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<div class="contents">
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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/findpath.h File Reference</h1>
<p>Compute direct refolding paths between two secondary structures.
-<a href="#details">More...</a></p>
-<div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for findpath.h:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<div class="center"><img src="findpath_8h__incl.png" border="0" usemap="#_2home_2mescalin_2ronny_2public__html_2programs_2ViennaRNA_2H_2findpath_8h" alt=""/></div>
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-<area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found here." alt="" coords="27,109,161,136"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="35,184,155,211"/></map>
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+<a href="#_details">More...</a></p>
+<div class="dynheader">
+Include dependency graph for findpath.h:</div>
+<div class="dynsection">
+<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>
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</div>
+
<p><a href="findpath_8h_source.html">Go to the source code of this file.</a></p>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:ad0e14268e309af773ecd1fce6244ee50"><td class="memItemLeft" align="right" valign="top">int </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>
-<tr class="memdesc:ad0e14268e309af773ecd1fce6244ee50"><td class="mdescLeft"> </td><td class="mdescRight">Find energy of a saddle point between 2 structures (serch only direct path) <a href="#ad0e14268e309af773ecd1fce6244ee50"></a><br/></td></tr>
-<tr class="memitem:a0ff35d65c892a3403af937c00a867ef9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structpath__t.html">path_t</a> * </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>
-<tr class="memdesc:a0ff35d65c892a3403af937c00a867ef9"><td class="mdescLeft"> </td><td class="mdescRight">Find refolding path between 2 structures (serch only direct path) <a href="#a0ff35d65c892a3403af937c00a867ef9"></a><br/></td></tr>
-<tr class="memitem:a326e6d1640bbfd035e3869f5f4c188f7"><td class="memItemLeft" align="right" valign="top">void </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>
-<tr class="memdesc:a326e6d1640bbfd035e3869f5f4c188f7"><td class="mdescLeft"> </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>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Find energy of a saddle point between 2 structures (serch only direct path). <a href="#ad0e14268e309af773ecd1fce6244ee50"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structpath__t.html">path_t</a> * </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Find refolding path between 2 structures (serch only direct path). <a href="#a0ff35d65c892a3403af937c00a867ef9"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </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>
+<tr><td class="mdescLeft"> </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>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Compute direct refolding paths between two secondary structures. </p>
-</div><hr/><h2>Function Documentation</h2>
-<a class="anchor" id="ad0e14268e309af773ecd1fce6244ee50"></a>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Compute direct refolding paths between two secondary structures. </p>
+<hr/><h2>Function Documentation</h2>
+<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)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int find_saddle </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>seq</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>struc1</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>struc1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>struc2</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>struc2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>max</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>max</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
-<p>Find energy of a saddle point between 2 structures (serch only direct path) </p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">seq</td><td>RNA sequence </td></tr>
- <tr><td class="paramname">struc1</td><td>A pointer to the character array where the first secondary structure in dot-bracket notation will be written to </td></tr>
- <tr><td class="paramname">struc2</td><td>A pointer to the character array where the second secondary structure in dot-bracket notation will be written to </td></tr>
- <tr><td class="paramname">max</td><td>integer how many strutures are being kept during the search </td></tr>
+<p>Find energy of a saddle point between 2 structures (serch only direct path). </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>seq</em> </td><td>RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>struc1</em> </td><td>A pointer to the character array where the first secondary structure in dot-bracket notation will be written to </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>struc2</em> </td><td>A pointer to the character array where the second secondary structure in dot-bracket notation will be written to </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>max</em> </td><td>integer how many strutures are being kept during the search </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>the saddle energy in 10cal/mol </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>the saddle energy in 10cal/mol </dd></dl>
</div>
</div>
-<a class="anchor" id="a0ff35d65c892a3403af937c00a867ef9"></a>
+<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)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structpath__t.html">path_t</a>* get_path </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>seq</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>seq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>s1</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>s1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>s2</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>s2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>maxkeep</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>maxkeep</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
-<p>Find refolding path between 2 structures (serch only direct path) </p>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">seq</td><td>RNA sequence </td></tr>
- <tr><td class="paramname">s1</td><td>A pointer to the character array where the first secondary structure in dot-bracket notation will be written to </td></tr>
- <tr><td class="paramname">s2</td><td>A pointer to the character array where the second secondary structure in dot-bracket notation will be written to </td></tr>
- <tr><td class="paramname">maxkeep</td><td>integer how many strutures are being kept during the search </td></tr>
+<p>Find refolding path between 2 structures (serch only direct path). </p>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>seq</em> </td><td>RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s1</em> </td><td>A pointer to the character array where the first secondary structure in dot-bracket notation will be written to </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s2</em> </td><td>A pointer to the character array where the second secondary structure in dot-bracket notation will be written to </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>maxkeep</em> </td><td>integer how many strutures are being kept during the search </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>direct refolding path between two structures </dd></dl>
+<dl class="return"><dt><b>Returns:</b></dt><dd>direct refolding path between two structures </dd></dl>
</div>
</div>
-<a class="anchor" id="a326e6d1640bbfd035e3869f5f4c188f7"></a>
+<a class="anchor" id="a326e6d1640bbfd035e3869f5f4c188f7"></a><!-- doxytag: member="findpath.h::free_path" ref="a326e6d1640bbfd035e3869f5f4c188f7" args="(path_t *path)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void free_path </td>
<td>(</td>
- <td class="paramtype"><a class="el" href="structpath__t.html">path_t</a> * </td>
- <td class="paramname"><em>path</em></td><td>)</td>
+ <td class="paramtype"><a class="el" href="structpath__t.html">path_t</a> * </td>
+ <td class="paramname"> <em>path</em></td>
+ <td> ) </td>
<td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
-<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>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">path</td><td>pointer to memory to be freed </td></tr>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>path</em> </td><td>pointer to memory to be freed </td></tr>
</table>
</dd>
</dl>
</div>
</div>
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- <li class="footer">Generated on Wed Jul 24 2013 13:38:58 for RNAlib-2.1.2 by
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- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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