_e"><span>e</span></a></li>
  64       <li><a href="#index_f"><span>f</span></a></li>
  65       <li><a href="#index_g"><span>g</span></a></li>
  66       <li><a href="#index_h"><span>h</span></a></li>
  67       <li><a href="#index_i"><span>i</span></a></li>
  68       <li><a href="#index_l"><span>l</span></a></li>
  69       <li><a href="#index_m"><span>m</span></a></li>
  70       <li><a href="#index_n"><span>n</span></a></li>
  71       <li><a href="#index_p"><span>p</span></a></li>
  72       <li><a href="#index_r"><span>r</span></a></li>
  73       <li><a href="#index_s"><span>s</span></a></li>
  74       <li><a href="#index_t"><span>t</span></a></li>
  75       <li><a href="#index_u"><span>u</span></a></li>
  76       <li><a href="#index_w"><span>w</span></a></li>
  77       <li><a href="#index_x"><span>x</span></a></li>
  78       <li><a href="#index_z"><span>z</span></a></li>
  79     </ul>
  80   </div>
  81 </div><!-- top -->
  82 <div id="side-nav" class="ui-resizable side-nav-resizable">
  83   <div id="nav-tree">
  84     <div id="nav-tree-contents">
  85     </div>
  86   </div>
  87   <div id="splitbar" style="-moz-user-select:none;"
  88        class="ui-resizable-handle">
  89   </div>
  90 </div>
  91 <script type="text/javascript">
  92 $(document).ready(function(){initNavTree('globals_func.html','');});
  93 </script>
  94 <div id="doc-content">
  95 <div class="contents">
  96 &#160;
  97
  98 <h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
  99 <li>add_root()
 100 : <a class="el" href="RNAstruct_8h.html#a880d33066dd95441e5fbb73c57ed1c3e">RNAstruct.h</a>
 101 </li>
 102 <li>alifold()
 103 : <a class="el" href="group__consensus__mfe__fold.html#ga4cf00f0659e5f0480335d69e797f05b1">alifold.h</a>
 104 </li>
 105 <li>aliLfold()
 106 : <a class="el" href="group__local__consensus__fold.html#ga20a173a3cdb83f5d1778e36c1a6b1f2b">Lfold.h</a>
 107 </li>
 108 <li>alimake_pair_table()
 109 : <a class="el" href="utils_8h.html#a3c81b3967056c3888b8472b65fbb16f5">utils.h</a>
 110 </li>
 111 <li>alipbacktrack()
 112 : <a class="el" href="group__consensus__stochbt.html#ga0df40248788f0fb17ebdc59d74116d1c">alifold.h</a>
 113 </li>
 114 <li>alipf_circ_fold()
 115 : <a class="el" href="group__consensus__pf__fold.html#ga6b4dde1d43b79ab3753508c46cf50363">alifold.h</a>
 116 </li>
 117 <li>alipf_fold()
 118 : <a class="el" href="group__consensus__pf__fold.html#gad32ded7d753ccaf211ab35782d1f42a9">alifold.h</a>
 119 </li>
 120 <li>alipf_fold_par()
 121 : <a class="el" href="group__consensus__pf__fold.html#ga4d2ff54d8210fc7cceeeff389d4dbd1d">alifold.h</a>
 122 </li>
 123 <li>aliPS_color_aln()
 124 : <a class="el" href="PS__dot_8h.html#aab48d4dac655d688abe921389ac2847c">PS_dot.h</a>
 125 </li>
 126 <li>alloc_sequence_arrays()
 127 : <a class="el" href="group__consensus__fold.html#ga8a560930f7f2582cc3967723a86cfdfa">alifold.h</a>
 128 </li>
 129 <li>assign_plist_from_db()
 130 : <a class="el" href="fold_8h.html#adaa59b81664e2e36cb9932e891558fae">fold.h</a>
 131 </li>
 132 <li>assign_plist_from_pr()
 133 : <a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">part_func.h</a>
 134 </li>
 135 </ul>
 136
 137
 138 <h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
 139 <li>b2C()
 140 : <a class="el" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0">RNAstruct.h</a>
 141 </li>
 142 <li>b2HIT()
 143 : <a class="el" href="RNAstruct_8h.html#a07b7e90e712559a1992fba3ac6d21bbd">RNAstruct.h</a>
 144 </li>
 145 <li>b2Shapiro()
 146 : <a class="el" href="RNAstruct_8h.html#a5cd2feb367feeacad0c03cb7ddba5f10">RNAstruct.h</a>
 147 </li>
 148 <li>backtrack_GQuad_IntLoop()
 149 : <a class="el" href="gquad_8h.html#a54475a8eb898fa1e8af8ab5f5375f3be">gquad.h</a>
 150 </li>
 151 <li>backtrack_GQuad_IntLoop_L()
 152 : <a class="el" href="gquad_8h.html#a118ec7289f1936bd810be7fe50b98212">gquad.h</a>
 153 </li>
 154 <li>bppm_symbol()
 155 : <a class="el" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d">part_func.h</a>
 156 </li>
 157 <li>bppm_to_structure()
 158 : <a class="el" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38">part_func.h</a>
 159 </li>
 160 </ul>
 161
 162
 163 <h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
 164 <li>centroid()
 165 : <a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">part_func.h</a>
 166 </li>
 167 <li>circalifold()
 168 : <a class="el" href="group__consensus__mfe__fold.html#gadbd3b0b1c144cbfb4efe704b2b260f96">alifold.h</a>
 169 </li>
 170 <li>circfold()
 171 : <a class="el" href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423">fold.h</a>
 172 </li>
 173 <li>co_pf_fold()
 174 : <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b">part_func_co.h</a>
 175 </li>
 176 <li>co_pf_fold_par()
 177 : <a class="el" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21">part_func_co.h</a>
 178 </li>
 179 <li>cofold()
 180 : <a class="el" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52">cofold.h</a>
 181 </li>
 182 <li>cofold_par()
 183 : <a class="el" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f">cofold.h</a>
 184 </li>
 185 <li>compute_probabilities()
 186 : <a class="el" href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617">part_func_co.h</a>
 187 </li>
 188 <li>constrain_ptypes()
 189 : <a class="el" href="utils_8h.html#a36c3a6c3218b041f992052767bc74549">utils.h</a>
 190 </li>
 191 <li>convert_parameter_file()
 192 : <a class="el" href="group__energy__parameters__convert.html#gafbe538bc4eb2cf2a33326e1010005f8a">convert_epars.h</a>
 193 </li>
 194 <li>copy_pair_table()
 195 : <a class="el" href="utils_8h.html#afeaa6d68eef3a99d0a7aa08aa91c6601">utils.h</a>
 196 </li>
 197 </ul>
 198
 199
 200 <h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
 201 <li>destroy_TwoDfold_variables()
 202 : <a class="el" href="group__kl__neighborhood__mfe.html#ga05bf4f31d216b1b160fd2d3d68e9b487">2Dfold.h</a>
 203 </li>
 204 <li>destroy_TwoDpfold_variables()
 205 : <a class="el" href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15">2Dpfold.h</a>
 206 </li>
 207 </ul>
 208
 209
 210 <h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
 211 <li>E_Hairpin()
 212 : <a class="el" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">loop_energies.h</a>
 213 </li>
 214 <li>E_IntLoop()
 215 : <a class="el" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">loop_energies.h</a>
 216 </li>
 217 <li>E_Stem()
 218 : <a class="el" href="loop__energies_8h.html#af5a6594eba9b2622cb47076650c69819">loop_energies.h</a>
 219 </li>
 220 <li>encode_ali_sequence()
 221 : <a class="el" href="group__consensus__fold.html#gaa3e40277c837d6f7603afe319884c786">alifold.h</a>
 222 </li>
 223 <li>energy_of_alistruct()
 224 : <a class="el" href="group__consensus__fold.html#ga1c48869c03b49a342bf4cbdd61900081">alifold.h</a>
 225 </li>
 226 <li>energy_of_circ_struct()
 227 : <a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">fold.h</a>
 228 </li>
 229 <li>energy_of_circ_struct_par()
 230 : <a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5">fold.h</a>
 231 </li>
 232 <li>energy_of_circ_structure()
 233 : <a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">fold.h</a>
 234 </li>
 235 <li>energy_of_move()
 236 : <a class="el" href="fold_8h.html#a539ecaed89730f7644c202f304d7529b">fold.h</a>
 237 </li>
 238 <li>energy_of_move_pt()
 239 : <a class="el" href="fold_8h.html#a49e0ee561be69faf0568213546f6a53f">fold.h</a>
 240 </li>
 241 <li>energy_of_struct()
 242 : <a class="el" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">fold.h</a>
 243 </li>
 244 <li>energy_of_struct_par()
 245 : <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40">fold.h</a>
 246 </li>
 247 <li>energy_of_struct_pt()
 248 : <a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">fold.h</a>
 249 </li>
 250 <li>energy_of_struct_pt_par()
 251 : <a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e">fold.h</a>
 252 </li>
 253 <li>energy_of_structure()
 254 : <a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">fold.h</a>
 255 </li>
 256 <li>energy_of_structure_pt()
 257 : <a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">fold.h</a>
 258 </li>
 259 <li>exp_E_Hairpin()
 260 : <a class="el" href="loop__energies_8h.html#a0e128184bb097dc2da33706f33b555a6">loop_energies.h</a>
 261 </li>
 262 <li>exp_E_IntLoop()
 263 : <a class="el" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">loop_energies.h</a>
 264 </li>
 265 <li>exp_E_Stem()
 266 : <a class="el" href="loop__energies_8h.html#a76cc24ec96199e04beddad13e7891e21">loop_energies.h</a>
 267 </li>
 268 <li>expand_Full()
 269 : <a class="el" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f">RNAstruct.h</a>
 270 </li>
 271 <li>expand_Shapiro()
 272 : <a class="el" href="RNAstruct_8h.html#abe3d815b420dc4553bfb23511198b4c6">RNAstruct.h</a>
 273 </li>
 274 <li>expHairpinEnergy()
 275 : <a class="el" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">part_func.h</a>
 276 </li>
 277 <li>expLoopEnergy()
 278 : <a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">part_func.h</a>
 279 </li>
 280 <li>export_ali_bppm()
 281 : <a class="el" href="group__consensus__pf__fold.html#gadaaf83394216413505e48d913dbc1b4e">alifold.h</a>
 282 </li>
 283 <li>export_bppm()
 284 : <a class="el" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115">part_func.h</a>
 285 </li>
 286 <li>export_co_bppm()
 287 : <a class="el" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c">part_func_co.h</a>
 288 </li>
 289 <li>export_cofold_arrays()
 290 : <a class="el" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482">cofold.h</a>
 291 </li>
 292 <li>export_cofold_arrays_gq()
 293 : <a class="el" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48">cofold.h</a>
 294 </li>
 295 </ul>
 296
 297
 298 <h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
 299 <li>find_saddle()
 300 : <a class="el" href="findpath_8h.html#ad0e14268e309af773ecd1fce6244ee50">findpath.h</a>
 301 </li>
 302 <li>fold()
 303 : <a class="el" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b">fold.h</a>
 304 </li>
 305 <li>fold_par()
 306 : <a class="el" href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e">fold.h</a>
 307 </li>
 308 <li>free_alifold_arrays()
 309 : <a class="el" href="group__consensus__mfe__fold.html#ga72095e4554b5d577250ea14c42acc49e">alifold.h</a>
 310 </li>
 311 <li>free_arrays()
 312 : <a class="el" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7">fold.h</a>
 313 </li>
 314 <li>free_co_arrays()
 315 : <a class="el" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a">cofold.h</a>
 316 </li>
 317 <li>free_co_pf_arrays()
 318 : <a class="el" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247">part_func_co.h</a>
 319 </li>
 320 <li>free_interact()
 321 : <a class="el" href="group__up__cofold.html#gadde308fd5f696dc271b1532aa96fd12f">part_func_up.h</a>
 322 </li>
 323 <li>free_path()
 324 : <a class="el" href="findpath_8h.html#a326e6d1640bbfd035e3869f5f4c188f7">findpath.h</a>
 325 </li>
 326 <li>free_pf_arrays()
 327 : <a class="el" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd">part_func.h</a>
 328 </li>
 329 <li>free_profile()
 330 : <a class="el" href="profiledist_8h.html#a9b0b84a5a45761bf42d7c835dcdb3b85">profiledist.h</a>
 331 </li>
 332 <li>free_pu_contrib_struct()
 333 : <a class="el" href="group__up__cofold.html#gac20bd61824981d45ce0dc9934aa56df8">part_func_up.h</a>
 334 </li>
 335 <li>free_sequence_arrays()
 336 : <a class="el" href="group__consensus__fold.html#ga298a420a8c879202e2617b3f724fde38">alifold.h</a>
 337 </li>
 338 <li>free_tree()
 339 : <a class="el" href="treedist_8h.html#acbc1cb9bce582ea945e4a467c76a57aa">treedist.h</a>
 340 </li>
 341 </ul>
 342
 343
 344 <h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
 345 <li>get_alipf_arrays()
 346 : <a class="el" href="group__consensus__fold.html#ga0cc49457fd79eeb04d4a7f97c868b09b">alifold.h</a>
 347 </li>
 348 <li>get_boltzmann_factor_copy()
 349 : <a class="el" href="group__energy__parameters.html#gacba212326a051734797e65987260fdd0">params.h</a>
 350 </li>
 351 <li>get_boltzmann_factors()
 352 : <a class="el" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d">params.h</a>
 353 </li>
 354 <li>get_boltzmann_factors_ali()
 355 : <a class="el" href="group__energy__parameters.html#gaaa049a8c9f1c2ed4398cb1b5a3d65a66">params.h</a>
 356 </li>
 357 <li>get_centroid_struct_pl()
 358 : <a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6">part_func.h</a>
 359 </li>
 360 <li>get_centroid_struct_pr()
 361 : <a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38">part_func.h</a>
 362 </li>
 363 <li>get_concentrations()
 364 : <a class="el" href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7">part_func_co.h</a>
 365 </li>
 366 <li>get_gquad_matrix()
 367 : <a class="el" href="gquad_8h.html#a8b0784c14fa1208d0aebbebdc1318b7a">gquad.h</a>
 368 </li>
 369 <li>get_iindx()
 370 : <a class="el" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397">utils.h</a>
 371 </li>
 372 <li>get_indx()
 373 : <a class="el" href="utils_8h.html#a4d9ee1572c1bfcd02d3d3f2db8a6530f">utils.h</a>
 374 </li>
 375 <li>get_input_line()
 376 : <a class="el" href="utils_8h.html#a8ef1835eb83f542396f59f0b205965e5">utils.h</a>
 377 </li>
 378 <li>get_line()
 379 : <a class="el" href="utils_8h.html#abe51806d14cff0789a8c1df7dbc45b71">utils.h</a>
 380 </li>
 381 <li>get_monomere_mfes()
 382 : <a class="el" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79">cofold.h</a>
 383 </li>
 384 <li>get_mpi()
 385 : <a class="el" href="group__consensus__fold.html#gaa2d600be90844094ec145ea14a314d2f">alifold.h</a>
 386 </li>
 387 <li>get_path()
 388 : <a class="el" href="findpath_8h.html#a0ff35d65c892a3403af937c00a867ef9">findpath.h</a>
 389 </li>
 390 <li>get_pf_arrays()
 391 : <a class="el" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e">part_func.h</a>
 392 </li>
 393 <li>get_plist()
 394 : <a class="el" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">part_func_co.h</a>
 395 </li>
 396 <li>get_scaled_alipf_parameters()
 397 : <a class="el" href="group__energy__parameters.html#gaa6a4297a2b91d6f7ae47dd61ca1862a0">params.h</a>
 398 </li>
 399 <li>get_scaled_parameters()
 400 : <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72">params.h</a>
 401 </li>
 402 <li>get_scaled_pf_parameters()
 403 : <a class="el" href="group__energy__parameters.html#gab85f6b6da051f380371deb0d8921bdba">params.h</a>
 404 </li>
 405 <li>get_subseq_F()
 406 : <a class="el" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e">part_func.h</a>
 407 </li>
 408 <li>get_TwoDfold_variables()
 409 : <a class="el" href="group__kl__neighborhood__mfe.html#gac9284f132cf0eaa0a2f43590eda05488">2Dfold.h</a>
 410 </li>
 411 <li>get_TwoDpfold_variables()
 412 : <a class="el" href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64">2Dpfold.h</a>
 413 </li>
 414 <li>get_TwoDpfold_variables_from_MFE()
 415 : <a class="el" href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216">2Dpfold.h</a>
 416 </li>
 417 <li>gmlRNA()
 418 : <a class="el" href="PS__dot_8h.html#a70834bc8c0aad4fe6824ff76ccb8f329">PS_dot.h</a>
 419 </li>
 420 </ul>
 421
 422
 423 <h3><a class="anchor" id="index_h"></a>- h -</h3><ul>
 424 <li>HairpinE()
 425 : <a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">fold.h</a>
 426 </li>
 427 <li>hamming()
 428 : <a class="el" href="utils_8h.html#ad9dc7bfc9aa664dc6698f17ce07fc7e7">utils.h</a>
 429 </li>
 430 <li>hamming_bound()
 431 : <a class="el" href="utils_8h.html#a96d3c36717d624514055ce201cab1542">utils.h</a>
 432 </li>
 433 </ul>
 434
 435
 436 <h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
 437 <li>init_co_pf_fold()
 438 : <a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">part_func_co.h</a>
 439 </li>
 440 <li>init_pf_fold()
 441 : <a class="el" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af">part_func.h</a>
 442 </li>
 443 <li>init_pf_foldLP()
 444 : <a class="el" href="LPfold_8h.html#ae85bf55053e9fb295208be322e0fa07a">LPfold.h</a>
 445 </li>
 446 <li>init_rand()
 447 : <a class="el" href="utils_8h.html#a8aaa6d9be6f803f496d9b97375c371f3">utils.h</a>
 448 </li>
 449 <li>initialize_cofold()
 450 : <a class="el" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">cofold.h</a>
 451 </li>
 452 <li>initialize_fold()
 453 : <a class="el" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">fold.h</a>
 454 </li>
 455 <li>int_urn()
 456 : <a class="el" href="utils_8h.html#a68ff0849d44f62fe491800378a5ffcb4">utils.h</a>
 457 </li>
 458 <li>inverse_fold()
 459 : <a class="el" href="group__inverse__fold.html#ga7af026de55d4babad879f2c92559cbbc">inverse.h</a>
 460 </li>
 461 <li>inverse_pf_fold()
 462 : <a class="el" href="group__inverse__fold.html#gaeef52ecbf2a2450ad585a344f9826806">inverse.h</a>
 463 </li>
 464 </ul>
 465
 466
 467 <h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
 468 <li>Lfold()
 469 : <a class="el" href="group__local__mfe__fold.html#ga16e5a70e60835bb969eaecbe6482f1be">Lfold.h</a>
 470 </li>
 471 <li>Lfoldz()
 472 : <a class="el" href="group__local__mfe__fold.html#gab6d79eecc180f586679f7b85cce5cbe9">Lfold.h</a>
 473 </li>
 474 <li>loop_energy()
 475 : <a class="el" href="fold_8h.html#a507d4fd93f4b398d793ba2402731388d">fold.h</a>
 476 </li>
 477 <li>LoopEnergy()
 478 : <a class="el" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">fold.h</a>
 479 </li>
 480 </ul>
 481
 482
 483 <h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
 484 <li>Make_bp_profile()
 485 : <a class="el" href="profiledist_8h.html#a904c7eaf4a2413567c00ac4891749d18">profiledist.h</a>
 486 </li>
 487 <li>Make_bp_profile_bppm()
 488 : <a class="el" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc">profiledist.h</a>
 489 </li>
 490 <li>make_loop_index_pt()
 491 : <a class="el" href="utils_8h.html#a4358e89f64cc87a563b7ef3855f75bed">utils.h</a>
 492 </li>
 493 <li>make_pair_table()
 494 : <a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a">utils.h</a>
 495 </li>
 496 <li>make_pair_table_snoop()
 497 : <a class="el" href="utils_8h.html#a9aa3bf3b4346bb7fb88efc154dd07a79">utils.h</a>
 498 </li>
 499 <li>Make_swString()
 500 : <a class="el" href="stringdist_8h.html#a3125991b3a403b3f89230474deb3f22e">stringdist.h</a>
 501 </li>
 502 <li>make_tree()
 503 : <a class="el" href="treedist_8h.html#a08fe4d5afd385dce593b86eaf010c6e3">treedist.h</a>
 504 </li>
 505 <li>MEA()
 506 : <a class="el" href="MEA_8h.html#a396ec6144c6a74fcbab4cea6b42d76c3">MEA.h</a>
 507 </li>
 508 <li>mean_bp_dist()
 509 : <a class="el" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">part_func.h</a>
 510 </li>
 511 <li>mean_bp_distance()
 512 : <a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">part_func.h</a>
 513 </li>
 514 <li>mean_bp_distance_pr()
 515 : <a class="el" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5">part_func.h</a>
 516 </li>
 517 </ul>
 518
 519
 520 <h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
 521 <li>nrerror()
 522 : <a class="el" href="utils_8h.html#a127ce946e56b5a5773781cabe68e38c5">utils.h</a>
 523 </li>
 524 </ul>
 525
 526
 527 <h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
 528 <li>pack_structure()
 529 : <a class="el" href="utils_8h.html#ac6dfa5e22928c087c6e09ff0054a7ced">utils.h</a>
 530 </li>
 531 <li>parenthesis_structure()
 532 : <a class="el" href="fold_8h.html#a87b7869bd1d8dc79c60775c74e009e9b">fold.h</a>
 533 </li>
 534 <li>parenthesis_zuker()
 535 : <a class="el" href="fold_8h.html#a325f3835c68f34fe833b2b7a5828857f">fold.h</a>
 536 </li>
 537 <li>parse_gquad()
 538 : <a class="el" href="gquad_8h.html#ae41763215b9c64d2a7b67f0df8a28078">gquad.h</a>
 539 </li>
 540 <li>parse_structure()
 541 : <a class="el" href="RNAstruct_8h.html#a3c79042e6bf6f01706bf30ec9e69e8ac">RNAstruct.h</a>
 542 </li>
 543 <li>pbacktrack()
 544 : <a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">part_func.h</a>
 545 </li>
 546 <li>pbacktrack_circ()
 547 : <a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">part_func.h</a>
 548 </li>
 549 <li>pf_circ_fold()
 550 : <a class="el" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735">part_func.h</a>
 551 </li>
 552 <li>pf_fold()
 553 : <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2">part_func.h</a>
 554 </li>
 555 <li>pf_fold_par()
 556 : <a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823">part_func.h</a>
 557 </li>
 558 <li>pf_interact()
 559 : <a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00">part_func_up.h</a>
 560 </li>
 561 <li>pf_unstru()
 562 : <a class="el" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf">part_func_up.h</a>
 563 </li>
 564 <li>pfl_fold()
 565 : <a class="el" href="group__local__pf__fold.html#gaa1ecd401617ebc748a0220026543c777">LPfold.h</a>
 566 </li>
 567 <li>pfl_fold_par()
 568 : <a class="el" href="group__local__pf__fold.html#gab354507e8028f3e1c52ef96bb1eb9df8">LPfold.h</a>
 569 </li>
 570 <li>print_bppm()
 571 : <a class="el" href="profiledist_8h.html#a8e0b4fe3698b3502945116ecc0ba6160">profiledist.h</a>
 572 </li>
 573 <li>print_tree()
 574 : <a class="el" href="treedist_8h.html#a21ad4de3ba4055aeef08b28c9ad48894">treedist.h</a>
 575 </li>
 576 <li>print_tty_constraint()
 577 : <a class="el" href="utils_8h.html#a4d167deb70bb51723e44374dc981deb2">utils.h</a>
 578 </li>
 579 <li>print_tty_constraint_full()
 580 : <a class="el" href="utils_8h.html#ae8ae8a34962b9959be3f6c40f0a80ac1">utils.h</a>
 581 </li>
 582 <li>print_tty_input_seq()
 583 : <a class="el" href="utils_8h.html#a6bf778117d31b7fd90db435323f4ef74">utils.h</a>
 584 </li>
 585 <li>print_tty_input_seq_str()
 586 : <a class="el" href="utils_8h.html#ae4ef89b662a3e9b5b5f0781d9757aba0">utils.h</a>
 587 </li>
 588 <li>profile_edit_distance()
 589 : <a class="el" href="profiledist_8h.html#abe75e90e00a1e5dd8862944ed53dad5d">profiledist.h</a>
 590 </li>
 591 <li>PS_dot_plot()
 592 : <a class="el" href="PS__dot_8h.html#a689a97a7e3b8a2df14728b8204d9d57b">PS_dot.h</a>
 593 </li>
 594 <li>PS_dot_plot_list()
 595 : <a class="el" href="PS__dot_8h.html#a00ea223b5cf02eb2faae5ff29f0d5e12">PS_dot.h</a>
 596 </li>
 597 <li>PS_rna_plot()
 598 : <a class="el" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9">PS_dot.h</a>
 599 </li>
 600 <li>PS_rna_plot_a()
 601 : <a class="el" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271">PS_dot.h</a>
 602 </li>
 603 <li>putoutpU_prob()
 604 : <a class="el" href="group__local__pf__fold.html#ga0bcb751860bbf34e3dfee8c2fbdb3ef3">LPfold.h</a>
 605 </li>
 606 <li>putoutpU_prob_bin()
 607 : <a class="el" href="group__local__pf__fold.html#ga9acb00ee10e96b1ca4ea394cd8bcec75">LPfold.h</a>
 608 </li>
 609 </ul>
 610
 611
 612 <h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
 613 <li>random_string()
 614 : <a class="el" href="utils_8h.html#a1b95eac365a021572e1c37e5993a89be">utils.h</a>
 615 </li>
 616 <li>read_parameter_file()
 617 : <a class="el" href="group__energy__parameters__rw.html#ga165a142a3c68fb6655c69ef4ab7cd749">read_epars.h</a>
 618 </li>
 619 <li>read_record()
 620 : <a class="el" href="utils_8h.html#afd194a69af9d92b5b0412a7627ac1595">utils.h</a>
 621 </li>
 622 <li>readribosum()
 623 : <a class="el" href="group__consensus__fold.html#ga5e125c9586fcd4e2e1559fe76f7289cc">alifold.h</a>
 624 </li>
 625 </ul>
 626
 627
 628 <h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
 629 <li>scale_parameters()
 630 : <a class="el" href="group__energy__parameters.html#ga527ef619cd8210b84d5d53be1e0e29b6">params.h</a>
 631 </li>
 632 <li>set_model_details()
 633 : <a class="el" href="fold__vars_8h.html#a4c3257186a796182462f18a5480ac8b3">fold_vars.h</a>
 634 </li>
 635 <li>simple_circplot_coordinates()
 636 : <a class="el" href="plot__layouts_8h.html#ac4ea13d35308f09940178d2b05a248c2">plot_layouts.h</a>
 637 </li>
 638 <li>simple_xy_coordinates()
 639 : <a class="el" href="plot__layouts_8h.html#af4b9173e7d3fd361c3c85e6def194123">plot_layouts.h</a>
 640 </li>
 641 <li>space()
 642 : <a class="el" href="utils_8h.html#ad7e1e137b3bf1f7108933d302a7f0177">utils.h</a>
 643 </li>
 644 <li>ssv_rna_plot()
 645 : <a class="el" href="PS__dot_8h.html#add368528755f9a830727b680243541df">PS_dot.h</a>
 646 </li>
 647 <li>str_DNA2RNA()
 648 : <a class="el" href="utils_8h.html#ad3f18dd83f958f18b2f26ecb99305208">utils.h</a>
 649 </li>
 650 <li>str_uppercase()
 651 : <a class="el" href="utils_8h.html#a17b796b806f96b70382077fb5bc519bb">utils.h</a>
 652 </li>
 653 <li>string_edit_distance()
 654 : <a class="el" href="stringdist_8h.html#a89e3c335ef17780576d7c0e713830db9">stringdist.h</a>
 655 </li>
 656 <li>subopt()
 657 : <a class="el" href="group__subopt__wuchty.html#ga700f662506a233e42dd7fda74fafd40e">subopt.h</a>
 658 </li>
 659 <li>subopt_circ()
 660 : <a class="el" href="group__subopt__wuchty.html#ga8634516e4740e0b6c9a46d2bae940340">subopt.h</a>
 661 </li>
 662 <li>subopt_par()
 663 : <a class="el" href="group__subopt__wuchty.html#ga554dedfcdb249fdf151caade58666e4d">subopt.h</a>
 664 </li>
 665 <li>svg_rna_plot()
 666 : <a class="el" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304">PS_dot.h</a>
 667 </li>
 668 </ul>
 669
 670
 671 <h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
 672 <li>time_stamp()
 673 : <a class="el" href="utils_8h.html#a7afeb906cb36e9d77379eabc6907ac46">utils.h</a>
 674 </li>
 675 <li>tree_edit_distance()
 676 : <a class="el" href="treedist_8h.html#a3b21f1925f7071f46d93431a835217bb">treedist.h</a>
 677 </li>
 678 <li>TwoDfold_backtrack_f5()
 679 : <a class="el" href="group__kl__neighborhood__mfe.html#gaf4dc05bf8fc1ea53acd7aeb798ba80c2">2Dfold.h</a>
 680 </li>
 681 <li>TwoDfoldList()
 682 : <a class="el" href="group__kl__neighborhood__mfe.html#ga47da790166020558d27323aef489703e">2Dfold.h</a>
 683 </li>
 684 <li>TwoDpfold_pbacktrack()
 685 : <a class="el" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71">2Dpfold.h</a>
 686 </li>
 687 <li>TwoDpfold_pbacktrack5()
 688 : <a class="el" href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7">2Dpfold.h</a>
 689 </li>
 690 <li>TwoDpfoldList()
 691 : <a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb">2Dpfold.h</a>
 692 </li>
 693 </ul>
 694
 695
 696 <h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
 697 <li>unexpand_aligned_F()
 698 : <a class="el" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a">RNAstruct.h</a>
 699 </li>
 700 <li>unexpand_Full()
 701 : <a class="el" href="RNAstruct_8h.html#a260c4b622093b76a883bf96628280de1">RNAstruct.h</a>
 702 </li>
 703 <li>unpack_structure()
 704 : <a class="el" href="utils_8h.html#a071c6921efe1eb974f115ee6fefa3c39">utils.h</a>
 705 </li>
 706 <li>unweight()
 707 : <a class="el" href="RNAstruct_8h.html#a09a80253ac7b6bae606871ba7c6e5136">RNAstruct.h</a>
 708 </li>
 709 <li>update_alifold_params()
 710 : <a class="el" href="alifold_8h.html#ac484c6bd429bafbd353b91044508d8e9">alifold.h</a>
 711 </li>
 712 <li>update_co_pf_params()
 713 : <a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5">part_func_co.h</a>
 714 </li>
 715 <li>update_co_pf_params_par()
 716 : <a class="el" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53">part_func_co.h</a>
 717 </li>
 718 <li>update_cofold_params()
 719 : <a class="el" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57">cofold.h</a>
 720 </li>
 721 <li>update_fold_params()
 722 : <a class="el" href="group__mfe__fold.html#ga41bf8f6fa15b94471f7095cad9f0ccf3">fold.h</a>
 723 </li>
 724 <li>update_pf_params()
 725 : <a class="el" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28">part_func.h</a>
 726 </li>
 727 <li>update_pf_params_par()
 728 : <a class="el" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc">part_func.h</a>
 729 </li>
 730 <li>update_pf_paramsLP()
 731 : <a class="el" href="group__local__pf__fold.html#ga5a019014d37fe6105131dfc2fc447880">LPfold.h</a>
 732 </li>
 733 <li>urn()
 734 : <a class="el" href="utils_8h.html#aaa328491c84996e445d027fde9800f2e">utils.h</a>
 735 </li>
 736 </ul>
 737
 738
 739 <h3><a class="anchor" id="index_w"></a>- w -</h3><ul>
 740 <li>warn_user()
 741 : <a class="el" href="utils_8h.html#af2355fa8746f2f30fbe71db65dea3d51">utils.h</a>
 742 </li>
 743 <li>write_parameter_file()
 744 : <a class="el" href="group__energy__parameters__rw.html#ga8a43459be386a7489feeab68dc2c6c76">read_epars.h</a>
 745 </li>
 746 </ul>
 747
 748
 749 <h3><a class="anchor" id="index_x"></a>- x -</h3><ul>
 750 <li>xrealloc()
 751 : <a class="el" href="utils_8h.html#a9037ada838835b1b9db41581a021b0c8">utils.h</a>
 752 </li>
 753 <li>xrna_plot()
 754 : <a class="el" href="PS__dot_8h.html#a2f6d5953e6a323df898896b8d6614483">PS_dot.h</a>
 755 </li>
 756 </ul>
 757
 758
 759 <h3><a class="anchor" id="index_z"></a>- z -</h3><ul>
 760 <li>zukersubopt()
 761 : <a class="el" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90">cofold.h</a>
 762 </li>
 763 <li>zukersubopt_par()
 764 : <a class="el" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c">cofold.h</a>
 765 </li>
 766 </ul>
 767 </div><!-- contents -->
 768 </div><!-- doc-content -->
 769 <!-- start footer part -->
 770 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
 771   <ul>
 772     <li class="footer">Generated on Wed Jul 24 2013 13:39:00 for RNAlib-2.1.2 by
 773     <a href="http://www.doxygen.org/index.html">
 774     <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
 775   </ul>
 776 </div>
 777 </body>
 778 </html>