binaries/src/ViennaRNA/doc/html/findpath_8h.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 <title>RNAlib-2.1.2: /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h File Reference</title>
   6 <link href="tabs.css" rel="stylesheet" type="text/css"/>
   7 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
   8 </head>
   9 <body>
  10 <!-- Generated by Doxygen 1.6.1 -->
  11 <script type="text/javascript">
  12 <!--
  13 function changeDisplayState (e){
  14   var num=this.id.replace(/[^[0-9]/g,'');
  15   var button=this.firstChild;
  16   var sectionDiv=document.getElementById('dynsection'+num);
  17   if (sectionDiv.style.display=='none'||sectionDiv.style.display==''){
  18     sectionDiv.style.display='block';
  19     button.src='open.gif';
  20   }else{
  21     sectionDiv.style.display='none';
  22     button.src='closed.gif';
  23   }
  24 }
  25 function initDynSections(){
  26   var divs=document.getElementsByTagName('div');
  27   var sectionCounter=1;
  28   for(var i=0;i<divs.length-1;i++){
  29     if(divs[i].className=='dynheader'&&divs[i+1].className=='dynsection'){
  30       var header=divs[i];
  31       var section=divs[i+1];
  32       var button=header.firstChild;
  33       if (button!='IMG'){
  34         divs[i].insertBefore(document.createTextNode(' '),divs[i].firstChild);
  35         button=document.createElement('img');
  36         divs[i].insertBefore(button,divs[i].firstChild);
  37       }
  38       header.style.cursor='pointer';
  39       header.onclick=changeDisplayState;
  40       header.id='dynheader'+sectionCounter;
  41       button.src='closed.gif';
  42       section.id='dynsection'+sectionCounter;
  43       section.style.display='none';
  44       section.style.marginLeft='14px';
  45       sectionCounter++;
  46     }
  47   }
  48 }
  49 window.onload = initDynSections;
  50 -->
  51 </script>
  52 <div class="navigation" id="top">
  53   <div class="tabs">
  54     <ul>
  55       <li><a href="main.html"><span>Main&nbsp;Page</span></a></li>
  56       <li><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
  57       <li><a href="modules.html"><span>Modules</span></a></li>
  58       <li><a href="annotated.html"><span>Data&nbsp;Structures</span></a></li>
  59       <li class="current"><a href="files.html"><span>Files</span></a></li>
  60     </ul>
  61   </div>
  62   <div class="tabs">
  63     <ul>
  64       <li><a href="files.html"><span>File&nbsp;List</span></a></li>
  65       <li><a href="globals.html"><span>Globals</span></a></li>
  66     </ul>
  67   </div>
  68 </div>
  69 <div class="contents">
  70 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h File Reference</h1>
  71 <p>Compute direct refolding paths between two secondary structures.
  72 <a href="#_details">More...</a></p>
  73 <div class="dynheader">
  74 Include dependency graph for findpath.h:</div>
  75 <div class="dynsection">
  76 <div class="center"><img src="findpath_8h__incl.png" border="0" usemap="#_2homes_2fmmarquesmadeira_2Projects_2jabaws_2binaries_2src_2ViennaRNA_2H_2findpath_8h_map" alt=""/></div>
  77 <map name="_2homes_2fmmarquesmadeira_2Projects_2jabaws_2binaries_2src_2ViennaRNA_2H_2findpath_8h_map" id="_2homes_2fmmarquesmadeira_2Projects_2jabaws_2binaries_2src_2ViennaRNA_2H_2findpath_8h">
  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="197,86,320,117"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="203,166,315,197"/></map>
  79 </div>
  80
  81 <p><a href="findpath_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">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="findpath_8h.html#ad0e14268e309af773ecd1fce6244ee50">find_saddle</a> (const char *seq, const char *struc1, const char *struc2, int max)</td></tr>
  85 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Find energy of a saddle point between 2 structures (serch only direct path).  <a href="#ad0e14268e309af773ecd1fce6244ee50"></a><br/></td></tr>
  86 <tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structpath__t.html">path_t</a> *&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="findpath_8h.html#a0ff35d65c892a3403af937c00a867ef9">get_path</a> (const char *seq, const char *s1, const char *s2, int maxkeep)</td></tr>
  87 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Find refolding path between 2 structures (serch only direct path).  <a href="#a0ff35d65c892a3403af937c00a867ef9"></a><br/></td></tr>
  88 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="findpath_8h.html#a326e6d1640bbfd035e3869f5f4c188f7">free_path</a> (<a class="el" href="structpath__t.html">path_t</a> *path)</td></tr>
  89 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Free memory allocated by <a class="el" href="findpath_8h.html#a0ff35d65c892a3403af937c00a867ef9" title="Find refolding path between 2 structures (serch only direct path).">get_path()</a> function.  <a href="#a326e6d1640bbfd035e3869f5f4c188f7"></a><br/></td></tr>
  90 </table>
  91 <hr/><a name="_details"></a><h2>Detailed Description</h2>
  92 <p>Compute direct refolding paths between two secondary structures. </p>
  93 <hr/><h2>Function Documentation</h2>
  94 <a class="anchor" id="ad0e14268e309af773ecd1fce6244ee50"></a><!-- doxytag: member="findpath.h::find_saddle" ref="ad0e14268e309af773ecd1fce6244ee50" args="(const char *seq, const char *struc1, const char *struc2, int max)" -->
  95 <div class="memitem">
  96 <div class="memproto">
  97       <table class="memname">
  98         <tr>
  99           <td class="memname">int find_saddle </td>
 100           <td>(</td>
 101           <td class="paramtype">const char *&nbsp;</td>
 102           <td class="paramname"> <em>seq</em>, </td>
 103         </tr>
 104         <tr>
 105           <td class="paramkey"></td>
 106           <td></td>
 107           <td class="paramtype">const char *&nbsp;</td>
 108           <td class="paramname"> <em>struc1</em>, </td>
 109         </tr>
 110         <tr>
 111           <td class="paramkey"></td>
 112           <td></td>
 113           <td class="paramtype">const char *&nbsp;</td>
 114           <td class="paramname"> <em>struc2</em>, </td>
 115         </tr>
 116         <tr>
 117           <td class="paramkey"></td>
 118           <td></td>
 119           <td class="paramtype">int&nbsp;</td>
 120           <td class="paramname"> <em>max</em></td><td>&nbsp;</td>
 121         </tr>
 122         <tr>
 123           <td></td>
 124           <td>)</td>
 125           <td></td><td></td><td></td>
 126         </tr>
 127       </table>
 128 </div>
 129 <div class="memdoc">
 130
 131 <p>Find energy of a saddle point between 2 structures (serch only direct path). </p>
 132 <dl><dt><b>Parameters:</b></dt><dd>
 133   <table border="0" cellspacing="2" cellpadding="0">
 134     <tr><td valign="top"></td><td valign="top"><em>seq</em>&nbsp;</td><td>RNA sequence </td></tr>
 135     <tr><td valign="top"></td><td valign="top"><em>struc1</em>&nbsp;</td><td>A pointer to the character array where the first secondary structure in dot-bracket notation will be written to </td></tr>
 136     <tr><td valign="top"></td><td valign="top"><em>struc2</em>&nbsp;</td><td>A pointer to the character array where the second secondary structure in dot-bracket notation will be written to </td></tr>
 137     <tr><td valign="top"></td><td valign="top"><em>max</em>&nbsp;</td><td>integer how many strutures are being kept during the search </td></tr>
 138   </table>
 139   </dd>
 140 </dl>
 141 <dl class="return"><dt><b>Returns:</b></dt><dd>the saddle energy in 10cal/mol </dd></dl>
 142
 143 </div>
 144 </div>
 145 <a class="anchor" id="a0ff35d65c892a3403af937c00a867ef9"></a><!-- doxytag: member="findpath.h::get_path" ref="a0ff35d65c892a3403af937c00a867ef9" args="(const char *seq, const char *s1, const char *s2, int maxkeep)" -->
 146 <div class="memitem">
 147 <div class="memproto">
 148       <table class="memname">
 149         <tr>
 150           <td class="memname"><a class="el" href="structpath__t.html">path_t</a>* get_path </td>
 151           <td>(</td>
 152           <td class="paramtype">const char *&nbsp;</td>
 153           <td class="paramname"> <em>seq</em>, </td>
 154         </tr>
 155         <tr>
 156           <td class="paramkey"></td>
 157           <td></td>
 158           <td class="paramtype">const char *&nbsp;</td>
 159           <td class="paramname"> <em>s1</em>, </td>
 160         </tr>
 161         <tr>
 162           <td class="paramkey"></td>
 163           <td></td>
 164           <td class="paramtype">const char *&nbsp;</td>
 165           <td class="paramname"> <em>s2</em>, </td>
 166         </tr>
 167         <tr>
 168           <td class="paramkey"></td>
 169           <td></td>
 170           <td class="paramtype">int&nbsp;</td>
 171           <td class="paramname"> <em>maxkeep</em></td><td>&nbsp;</td>
 172         </tr>
 173         <tr>
 174           <td></td>
 175           <td>)</td>
 176           <td></td><td></td><td></td>
 177         </tr>
 178       </table>
 179 </div>
 180 <div class="memdoc">
 181
 182 <p>Find refolding path between 2 structures (serch only direct path). </p>
 183 <dl><dt><b>Parameters:</b></dt><dd>
 184   <table border="0" cellspacing="2" cellpadding="0">
 185     <tr><td valign="top"></td><td valign="top"><em>seq</em>&nbsp;</td><td>RNA sequence </td></tr>
 186     <tr><td valign="top"></td><td valign="top"><em>s1</em>&nbsp;</td><td>A pointer to the character array where the first secondary structure in dot-bracket notation will be written to </td></tr>
 187     <tr><td valign="top"></td><td valign="top"><em>s2</em>&nbsp;</td><td>A pointer to the character array where the second secondary structure in dot-bracket notation will be written to </td></tr>
 188     <tr><td valign="top"></td><td valign="top"><em>maxkeep</em>&nbsp;</td><td>integer how many strutures are being kept during the search </td></tr>
 189   </table>
 190   </dd>
 191 </dl>
 192 <dl class="return"><dt><b>Returns:</b></dt><dd>direct refolding path between two structures </dd></dl>
 193
 194 </div>
 195 </div>
 196 <a class="anchor" id="a326e6d1640bbfd035e3869f5f4c188f7"></a><!-- doxytag: member="findpath.h::free_path" ref="a326e6d1640bbfd035e3869f5f4c188f7" args="(path_t *path)" -->
 197 <div class="memitem">
 198 <div class="memproto">
 199       <table class="memname">
 200         <tr>
 201           <td class="memname">void free_path </td>
 202           <td>(</td>
 203           <td class="paramtype"><a class="el" href="structpath__t.html">path_t</a> *&nbsp;</td>
 204           <td class="paramname"> <em>path</em></td>
 205           <td>&nbsp;)&nbsp;</td>
 206           <td></td>
 207         </tr>
 208       </table>
 209 </div>
 210 <div class="memdoc">
 211
 212 <p>Free memory allocated by <a class="el" href="findpath_8h.html#a0ff35d65c892a3403af937c00a867ef9" title="Find refolding path between 2 structures (serch only direct path).">get_path()</a> function. </p>
 213 <dl><dt><b>Parameters:</b></dt><dd>
 214   <table border="0" cellspacing="2" cellpadding="0">
 215     <tr><td valign="top"></td><td valign="top"><em>path</em>&nbsp;</td><td>pointer to memory to be freed </td></tr>
 216   </table>
 217   </dd>
 218 </dl>
 219
 220 </div>
 221 </div>
 222 </div>
 223 <hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
 224 <a href="http://www.doxygen.org/index.html">
 225 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 226 </body>
 227 </html>