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

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   5 <title>RNAlib-2.1.2: Energy evaluation</title>
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  63 <div class="contents">
  64 <h1>Energy evaluation<br/>
  65 <small>
  66 [<a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a>]</small>
  67 </h1>
  68 <p>This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
  69 <a href="#_details">More...</a></p>
  70
  71 <p><div class="dynheader">
  72 Collaboration diagram for Energy evaluation:</div>
  73 <div class="dynsection">
  74 <center><table><tr><td><img src="group__eval.png" border="0" alt="" usemap="#group____eval_map"/>
  75 <map name="group____eval_map" id="group____eval">
  76 <area shape="rect" id="node2" href="group__folding__routines.html" title="This module contains all functions related to thermodynamic folding of RNAs." alt="" coords="5,5,229,35"/></map></td></tr></table></center>
  77 </div>
  78 </p>
  79 <table border="0" cellpadding="0" cellspacing="0">
  80 <tr><td colspan="2"><h2>Functions</h2></td></tr>
  81 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</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><td class="mdescLeft">&nbsp;</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><td class="memItemLeft" align="right" valign="top">float&nbsp;</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><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
  85 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</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><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded circular RNA.  <a href="#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
  87 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</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><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded circular RNA.  <a href="#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
  89 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</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><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
  91 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</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><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
  93 <tr><td colspan="2"><h2>Variables</h2></td></tr>
  94 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a><!-- doxytag: member="eval::eos_debug" ref="ga567530678f6260a1a649a5beca5da4c5" args="" -->
  95 int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
  96 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>
  97 </table>
  98 <hr/><a name="_details"></a><h2>Detailed Description</h2>
  99 <p>This module contains all functions and variables related to energy evaluation of sequence/structure pairs. </p>
 100 <hr/><h2>Function Documentation</h2>
 101 <a class="anchor" id="gaf93986cb3cb29770ec9cca69c9fab8cf"></a><!-- doxytag: member="fold.h::energy_of_structure" ref="gaf93986cb3cb29770ec9cca69c9fab8cf" args="(const char *string, const char *structure, int verbosity_level)" -->
 102 <div class="memitem">
 103 <div class="memproto">
 104       <table class="memname">
 105         <tr>
 106           <td class="memname">float energy_of_structure </td>
 107           <td>(</td>
 108           <td class="paramtype">const char *&nbsp;</td>
 109           <td class="paramname"> <em>string</em>, </td>
 110         </tr>
 111         <tr>
 112           <td class="paramkey"></td>
 113           <td></td>
 114           <td class="paramtype">const char *&nbsp;</td>
 115           <td class="paramname"> <em>structure</em>, </td>
 116         </tr>
 117         <tr>
 118           <td class="paramkey"></td>
 119           <td></td>
 120           <td class="paramtype">int&nbsp;</td>
 121           <td class="paramname"> <em>verbosity_level</em></td><td>&nbsp;</td>
 122         </tr>
 123         <tr>
 124           <td></td>
 125           <td>)</td>
 126           <td></td><td></td><td></td>
 127         </tr>
 128       </table>
 129 </div>
 130 <div class="memdoc">
 131
 132 <p>Calculate the free energy of an already folded RNA using global model detail settings. </p>
 133 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 134 <dl class="note"><dt><b>Note:</b></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>
 135 <dl class="see"><dt><b>See also:</b></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>
 136 <dl><dt><b>Parameters:</b></dt><dd>
 137   <table border="0" cellspacing="2" cellpadding="0">
 138     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 139     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>secondary structure in dot-bracket notation </td></tr>
 140     <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em>&nbsp;</td><td>a flag to turn verbose output on/off </td></tr>
 141   </table>
 142   </dd>
 143 </dl>
 144 <dl class="return"><dt><b>Returns:</b></dt><dd>the free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 145
 146 </div>
 147 </div>
 148 <a class="anchor" id="gab5169ea4f72f250e43811463a33f4e40"></a><!-- doxytag: member="fold.h::energy_of_struct_par" ref="gab5169ea4f72f250e43811463a33f4e40" args="(const char *string, const char *structure, paramT *parameters, int verbosity_level)" -->
 149 <div class="memitem">
 150 <div class="memproto">
 151       <table class="memname">
 152         <tr>
 153           <td class="memname">float energy_of_struct_par </td>
 154           <td>(</td>
 155           <td class="paramtype">const char *&nbsp;</td>
 156           <td class="paramname"> <em>string</em>, </td>
 157         </tr>
 158         <tr>
 159           <td class="paramkey"></td>
 160           <td></td>
 161           <td class="paramtype">const char *&nbsp;</td>
 162           <td class="paramname"> <em>structure</em>, </td>
 163         </tr>
 164         <tr>
 165           <td class="paramkey"></td>
 166           <td></td>
 167           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&nbsp;</td>
 168           <td class="paramname"> <em>parameters</em>, </td>
 169         </tr>
 170         <tr>
 171           <td class="paramkey"></td>
 172           <td></td>
 173           <td class="paramtype">int&nbsp;</td>
 174           <td class="paramname"> <em>verbosity_level</em></td><td>&nbsp;</td>
 175         </tr>
 176         <tr>
 177           <td></td>
 178           <td>)</td>
 179           <td></td><td></td><td></td>
 180         </tr>
 181       </table>
 182 </div>
 183 <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="see"><dt><b>See also:</b></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><dt><b>Parameters:</b></dt><dd>
 189   <table border="0" cellspacing="2" cellpadding="0">
 190     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence in uppercase letters </td></tr>
 191     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>Secondary structure in dot-bracket notation </td></tr>
 192     <tr><td valign="top"></td><td valign="top"><em>parameters</em>&nbsp;</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
 193     <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em>&nbsp;</td><td>A flag to turn verbose output on/off </td></tr>
 194   </table>
 195   </dd>
 196 </dl>
 197 <dl class="return"><dt><b>Returns:</b></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><!-- doxytag: member="fold.h::energy_of_circ_structure" ref="gaeb14f3664aec67fc03268ac75253f0f8" args="(const char *string, const char *structure, int verbosity_level)" -->
 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 *&nbsp;</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 *&nbsp;</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&nbsp;</td>
 221           <td class="paramname"> <em>verbosity_level</em></td><td>&nbsp;</td>
 222         </tr>
 223         <tr>
 224           <td></td>
 225           <td>)</td>
 226           <td></td><td></td><td></td>
 227         </tr>
 228       </table>
 229 </div>
 230 <div class="memdoc">
 231
 232 <p>Calculate the free energy of an already folded circular RNA. </p>
 233 <dl class="note"><dt><b>Note:</b></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>
 234 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 235 <dl class="see"><dt><b>See also:</b></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>
 236 <dl><dt><b>Parameters:</b></dt><dd>
 237   <table border="0" cellspacing="2" cellpadding="0">
 238     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 239     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>Secondary structure in dot-bracket notation </td></tr>
 240     <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em>&nbsp;</td><td>A flag to turn verbose output on/off </td></tr>
 241   </table>
 242   </dd>
 243 </dl>
 244 <dl class="return"><dt><b>Returns:</b></dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 245
 246 </div>
 247 </div>
 248 <a class="anchor" id="ga75dc765ee4a1177832bc817c94cf88e5"></a><!-- doxytag: member="fold.h::energy_of_circ_struct_par" ref="ga75dc765ee4a1177832bc817c94cf88e5" args="(const char *string, const char *structure, paramT *parameters, int verbosity_level)" -->
 249 <div class="memitem">
 250 <div class="memproto">
 251       <table class="memname">
 252         <tr>
 253           <td class="memname">float energy_of_circ_struct_par </td>
 254           <td>(</td>
 255           <td class="paramtype">const char *&nbsp;</td>
 256           <td class="paramname"> <em>string</em>, </td>
 257         </tr>
 258         <tr>
 259           <td class="paramkey"></td>
 260           <td></td>
 261           <td class="paramtype">const char *&nbsp;</td>
 262           <td class="paramname"> <em>structure</em>, </td>
 263         </tr>
 264         <tr>
 265           <td class="paramkey"></td>
 266           <td></td>
 267           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&nbsp;</td>
 268           <td class="paramname"> <em>parameters</em>, </td>
 269         </tr>
 270         <tr>
 271           <td class="paramkey"></td>
 272           <td></td>
 273           <td class="paramtype">int&nbsp;</td>
 274           <td class="paramname"> <em>verbosity_level</em></td><td>&nbsp;</td>
 275         </tr>
 276         <tr>
 277           <td></td>
 278           <td>)</td>
 279           <td></td><td></td><td></td>
 280         </tr>
 281       </table>
 282 </div>
 283 <div class="memdoc">
 284
 285 <p>Calculate the free energy of an already folded circular RNA. </p>
 286 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 287 <dl class="see"><dt><b>See also:</b></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>
 288 <dl><dt><b>Parameters:</b></dt><dd>
 289   <table border="0" cellspacing="2" cellpadding="0">
 290     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 291     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>Secondary structure in dot-bracket notation </td></tr>
 292     <tr><td valign="top"></td><td valign="top"><em>parameters</em>&nbsp;</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
 293     <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em>&nbsp;</td><td>A flag to turn verbose output on/off </td></tr>
 294   </table>
 295   </dd>
 296 </dl>
 297 <dl class="return"><dt><b>Returns:</b></dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
 298
 299 </div>
 300 </div>
 301 <a class="anchor" id="ga8831445966b761417e713360791299d8"></a><!-- doxytag: member="fold.h::energy_of_structure_pt" ref="ga8831445966b761417e713360791299d8" args="(const char *string, short *ptable, short *s, short *s1, int verbosity_level)" -->
 302 <div class="memitem">
 303 <div class="memproto">
 304       <table class="memname">
 305         <tr>
 306           <td class="memname">int energy_of_structure_pt </td>
 307           <td>(</td>
 308           <td class="paramtype">const char *&nbsp;</td>
 309           <td class="paramname"> <em>string</em>, </td>
 310         </tr>
 311         <tr>
 312           <td class="paramkey"></td>
 313           <td></td>
 314           <td class="paramtype">short *&nbsp;</td>
 315           <td class="paramname"> <em>ptable</em>, </td>
 316         </tr>
 317         <tr>
 318           <td class="paramkey"></td>
 319           <td></td>
 320           <td class="paramtype">short *&nbsp;</td>
 321           <td class="paramname"> <em>s</em>, </td>
 322         </tr>
 323         <tr>
 324           <td class="paramkey"></td>
 325           <td></td>
 326           <td class="paramtype">short *&nbsp;</td>
 327           <td class="paramname"> <em>s1</em>, </td>
 328         </tr>
 329         <tr>
 330           <td class="paramkey"></td>
 331           <td></td>
 332           <td class="paramtype">int&nbsp;</td>
 333           <td class="paramname"> <em>verbosity_level</em></td><td>&nbsp;</td>
 334         </tr>
 335         <tr>
 336           <td></td>
 337           <td>)</td>
 338           <td></td><td></td><td></td>
 339         </tr>
 340       </table>
 341 </div>
 342 <div class="memdoc">
 343
 344 <p>Calculate the free energy of an already folded RNA. </p>
 345 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 346 <dl class="note"><dt><b>Note:</b></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>
 347 <dl class="see"><dt><b>See also:</b></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>
 348 <dl><dt><b>Parameters:</b></dt><dd>
 349   <table border="0" cellspacing="2" cellpadding="0">
 350     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 351     <tr><td valign="top"></td><td valign="top"><em>ptable</em>&nbsp;</td><td>the pair table of the secondary structure </td></tr>
 352     <tr><td valign="top"></td><td valign="top"><em>s</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 353     <tr><td valign="top"></td><td valign="top"><em>s1</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 354     <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em>&nbsp;</td><td>a flag to turn verbose output on/off </td></tr>
 355   </table>
 356   </dd>
 357 </dl>
 358 <dl class="return"><dt><b>Returns:</b></dt><dd>the free energy of the input structure given the input sequence in 10kcal/mol </dd></dl>
 359
 360 </div>
 361 </div>
 362 <a class="anchor" id="gada4701dd7519b29da75ceac147601f4e"></a><!-- doxytag: member="fold.h::energy_of_struct_pt_par" ref="gada4701dd7519b29da75ceac147601f4e" args="(const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level)" -->
 363 <div class="memitem">
 364 <div class="memproto">
 365       <table class="memname">
 366         <tr>
 367           <td class="memname">int energy_of_struct_pt_par </td>
 368           <td>(</td>
 369           <td class="paramtype">const char *&nbsp;</td>
 370           <td class="paramname"> <em>string</em>, </td>
 371         </tr>
 372         <tr>
 373           <td class="paramkey"></td>
 374           <td></td>
 375           <td class="paramtype">short *&nbsp;</td>
 376           <td class="paramname"> <em>ptable</em>, </td>
 377         </tr>
 378         <tr>
 379           <td class="paramkey"></td>
 380           <td></td>
 381           <td class="paramtype">short *&nbsp;</td>
 382           <td class="paramname"> <em>s</em>, </td>
 383         </tr>
 384         <tr>
 385           <td class="paramkey"></td>
 386           <td></td>
 387           <td class="paramtype">short *&nbsp;</td>
 388           <td class="paramname"> <em>s1</em>, </td>
 389         </tr>
 390         <tr>
 391           <td class="paramkey"></td>
 392           <td></td>
 393           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&nbsp;</td>
 394           <td class="paramname"> <em>parameters</em>, </td>
 395         </tr>
 396         <tr>
 397           <td class="paramkey"></td>
 398           <td></td>
 399           <td class="paramtype">int&nbsp;</td>
 400           <td class="paramname"> <em>verbosity_level</em></td><td>&nbsp;</td>
 401         </tr>
 402         <tr>
 403           <td></td>
 404           <td>)</td>
 405           <td></td><td></td><td></td>
 406         </tr>
 407       </table>
 408 </div>
 409 <div class="memdoc">
 410
 411 <p>Calculate the free energy of an already folded RNA. </p>
 412 <p>If verbosity level is set to a value &gt;0, energies of structure elements are printed to stdout</p>
 413 <dl class="see"><dt><b>See also:</b></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>
 414 <dl><dt><b>Parameters:</b></dt><dd>
 415   <table border="0" cellspacing="2" cellpadding="0">
 416     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence in uppercase letters </td></tr>
 417     <tr><td valign="top"></td><td valign="top"><em>ptable</em>&nbsp;</td><td>The pair table of the secondary structure </td></tr>
 418     <tr><td valign="top"></td><td valign="top"><em>s</em>&nbsp;</td><td>Encoded RNA sequence </td></tr>
 419     <tr><td valign="top"></td><td valign="top"><em>s1</em>&nbsp;</td><td>Encoded RNA sequence </td></tr>
 420     <tr><td valign="top"></td><td valign="top"><em>parameters</em>&nbsp;</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
 421     <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em>&nbsp;</td><td>A flag to turn verbose output on/off </td></tr>
 422   </table>
 423   </dd>
 424 </dl>
 425 <dl class="return"><dt><b>Returns:</b></dt><dd>The free energy of the input structure given the input sequence in 10kcal/mol </dd></dl>
 426
 427 </div>
 428 </div>
 429 </div>
 430 <hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
 431 <a href="http://www.doxygen.org/index.html">
 432 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 433 </body>
 434 </html>