binaries/src/ViennaRNA/doc/html/group__eval.html

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  59 <a href="#func-members">Functions</a> &#124;
  60 <a href="#var-members">Variables</a>  </div>
  61   <div class="headertitle">
  62 <div class="title">Energy evaluation</div>  </div>
  63 <div class="ingroups"><a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a></div></div><!--header-->
  64 <div class="contents">
  65
  66 <p>This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
  67 <a href="#details">More...</a></p>
  68 <div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
  69   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Energy evaluation:</div>
  70 <div id="dynsection-0-summary" class="dynsummary" style="display:block;">
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  73 <center><table><tr><td><img src="group__eval.png" border="0" alt="" usemap="#group____eval"/>
  74 <map name="group____eval" id="group____eval">
  75 <area shape="rect" id="node2" href="group__folding__routines.html" title="This module contains all functions related to thermodynamic folding of RNAs." alt="" coords="6,5,191,46"/></map>
  76 </td></tr></table></center>
  77 </div>
  78 <table class="memberdecls">
  79 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  80 Functions</h2></td></tr>
  81 <tr class="memitem:gaf93986cb3cb29770ec9cca69c9fab8cf"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">energy_of_structure</a> (const char *string, const char *structure, int verbosity_level)</td></tr>
  82 <tr class="memdesc:gaf93986cb3cb29770ec9cca69c9fab8cf"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the free energy of an already folded RNA using global model detail settings.  <a href="#gaf93986cb3cb29770ec9cca69c9fab8cf"></a><br/></td></tr>
  83 <tr class="memitem:gab5169ea4f72f250e43811463a33f4e40"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40">energy_of_struct_par</a> (const char *string, const char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
  84 <tr class="memdesc:gab5169ea4f72f250e43811463a33f4e40"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
  85 <tr class="memitem:gaeb14f3664aec67fc03268ac75253f0f8"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">energy_of_circ_structure</a> (const char *string, const char *structure, int verbosity_level)</td></tr>
  86 <tr class="memdesc:gaeb14f3664aec67fc03268ac75253f0f8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the free energy of an already folded circular RNA.  <a href="#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
  87 <tr class="memitem:ga75dc765ee4a1177832bc817c94cf88e5"><td class="memItemLeft" align="right" valign="top">float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5">energy_of_circ_struct_par</a> (const char *string, const char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
  88 <tr class="memdesc:ga75dc765ee4a1177832bc817c94cf88e5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the free energy of an already folded circular RNA.  <a href="#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
  89 <tr class="memitem:ga8831445966b761417e713360791299d8"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">energy_of_structure_pt</a> (const char *string, short *ptable, short *s, short *s1, int verbosity_level)</td></tr>
  90 <tr class="memdesc:ga8831445966b761417e713360791299d8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
  91 <tr class="memitem:gada4701dd7519b29da75ceac147601f4e"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e">energy_of_struct_pt_par</a> (const char *string, short *ptable, short *s, short *s1, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
  92 <tr class="memdesc:gada4701dd7519b29da75ceac147601f4e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
  93 </table><table class="memberdecls">
  94 <tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
  95 Variables</h2></td></tr>
  96 <tr class="memitem:ga567530678f6260a1a649a5beca5da4c5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a>
  97 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
  98 <tr class="memdesc:ga567530678f6260a1a649a5beca5da4c5"><td class="mdescLeft">&#160;</td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>
  99 </table>
 100 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
 101 <p>This module contains all functions and variables related to energy evaluation of sequence/structure pairs. </p>
 102 <hr/><h2>Function Documentation</h2>
 103 <a class="anchor" id="gaf93986cb3cb29770ec9cca69c9fab8cf"></a>
 104 <div class="memitem">
 105 <div class="memproto">
 106       <table class="memname">
 107         <tr>
 108           <td class="memname">float energy_of_structure </td>
 109           <td>(</td>
 110           <td class="paramtype">const char *&#160;</td>
 111           <td class="paramname"><em>string</em>, </td>
 112         </tr>
 113         <tr>
 114           <td class="paramkey"></td>
 115           <td></td>
 116           <td class="paramtype">const char *&#160;</td>
 117           <td class="paramname"><em>structure</em>, </td>
 118         </tr>
 119         <tr>
 120           <td class="paramkey"></td>
 121           <td></td>
 122           <td class="paramtype">int&#160;</td>
 123           <td class="paramname"><em>verbosity_level</em>&#160;</td>
 124         </tr>
 125         <tr>
 126           <td></td>
 127           <td>)</td>
 128           <td></td><td></td>
 129         </tr>
 130       </table>
 131 </div><div class="memdoc">
 132
 133 <p>Calculate the free energy of an already folded RNA using global model detail settings. </p>
 134 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 135 <dl class="section note"><dt>Note:</dt><dd>OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a> for a completely threadsafe implementation.</dd></dl>
 136 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a>, <a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_structure()</a></dd></dl>
 137 <dl class="params"><dt>Parameters:</dt><dd>
 138   <table class="params">
 139     <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
 140     <tr><td class="paramname">structure</td><td>secondary structure in dot-bracket notation </td></tr>
 141     <tr><td class="paramname">verbosity_level</td><td>a flag to turn verbose output on/off </td></tr>
 142   </table>
 143   </dd>
 144 </dl>
 145 <dl class="section return"><dt>Returns:</dt><dd>the free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 146
 147 </div>
 148 </div>
 149 <a class="anchor" id="gab5169ea4f72f250e43811463a33f4e40"></a>
 150 <div class="memitem">
 151 <div class="memproto">
 152       <table class="memname">
 153         <tr>
 154           <td class="memname">float energy_of_struct_par </td>
 155           <td>(</td>
 156           <td class="paramtype">const char *&#160;</td>
 157           <td class="paramname"><em>string</em>, </td>
 158         </tr>
 159         <tr>
 160           <td class="paramkey"></td>
 161           <td></td>
 162           <td class="paramtype">const char *&#160;</td>
 163           <td class="paramname"><em>structure</em>, </td>
 164         </tr>
 165         <tr>
 166           <td class="paramkey"></td>
 167           <td></td>
 168           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&#160;</td>
 169           <td class="paramname"><em>parameters</em>, </td>
 170         </tr>
 171         <tr>
 172           <td class="paramkey"></td>
 173           <td></td>
 174           <td class="paramtype">int&#160;</td>
 175           <td class="paramname"><em>verbosity_level</em>&#160;</td>
 176         </tr>
 177         <tr>
 178           <td></td>
 179           <td>)</td>
 180           <td></td><td></td>
 181         </tr>
 182       </table>
 183 </div><div class="memdoc">
 184
 185 <p>Calculate the free energy of an already folded RNA. </p>
 186 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 187 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_structure()</a>, <a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8" title="Calculate the free energy of an already folded RNA.">energy_of_structure_pt()</a>, <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters()</a></dd></dl>
 188 <dl class="params"><dt>Parameters:</dt><dd>
 189   <table class="params">
 190     <tr><td class="paramname">string</td><td>RNA sequence in uppercase letters </td></tr>
 191     <tr><td class="paramname">structure</td><td>Secondary structure in dot-bracket notation </td></tr>
 192     <tr><td class="paramname">parameters</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
 193     <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
 194   </table>
 195   </dd>
 196 </dl>
 197 <dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 198
 199 </div>
 200 </div>
 201 <a class="anchor" id="gaeb14f3664aec67fc03268ac75253f0f8"></a>
 202 <div class="memitem">
 203 <div class="memproto">
 204       <table class="memname">
 205         <tr>
 206           <td class="memname">float energy_of_circ_structure </td>
 207           <td>(</td>
 208           <td class="paramtype">const char *&#160;</td>
 209           <td class="paramname"><em>string</em>, </td>
 210         </tr>
 211         <tr>
 212           <td class="paramkey"></td>
 213           <td></td>
 214           <td class="paramtype">const char *&#160;</td>
 215           <td class="paramname"><em>structure</em>, </td>
 216         </tr>
 217         <tr>
 218           <td class="paramkey"></td>
 219           <td></td>
 220           <td class="paramtype">int&#160;</td>
 221           <td class="paramname"><em>verbosity_level</em>&#160;</td>
 222         </tr>
 223         <tr>
 224           <td></td>
 225           <td>)</td>
 226           <td></td><td></td>
 227         </tr>
 228       </table>
 229 </div><div class="memdoc">
 230
 231 <p>Calculate the free energy of an already folded circular RNA. </p>
 232 <dl class="section note"><dt>Note:</dt><dd>OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See <a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_struct_par()</a> for a completely threadsafe implementation.</dd></dl>
 233 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 234 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_struct_par()</a>, <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a></dd></dl>
 235 <dl class="params"><dt>Parameters:</dt><dd>
 236   <table class="params">
 237     <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
 238     <tr><td class="paramname">structure</td><td>Secondary structure in dot-bracket notation </td></tr>
 239     <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
 240   </table>
 241   </dd>
 242 </dl>
 243 <dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 244
 245 </div>
 246 </div>
 247 <a class="anchor" id="ga75dc765ee4a1177832bc817c94cf88e5"></a>
 248 <div class="memitem">
 249 <div class="memproto">
 250       <table class="memname">
 251         <tr>
 252           <td class="memname">float energy_of_circ_struct_par </td>
 253           <td>(</td>
 254           <td class="paramtype">const char *&#160;</td>
 255           <td class="paramname"><em>string</em>, </td>
 256         </tr>
 257         <tr>
 258           <td class="paramkey"></td>
 259           <td></td>
 260           <td class="paramtype">const char *&#160;</td>
 261           <td class="paramname"><em>structure</em>, </td>
 262         </tr>
 263         <tr>
 264           <td class="paramkey"></td>
 265           <td></td>
 266           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&#160;</td>
 267           <td class="paramname"><em>parameters</em>, </td>
 268         </tr>
 269         <tr>
 270           <td class="paramkey"></td>
 271           <td></td>
 272           <td class="paramtype">int&#160;</td>
 273           <td class="paramname"><em>verbosity_level</em>&#160;</td>
 274         </tr>
 275         <tr>
 276           <td></td>
 277           <td>)</td>
 278           <td></td><td></td>
 279         </tr>
 280       </table>
 281 </div><div class="memdoc">
 282
 283 <p>Calculate the free energy of an already folded circular RNA. </p>
 284 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 285 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a>, <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters()</a></dd></dl>
 286 <dl class="params"><dt>Parameters:</dt><dd>
 287   <table class="params">
 288     <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
 289     <tr><td class="paramname">structure</td><td>Secondary structure in dot-bracket notation </td></tr>
 290     <tr><td class="paramname">parameters</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
 291     <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
 292   </table>
 293   </dd>
 294 </dl>
 295 <dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 296
 297 </div>
 298 </div>
 299 <a class="anchor" id="ga8831445966b761417e713360791299d8"></a>
 300 <div class="memitem">
 301 <div class="memproto">
 302       <table class="memname">
 303         <tr>
 304           <td class="memname">int energy_of_structure_pt </td>
 305           <td>(</td>
 306           <td class="paramtype">const char *&#160;</td>
 307           <td class="paramname"><em>string</em>, </td>
 308         </tr>
 309         <tr>
 310           <td class="paramkey"></td>
 311           <td></td>
 312           <td class="paramtype">short *&#160;</td>
 313           <td class="paramname"><em>ptable</em>, </td>
 314         </tr>
 315         <tr>
 316           <td class="paramkey"></td>
 317           <td></td>
 318           <td class="paramtype">short *&#160;</td>
 319           <td class="paramname"><em>s</em>, </td>
 320         </tr>
 321         <tr>
 322           <td class="paramkey"></td>
 323           <td></td>
 324           <td class="paramtype">short *&#160;</td>
 325           <td class="paramname"><em>s1</em>, </td>
 326         </tr>
 327         <tr>
 328           <td class="paramkey"></td>
 329           <td></td>
 330           <td class="paramtype">int&#160;</td>
 331           <td class="paramname"><em>verbosity_level</em>&#160;</td>
 332         </tr>
 333         <tr>
 334           <td></td>
 335           <td>)</td>
 336           <td></td><td></td>
 337         </tr>
 338       </table>
 339 </div><div class="memdoc">
 340
 341 <p>Calculate the free energy of an already folded RNA. </p>
 342 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 343 <dl class="section note"><dt>Note:</dt><dd>OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See <a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e" title="Calculate the free energy of an already folded RNA.">energy_of_struct_pt_par()</a> for a completely threadsafe implementation.</dd></dl>
 344 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table()</a>, <a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e" title="Calculate the free energy of an already folded RNA.">energy_of_struct_pt_par()</a></dd></dl>
 345 <dl class="params"><dt>Parameters:</dt><dd>
 346   <table class="params">
 347     <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
 348     <tr><td class="paramname">ptable</td><td>the pair table of the secondary structure </td></tr>
 349     <tr><td class="paramname">s</td><td>encoded RNA sequence </td></tr>
 350     <tr><td class="paramname">s1</td><td>encoded RNA sequence </td></tr>
 351     <tr><td class="paramname">verbosity_level</td><td>a flag to turn verbose output on/off </td></tr>
 352   </table>
 353   </dd>
 354 </dl>
 355 <dl class="section return"><dt>Returns:</dt><dd>the free energy of the input structure given the input sequence in 10kcal/mol </dd></dl>
 356
 357 </div>
 358 </div>
 359 <a class="anchor" id="gada4701dd7519b29da75ceac147601f4e"></a>
 360 <div class="memitem">
 361 <div class="memproto">
 362       <table class="memname">
 363         <tr>
 364           <td class="memname">int energy_of_struct_pt_par </td>
 365           <td>(</td>
 366           <td class="paramtype">const char *&#160;</td>
 367           <td class="paramname"><em>string</em>, </td>
 368         </tr>
 369         <tr>
 370           <td class="paramkey"></td>
 371           <td></td>
 372           <td class="paramtype">short *&#160;</td>
 373           <td class="paramname"><em>ptable</em>, </td>
 374         </tr>
 375         <tr>
 376           <td class="paramkey"></td>
 377           <td></td>
 378           <td class="paramtype">short *&#160;</td>
 379           <td class="paramname"><em>s</em>, </td>
 380         </tr>
 381         <tr>
 382           <td class="paramkey"></td>
 383           <td></td>
 384           <td class="paramtype">short *&#160;</td>
 385           <td class="paramname"><em>s1</em>, </td>
 386         </tr>
 387         <tr>
 388           <td class="paramkey"></td>
 389           <td></td>
 390           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&#160;</td>
 391           <td class="paramname"><em>parameters</em>, </td>
 392         </tr>
 393         <tr>
 394           <td class="paramkey"></td>
 395           <td></td>
 396           <td class="paramtype">int&#160;</td>
 397           <td class="paramname"><em>verbosity_level</em>&#160;</td>
 398         </tr>
 399         <tr>
 400           <td></td>
 401           <td>)</td>
 402           <td></td><td></td>
 403         </tr>
 404       </table>
 405 </div><div class="memdoc">
 406
 407 <p>Calculate the free energy of an already folded RNA. </p>
 408 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 409 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table()</a>, <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a>, <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters()</a></dd></dl>
 410 <dl class="params"><dt>Parameters:</dt><dd>
 411   <table class="params">
 412     <tr><td class="paramname">string</td><td>RNA sequence in uppercase letters </td></tr>
 413     <tr><td class="paramname">ptable</td><td>The pair table of the secondary structure </td></tr>
 414     <tr><td class="paramname">s</td><td>Encoded RNA sequence </td></tr>
 415     <tr><td class="paramname">s1</td><td>Encoded RNA sequence </td></tr>
 416     <tr><td class="paramname">parameters</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
 417     <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
 418   </table>
 419   </dd>
 420 </dl>
 421 <dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in 10kcal/mol </dd></dl>
 422
 423 </div>
 424 </div>
 425 </div><!-- contents -->
 426 </div><!-- doc-content -->
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 432     <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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