binaries/src/ViennaRNA/doc/html/fold_8h.html

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  70 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h File Reference</h1>
  71 <p>MFE calculations and energy evaluations for single RNA sequences.
  72 <a href="#_details">More...</a></p>
  73 <div class="dynheader">
  74 Include dependency graph for fold.h:</div>
  75 <div class="dynsection">
  76 <div class="center"><img src="fold_8h__incl.png" border="0" usemap="#_2homes_2fmmarquesmadeira_2Projects_2jabaws_2binaries_2src_2ViennaRNA_2H_2fold_8h_map" alt=""/></div>
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  78 <area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found..." alt="" coords="185,86,308,117"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="191,166,303,197"/></map>
  79 </div>
  80
  81 <p><a href="fold_8h_source.html">Go to the source code of this file.</a></p>
  82 <table border="0" cellpadding="0" cellspacing="0">
  83 <tr><td colspan="2"><h2>Functions</h2></td></tr>
  84 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e">fold_par</a> (const char *sequence, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int is_constrained, int is_circular)</td></tr>
  85 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of an RNA sequence.  <a href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e"></a><br/></td></tr>
  86 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b">fold</a> (const char *sequence, char *structure)</td></tr>
  87 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of an RNA sequence.  <a href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b"></a><br/></td></tr>
  88 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423">circfold</a> (const char *sequence, char *structure)</td></tr>
  89 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.  <a href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423"></a><br/></td></tr>
  90 <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>
  91 <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="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf"></a><br/></td></tr>
  92 <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>
  93 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
  94 <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>
  95 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded circular RNA.  <a href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
  96 <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>
  97 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded circular RNA.  <a href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
  98 <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>
  99 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="group__eval.html#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
 100 <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>
 101 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate the free energy of an already folded RNA.  <a href="group__eval.html#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
 102 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga107fdfe5fd641868156bfd849f6866c7"></a><!-- doxytag: member="fold.h::free_arrays" ref="ga107fdfe5fd641868156bfd849f6866c7" args="(void)" -->
 103 void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7">free_arrays</a> (void)</td></tr>
 104 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Free arrays for mfe folding. <br/></td></tr>
 105 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a87b7869bd1d8dc79c60775c74e009e9b">parenthesis_structure</a> (char *structure, <a class="el" href="structbondT.html">bondT</a> *bp, int length)</td></tr>
 106 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Create a dot-backet/parenthesis structure from backtracking stack.  <a href="#a87b7869bd1d8dc79c60775c74e009e9b"></a><br/></td></tr>
 107 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a325f3835c68f34fe833b2b7a5828857f">parenthesis_zuker</a> (char *structure, <a class="el" href="structbondT.html">bondT</a> *bp, int length)</td></tr>
 108 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.  <a href="#a325f3835c68f34fe833b2b7a5828857f"></a><br/></td></tr>
 109 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga41bf8f6fa15b94471f7095cad9f0ccf3"></a><!-- doxytag: member="fold.h::update_fold_params" ref="ga41bf8f6fa15b94471f7095cad9f0ccf3" args="(void)" -->
 110 void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga41bf8f6fa15b94471f7095cad9f0ccf3">update_fold_params</a> (void)</td></tr>
 111 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Recalculate energy parameters. <br/></td></tr>
 112 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a539ecaed89730f7644c202f304d7529b">energy_of_move</a> (const char *string, const char *structure, int m1, int m2)</td></tr>
 113 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate energy of a move (closing or opening of a base pair).  <a href="#a539ecaed89730f7644c202f304d7529b"></a><br/></td></tr>
 114 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a49e0ee561be69faf0568213546f6a53f">energy_of_move_pt</a> (short *pt, short *s, short *s1, int m1, int m2)</td></tr>
 115 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate energy of a move (closing or opening of a base pair).  <a href="#a49e0ee561be69faf0568213546f6a53f"></a><br/></td></tr>
 116 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a507d4fd93f4b398d793ba2402731388d">loop_energy</a> (short *ptable, short *s, short *s1, int i)</td></tr>
 117 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate energy of a loop.  <a href="#a507d4fd93f4b398d793ba2402731388d"></a><br/></td></tr>
 118 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#adaa59b81664e2e36cb9932e891558fae">assign_plist_from_db</a> (<a class="el" href="structplist.html">plist</a> **pl, const char *struc, float <a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
 119 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Create a <a class="el" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> from a dot-bracket string.  <a href="#adaa59b81664e2e36cb9932e891558fae"></a><br/></td></tr>
 120 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a> (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)</td></tr>
 121 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a> (int size, int type, int si1, int sj1, const char *string)</td></tr>
 122 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a> (int length)</td></tr>
 123 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a> (const char *string, const char *structure)</td></tr>
 124 <tr><td class="memItemLeft" align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a> (const char *string, short *ptable, short *s, short *s1)</td></tr>
 125 <tr><td class="memItemLeft" align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a> (const char *string, const char *structure)</td></tr>
 126 <tr><td colspan="2"><h2>Variables</h2></td></tr>
 127 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a80c3c5fd35e7479704cc91d2d0367743"></a><!-- doxytag: member="fold.h::logML" ref="a80c3c5fd35e7479704cc91d2d0367743" args="" -->
 128 int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743">logML</a></td></tr>
 129 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">if nonzero use logarithmic ML energy in energy_of_struct <br/></td></tr>
 130 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6c5655c8b272e3e6cab74dd0f540294f"></a><!-- doxytag: member="fold.h::uniq_ML" ref="a6c5655c8b272e3e6cab74dd0f540294f" args="" -->
 131 int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a6c5655c8b272e3e6cab74dd0f540294f">uniq_ML</a></td></tr>
 132 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">do ML decomposition uniquely (for subopt) <br/></td></tr>
 133 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ab9b2c3a37a5516614c06d0ab54b97cda"></a><!-- doxytag: member="fold.h::cut_point" ref="ab9b2c3a37a5516614c06d0ab54b97cda" args="" -->
 134 int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda">cut_point</a></td></tr>
 135 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">set to first pos of second seq for cofolding <br/></td></tr>
 136 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a><!-- doxytag: member="fold.h::eos_debug" ref="ga567530678f6260a1a649a5beca5da4c5" args="" -->
 137 int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
 138 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>
 139 </table>
 140 <hr/><a name="_details"></a><h2>Detailed Description</h2>
 141 <p>MFE calculations and energy evaluations for single RNA sequences. </p>
 142 <p>This file includes (almost) all function declarations within the RNAlib that are related to MFE folding... </p>
 143 <hr/><h2>Function Documentation</h2>
 144 <a class="anchor" id="a87b7869bd1d8dc79c60775c74e009e9b"></a><!-- doxytag: member="fold.h::parenthesis_structure" ref="a87b7869bd1d8dc79c60775c74e009e9b" args="(char *structure, bondT *bp, int length)" -->
 145 <div class="memitem">
 146 <div class="memproto">
 147       <table class="memname">
 148         <tr>
 149           <td class="memname">void parenthesis_structure </td>
 150           <td>(</td>
 151           <td class="paramtype">char *&nbsp;</td>
 152           <td class="paramname"> <em>structure</em>, </td>
 153         </tr>
 154         <tr>
 155           <td class="paramkey"></td>
 156           <td></td>
 157           <td class="paramtype"><a class="el" href="structbondT.html">bondT</a> *&nbsp;</td>
 158           <td class="paramname"> <em>bp</em>, </td>
 159         </tr>
 160         <tr>
 161           <td class="paramkey"></td>
 162           <td></td>
 163           <td class="paramtype">int&nbsp;</td>
 164           <td class="paramname"> <em>length</em></td><td>&nbsp;</td>
 165         </tr>
 166         <tr>
 167           <td></td>
 168           <td>)</td>
 169           <td></td><td></td><td></td>
 170         </tr>
 171       </table>
 172 </div>
 173 <div class="memdoc">
 174
 175 <p>Create a dot-backet/parenthesis structure from backtracking stack. </p>
 176 <dl class="note"><dt><b>Note:</b></dt><dd>This function is threadsafe </dd></dl>
 177
 178 </div>
 179 </div>
 180 <a class="anchor" id="a325f3835c68f34fe833b2b7a5828857f"></a><!-- doxytag: member="fold.h::parenthesis_zuker" ref="a325f3835c68f34fe833b2b7a5828857f" args="(char *structure, bondT *bp, int length)" -->
 181 <div class="memitem">
 182 <div class="memproto">
 183       <table class="memname">
 184         <tr>
 185           <td class="memname">void parenthesis_zuker </td>
 186           <td>(</td>
 187           <td class="paramtype">char *&nbsp;</td>
 188           <td class="paramname"> <em>structure</em>, </td>
 189         </tr>
 190         <tr>
 191           <td class="paramkey"></td>
 192           <td></td>
 193           <td class="paramtype"><a class="el" href="structbondT.html">bondT</a> *&nbsp;</td>
 194           <td class="paramname"> <em>bp</em>, </td>
 195         </tr>
 196         <tr>
 197           <td class="paramkey"></td>
 198           <td></td>
 199           <td class="paramtype">int&nbsp;</td>
 200           <td class="paramname"> <em>length</em></td><td>&nbsp;</td>
 201         </tr>
 202         <tr>
 203           <td></td>
 204           <td>)</td>
 205           <td></td><td></td><td></td>
 206         </tr>
 207       </table>
 208 </div>
 209 <div class="memdoc">
 210
 211 <p>Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. </p>
 212 <dl class="note"><dt><b>Note:</b></dt><dd>This function is threadsafe </dd></dl>
 213
 214 </div>
 215 </div>
 216 <a class="anchor" id="a539ecaed89730f7644c202f304d7529b"></a><!-- doxytag: member="fold.h::energy_of_move" ref="a539ecaed89730f7644c202f304d7529b" args="(const char *string, const char *structure, int m1, int m2)" -->
 217 <div class="memitem">
 218 <div class="memproto">
 219       <table class="memname">
 220         <tr>
 221           <td class="memname">float energy_of_move </td>
 222           <td>(</td>
 223           <td class="paramtype">const char *&nbsp;</td>
 224           <td class="paramname"> <em>string</em>, </td>
 225         </tr>
 226         <tr>
 227           <td class="paramkey"></td>
 228           <td></td>
 229           <td class="paramtype">const char *&nbsp;</td>
 230           <td class="paramname"> <em>structure</em>, </td>
 231         </tr>
 232         <tr>
 233           <td class="paramkey"></td>
 234           <td></td>
 235           <td class="paramtype">int&nbsp;</td>
 236           <td class="paramname"> <em>m1</em>, </td>
 237         </tr>
 238         <tr>
 239           <td class="paramkey"></td>
 240           <td></td>
 241           <td class="paramtype">int&nbsp;</td>
 242           <td class="paramname"> <em>m2</em></td><td>&nbsp;</td>
 243         </tr>
 244         <tr>
 245           <td></td>
 246           <td>)</td>
 247           <td></td><td></td><td></td>
 248         </tr>
 249       </table>
 250 </div>
 251 <div class="memdoc">
 252
 253 <p>Calculate energy of a move (closing or opening of a base pair). </p>
 254 <p>If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).</p>
 255 <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="fold_8h.html#a539ecaed89730f7644c202f304d7529b" title="Calculate energy of a move (closing or opening of a base pair).">energy_of_move()</a> </dd></dl>
 256 <dl><dt><b>Parameters:</b></dt><dd>
 257   <table border="0" cellspacing="2" cellpadding="0">
 258     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 259     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>secondary structure in dot-bracket notation </td></tr>
 260     <tr><td valign="top"></td><td valign="top"><em>m1</em>&nbsp;</td><td>first coordinate of base pair </td></tr>
 261     <tr><td valign="top"></td><td valign="top"><em>m2</em>&nbsp;</td><td>second coordinate of base pair </td></tr>
 262   </table>
 263   </dd>
 264 </dl>
 265 <dl class="return"><dt><b>Returns:</b></dt><dd>energy change of the move in kcal/mol </dd></dl>
 266
 267 </div>
 268 </div>
 269 <a class="anchor" id="a49e0ee561be69faf0568213546f6a53f"></a><!-- doxytag: member="fold.h::energy_of_move_pt" ref="a49e0ee561be69faf0568213546f6a53f" args="(short *pt, short *s, short *s1, int m1, int m2)" -->
 270 <div class="memitem">
 271 <div class="memproto">
 272       <table class="memname">
 273         <tr>
 274           <td class="memname">int energy_of_move_pt </td>
 275           <td>(</td>
 276           <td class="paramtype">short *&nbsp;</td>
 277           <td class="paramname"> <em>pt</em>, </td>
 278         </tr>
 279         <tr>
 280           <td class="paramkey"></td>
 281           <td></td>
 282           <td class="paramtype">short *&nbsp;</td>
 283           <td class="paramname"> <em>s</em>, </td>
 284         </tr>
 285         <tr>
 286           <td class="paramkey"></td>
 287           <td></td>
 288           <td class="paramtype">short *&nbsp;</td>
 289           <td class="paramname"> <em>s1</em>, </td>
 290         </tr>
 291         <tr>
 292           <td class="paramkey"></td>
 293           <td></td>
 294           <td class="paramtype">int&nbsp;</td>
 295           <td class="paramname"> <em>m1</em>, </td>
 296         </tr>
 297         <tr>
 298           <td class="paramkey"></td>
 299           <td></td>
 300           <td class="paramtype">int&nbsp;</td>
 301           <td class="paramname"> <em>m2</em></td><td>&nbsp;</td>
 302         </tr>
 303         <tr>
 304           <td></td>
 305           <td>)</td>
 306           <td></td><td></td><td></td>
 307         </tr>
 308       </table>
 309 </div>
 310 <div class="memdoc">
 311
 312 <p>Calculate energy of a move (closing or opening of a base pair). </p>
 313 <p>If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).</p>
 314 <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="fold_8h.html#a539ecaed89730f7644c202f304d7529b" title="Calculate energy of a move (closing or opening of a base pair).">energy_of_move()</a> </dd></dl>
 315 <dl><dt><b>Parameters:</b></dt><dd>
 316   <table border="0" cellspacing="2" cellpadding="0">
 317     <tr><td valign="top"></td><td valign="top"><em>pt</em>&nbsp;</td><td>the pair table of the secondary structure </td></tr>
 318     <tr><td valign="top"></td><td valign="top"><em>s</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 319     <tr><td valign="top"></td><td valign="top"><em>s1</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 320     <tr><td valign="top"></td><td valign="top"><em>m1</em>&nbsp;</td><td>first coordinate of base pair </td></tr>
 321     <tr><td valign="top"></td><td valign="top"><em>m2</em>&nbsp;</td><td>second coordinate of base pair </td></tr>
 322   </table>
 323   </dd>
 324 </dl>
 325 <dl class="return"><dt><b>Returns:</b></dt><dd>energy change of the move in 10cal/mol </dd></dl>
 326
 327 </div>
 328 </div>
 329 <a class="anchor" id="a507d4fd93f4b398d793ba2402731388d"></a><!-- doxytag: member="fold.h::loop_energy" ref="a507d4fd93f4b398d793ba2402731388d" args="(short *ptable, short *s, short *s1, int i)" -->
 330 <div class="memitem">
 331 <div class="memproto">
 332       <table class="memname">
 333         <tr>
 334           <td class="memname">int loop_energy </td>
 335           <td>(</td>
 336           <td class="paramtype">short *&nbsp;</td>
 337           <td class="paramname"> <em>ptable</em>, </td>
 338         </tr>
 339         <tr>
 340           <td class="paramkey"></td>
 341           <td></td>
 342           <td class="paramtype">short *&nbsp;</td>
 343           <td class="paramname"> <em>s</em>, </td>
 344         </tr>
 345         <tr>
 346           <td class="paramkey"></td>
 347           <td></td>
 348           <td class="paramtype">short *&nbsp;</td>
 349           <td class="paramname"> <em>s1</em>, </td>
 350         </tr>
 351         <tr>
 352           <td class="paramkey"></td>
 353           <td></td>
 354           <td class="paramtype">int&nbsp;</td>
 355           <td class="paramname"> <em>i</em></td><td>&nbsp;</td>
 356         </tr>
 357         <tr>
 358           <td></td>
 359           <td>)</td>
 360           <td></td><td></td><td></td>
 361         </tr>
 362       </table>
 363 </div>
 364 <div class="memdoc">
 365
 366 <p>Calculate energy of a loop. </p>
 367 <dl><dt><b>Parameters:</b></dt><dd>
 368   <table border="0" cellspacing="2" cellpadding="0">
 369     <tr><td valign="top"></td><td valign="top"><em>ptable</em>&nbsp;</td><td>the pair table of the secondary structure </td></tr>
 370     <tr><td valign="top"></td><td valign="top"><em>s</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 371     <tr><td valign="top"></td><td valign="top"><em>s1</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 372     <tr><td valign="top"></td><td valign="top"><em>i</em>&nbsp;</td><td>position of covering base pair </td></tr>
 373   </table>
 374   </dd>
 375 </dl>
 376 <dl class="return"><dt><b>Returns:</b></dt><dd>free energy of the loop in 10cal/mol </dd></dl>
 377
 378 </div>
 379 </div>
 380 <a class="anchor" id="adaa59b81664e2e36cb9932e891558fae"></a><!-- doxytag: member="fold.h::assign_plist_from_db" ref="adaa59b81664e2e36cb9932e891558fae" args="(plist **pl, const char *struc, float pr)" -->
 381 <div class="memitem">
 382 <div class="memproto">
 383       <table class="memname">
 384         <tr>
 385           <td class="memname">void assign_plist_from_db </td>
 386           <td>(</td>
 387           <td class="paramtype"><a class="el" href="structplist.html">plist</a> **&nbsp;</td>
 388           <td class="paramname"> <em>pl</em>, </td>
 389         </tr>
 390         <tr>
 391           <td class="paramkey"></td>
 392           <td></td>
 393           <td class="paramtype">const char *&nbsp;</td>
 394           <td class="paramname"> <em>struc</em>, </td>
 395         </tr>
 396         <tr>
 397           <td class="paramkey"></td>
 398           <td></td>
 399           <td class="paramtype">float&nbsp;</td>
 400           <td class="paramname"> <em>pr</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>Create a <a class="el" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> from a dot-bracket string. </p>
 412 <p>The dot-bracket string is parsed and for each base pair an entry in the <a class="el" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> is created. The probability of each pair in the list is set by a function parameter.</p>
 413 <p>The end of the <a class="el" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries</p>
 414 <p>This function is threadsafe</p>
 415 <dl><dt><b>Parameters:</b></dt><dd>
 416   <table border="0" cellspacing="2" cellpadding="0">
 417     <tr><td valign="top"></td><td valign="top"><em>pl</em>&nbsp;</td><td>A pointer to the <a class="el" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> that is to be created </td></tr>
 418     <tr><td valign="top"></td><td valign="top"><em>struc</em>&nbsp;</td><td>The secondary structure in dot-bracket notation </td></tr>
 419     <tr><td valign="top"></td><td valign="top"><em>pr</em>&nbsp;</td><td>The probability for each base pair </td></tr>
 420   </table>
 421   </dd>
 422 </dl>
 423
 424 </div>
 425 </div>
 426 <a class="anchor" id="a2163034a25c6115d894b199e97e03f6c"></a><!-- doxytag: member="fold.h::LoopEnergy" ref="a2163034a25c6115d894b199e97e03f6c" args="(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)" -->
 427 <div class="memitem">
 428 <div class="memproto">
 429       <table class="memname">
 430         <tr>
 431           <td class="memname">int LoopEnergy </td>
 432           <td>(</td>
 433           <td class="paramtype">int&nbsp;</td>
 434           <td class="paramname"> <em>n1</em>, </td>
 435         </tr>
 436         <tr>
 437           <td class="paramkey"></td>
 438           <td></td>
 439           <td class="paramtype">int&nbsp;</td>
 440           <td class="paramname"> <em>n2</em>, </td>
 441         </tr>
 442         <tr>
 443           <td class="paramkey"></td>
 444           <td></td>
 445           <td class="paramtype">int&nbsp;</td>
 446           <td class="paramname"> <em>type</em>, </td>
 447         </tr>
 448         <tr>
 449           <td class="paramkey"></td>
 450           <td></td>
 451           <td class="paramtype">int&nbsp;</td>
 452           <td class="paramname"> <em>type_2</em>, </td>
 453         </tr>
 454         <tr>
 455           <td class="paramkey"></td>
 456           <td></td>
 457           <td class="paramtype">int&nbsp;</td>
 458           <td class="paramname"> <em>si1</em>, </td>
 459         </tr>
 460         <tr>
 461           <td class="paramkey"></td>
 462           <td></td>
 463           <td class="paramtype">int&nbsp;</td>
 464           <td class="paramname"> <em>sj1</em>, </td>
 465         </tr>
 466         <tr>
 467           <td class="paramkey"></td>
 468           <td></td>
 469           <td class="paramtype">int&nbsp;</td>
 470           <td class="paramname"> <em>sp1</em>, </td>
 471         </tr>
 472         <tr>
 473           <td class="paramkey"></td>
 474           <td></td>
 475           <td class="paramtype">int&nbsp;</td>
 476           <td class="paramname"> <em>sq1</em></td><td>&nbsp;</td>
 477         </tr>
 478         <tr>
 479           <td></td>
 480           <td>)</td>
 481           <td></td><td></td><td></td>
 482         </tr>
 483       </table>
 484 </div>
 485 <div class="memdoc">
 486 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000002">Deprecated:</a></b></dt><dd>{This function is deprecated and will be removed soon. Use <a class="el" href="loop__energies_8h.html#a3e5ad89f451254b1fe366d77aa8ff7bd">E_IntLoop()</a> instead!} </dd></dl>
 487
 488 </div>
 489 </div>
 490 <a class="anchor" id="ab327ce11972f5ac069d52c8dedfdb700"></a><!-- doxytag: member="fold.h::HairpinE" ref="ab327ce11972f5ac069d52c8dedfdb700" args="(int size, int type, int si1, int sj1, const char *string)" -->
 491 <div class="memitem">
 492 <div class="memproto">
 493       <table class="memname">
 494         <tr>
 495           <td class="memname">int HairpinE </td>
 496           <td>(</td>
 497           <td class="paramtype">int&nbsp;</td>
 498           <td class="paramname"> <em>size</em>, </td>
 499         </tr>
 500         <tr>
 501           <td class="paramkey"></td>
 502           <td></td>
 503           <td class="paramtype">int&nbsp;</td>
 504           <td class="paramname"> <em>type</em>, </td>
 505         </tr>
 506         <tr>
 507           <td class="paramkey"></td>
 508           <td></td>
 509           <td class="paramtype">int&nbsp;</td>
 510           <td class="paramname"> <em>si1</em>, </td>
 511         </tr>
 512         <tr>
 513           <td class="paramkey"></td>
 514           <td></td>
 515           <td class="paramtype">int&nbsp;</td>
 516           <td class="paramname"> <em>sj1</em>, </td>
 517         </tr>
 518         <tr>
 519           <td class="paramkey"></td>
 520           <td></td>
 521           <td class="paramtype">const char *&nbsp;</td>
 522           <td class="paramname"> <em>string</em></td><td>&nbsp;</td>
 523         </tr>
 524         <tr>
 525           <td></td>
 526           <td>)</td>
 527           <td></td><td></td><td></td>
 528         </tr>
 529       </table>
 530 </div>
 531 <div class="memdoc">
 532 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000003">Deprecated:</a></b></dt><dd>{This function is deprecated and will be removed soon. Use <a class="el" href="loop__energies_8h.html#aa362183cf6db89a10cdb0f5c4bd180c6">E_Hairpin()</a> instead!} </dd></dl>
 533
 534 </div>
 535 </div>
 536 <a class="anchor" id="ac3f0a28d9cb609d388b155445073fd20"></a><!-- doxytag: member="fold.h::initialize_fold" ref="ac3f0a28d9cb609d388b155445073fd20" args="(int length)" -->
 537 <div class="memitem">
 538 <div class="memproto">
 539       <table class="memname">
 540         <tr>
 541           <td class="memname">void initialize_fold </td>
 542           <td>(</td>
 543           <td class="paramtype">int&nbsp;</td>
 544           <td class="paramname"> <em>length</em></td>
 545           <td>&nbsp;)&nbsp;</td>
 546           <td></td>
 547         </tr>
 548       </table>
 549 </div>
 550 <div class="memdoc">
 551 <p>Allocate arrays for folding<br/>
 552  </p>
 553 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000004">Deprecated:</a></b></dt><dd>{This function is deprecated and will be removed soon!}</dd></dl>
 554
 555 </div>
 556 </div>
 557 <a class="anchor" id="ac2b37fea2145c94d925a3f33378ef87b"></a><!-- doxytag: member="fold.h::energy_of_struct" ref="ac2b37fea2145c94d925a3f33378ef87b" args="(const char *string, const char *structure)" -->
 558 <div class="memitem">
 559 <div class="memproto">
 560       <table class="memname">
 561         <tr>
 562           <td class="memname">float energy_of_struct </td>
 563           <td>(</td>
 564           <td class="paramtype">const char *&nbsp;</td>
 565           <td class="paramname"> <em>string</em>, </td>
 566         </tr>
 567         <tr>
 568           <td class="paramkey"></td>
 569           <td></td>
 570           <td class="paramtype">const char *&nbsp;</td>
 571           <td class="paramname"> <em>structure</em></td><td>&nbsp;</td>
 572         </tr>
 573         <tr>
 574           <td></td>
 575           <td>)</td>
 576           <td></td><td></td><td></td>
 577         </tr>
 578       </table>
 579 </div>
 580 <div class="memdoc">
 581 <p>Calculate the free energy of an already folded RNA</p>
 582 <dl class="note"><dt><b>Note:</b></dt><dd>This function is not entirely threadsafe! Depending on the state of the global variable <a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a> it prints energy information to stdout or not...<br/>
 583 </dd></dl>
 584 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000005">Deprecated:</a></b></dt><dd>This function is deprecated and should not be used in future programs! Use <a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">energy_of_structure()</a> instead!</dd></dl>
 585 <dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf" title="Calculate the free energy of an already folded RNA using global model detail settings...">energy_of_structure</a>, <a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct()</a>, <a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt()</a> </dd></dl>
 586 <dl><dt><b>Parameters:</b></dt><dd>
 587   <table border="0" cellspacing="2" cellpadding="0">
 588     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 589     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>secondary structure in dot-bracket notation </td></tr>
 590   </table>
 591   </dd>
 592 </dl>
 593 <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>
 594
 595 </div>
 596 </div>
 597 <a class="anchor" id="a27ce6f68512d43bf1fe14a06c9d76d5c"></a><!-- doxytag: member="fold.h::energy_of_struct_pt" ref="a27ce6f68512d43bf1fe14a06c9d76d5c" args="(const char *string, short *ptable, short *s, short *s1)" -->
 598 <div class="memitem">
 599 <div class="memproto">
 600       <table class="memname">
 601         <tr>
 602           <td class="memname">int energy_of_struct_pt </td>
 603           <td>(</td>
 604           <td class="paramtype">const char *&nbsp;</td>
 605           <td class="paramname"> <em>string</em>, </td>
 606         </tr>
 607         <tr>
 608           <td class="paramkey"></td>
 609           <td></td>
 610           <td class="paramtype">short *&nbsp;</td>
 611           <td class="paramname"> <em>ptable</em>, </td>
 612         </tr>
 613         <tr>
 614           <td class="paramkey"></td>
 615           <td></td>
 616           <td class="paramtype">short *&nbsp;</td>
 617           <td class="paramname"> <em>s</em>, </td>
 618         </tr>
 619         <tr>
 620           <td class="paramkey"></td>
 621           <td></td>
 622           <td class="paramtype">short *&nbsp;</td>
 623           <td class="paramname"> <em>s1</em></td><td>&nbsp;</td>
 624         </tr>
 625         <tr>
 626           <td></td>
 627           <td>)</td>
 628           <td></td><td></td><td></td>
 629         </tr>
 630       </table>
 631 </div>
 632 <div class="memdoc">
 633 <p>Calculate the free energy of an already folded RNA</p>
 634 <dl class="note"><dt><b>Note:</b></dt><dd>This function is not entirely threadsafe! Depending on the state of the global variable <a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a> it prints energy information to stdout or not...<br/>
 635 </dd></dl>
 636 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000006">Deprecated:</a></b></dt><dd>This function is deprecated and should not be used in future programs! Use <a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">energy_of_structure_pt()</a> instead!</dd></dl>
 637 <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#gaf93986cb3cb29770ec9cca69c9fab8cf" title="Calculate the free energy of an already folded RNA using global model detail settings...">energy_of_structure()</a> </dd></dl>
 638 <dl><dt><b>Parameters:</b></dt><dd>
 639   <table border="0" cellspacing="2" cellpadding="0">
 640     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 641     <tr><td valign="top"></td><td valign="top"><em>ptable</em>&nbsp;</td><td>the pair table of the secondary structure </td></tr>
 642     <tr><td valign="top"></td><td valign="top"><em>s</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 643     <tr><td valign="top"></td><td valign="top"><em>s1</em>&nbsp;</td><td>encoded RNA sequence </td></tr>
 644   </table>
 645   </dd>
 646 </dl>
 647 <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>
 648
 649 </div>
 650 </div>
 651 <a class="anchor" id="a657222e2758c46bf13b416ef3032e417"></a><!-- doxytag: member="fold.h::energy_of_circ_struct" ref="a657222e2758c46bf13b416ef3032e417" args="(const char *string, const char *structure)" -->
 652 <div class="memitem">
 653 <div class="memproto">
 654       <table class="memname">
 655         <tr>
 656           <td class="memname">float energy_of_circ_struct </td>
 657           <td>(</td>
 658           <td class="paramtype">const char *&nbsp;</td>
 659           <td class="paramname"> <em>string</em>, </td>
 660         </tr>
 661         <tr>
 662           <td class="paramkey"></td>
 663           <td></td>
 664           <td class="paramtype">const char *&nbsp;</td>
 665           <td class="paramname"> <em>structure</em></td><td>&nbsp;</td>
 666         </tr>
 667         <tr>
 668           <td></td>
 669           <td>)</td>
 670           <td></td><td></td><td></td>
 671         </tr>
 672       </table>
 673 </div>
 674 <div class="memdoc">
 675 <p>Calculate the free energy of an already folded circular RNA</p>
 676 <dl class="note"><dt><b>Note:</b></dt><dd>This function is not entirely threadsafe! Depending on the state of the global variable <a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a> it prints energy information to stdout or not...<br/>
 677 </dd></dl>
 678 <dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000007">Deprecated:</a></b></dt><dd>This function is deprecated and should not be used in future programs Use <a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">energy_of_circ_structure()</a> instead!</dd></dl>
 679 <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="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct()</a>, <a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt()</a> </dd></dl>
 680 <dl><dt><b>Parameters:</b></dt><dd>
 681   <table border="0" cellspacing="2" cellpadding="0">
 682     <tr><td valign="top"></td><td valign="top"><em>string</em>&nbsp;</td><td>RNA sequence </td></tr>
 683     <tr><td valign="top"></td><td valign="top"><em>structure</em>&nbsp;</td><td>secondary structure in dot-bracket notation </td></tr>
 684   </table>
 685   </dd>
 686 </dl>
 687 <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>
 688
 689 </div>
 690 </div>
 691 </div>
 692 <hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
 693 <a href="http://www.doxygen.org/index.html">
 694 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 695 </body>
 696 </html>