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-<a href="#func-members">Functions</a> |
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-<div class="title">Energy evaluation</div> </div>
-<div class="ingroups"><a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a></div></div><!--header-->
<div class="contents">
-
+<h1>Energy evaluation<br/>
+<small>
+[<a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a>]</small>
+</h1>
<p>This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
-<a href="#details">More...</a></p>
-<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Energy evaluation:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
-<center><table><tr><td><img src="group__eval.png" border="0" alt="" usemap="#group____eval"/>
-<map name="group____eval" id="group____eval">
-<area shape="rect" id="node2" href="group__folding__routines.html" title="This module contains all functions related to thermodynamic folding of RNAs." alt="" coords="6,5,191,46"/></map>
-</td></tr></table></center>
+<a href="#_details">More...</a></p>
+
+<p><div class="dynheader">
+Collaboration diagram for Energy evaluation:</div>
+<div class="dynsection">
+<center><table><tr><td><img src="group__eval.png" border="0" alt="" usemap="#group____eval_map"/>
+<map name="group____eval_map" id="group____eval">
+<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>
</div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:gaf93986cb3cb29770ec9cca69c9fab8cf"><td class="memItemLeft" align="right" valign="top">float </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>
-<tr class="memdesc:gaf93986cb3cb29770ec9cca69c9fab8cf"><td class="mdescLeft"> </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>
-<tr class="memitem:gab5169ea4f72f250e43811463a33f4e40"><td class="memItemLeft" align="right" valign="top">float </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>
-<tr class="memdesc:gab5169ea4f72f250e43811463a33f4e40"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
-<tr class="memitem:gaeb14f3664aec67fc03268ac75253f0f8"><td class="memItemLeft" align="right" valign="top">float </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>
-<tr class="memdesc:gaeb14f3664aec67fc03268ac75253f0f8"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
-<tr class="memitem:ga75dc765ee4a1177832bc817c94cf88e5"><td class="memItemLeft" align="right" valign="top">float </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>
-<tr class="memdesc:ga75dc765ee4a1177832bc817c94cf88e5"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
-<tr class="memitem:ga8831445966b761417e713360791299d8"><td class="memItemLeft" align="right" valign="top">int </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>
-<tr class="memdesc:ga8831445966b761417e713360791299d8"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
-<tr class="memitem:gada4701dd7519b29da75ceac147601f4e"><td class="memItemLeft" align="right" valign="top">int </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>
-<tr class="memdesc:gada4701dd7519b29da75ceac147601f4e"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
-Variables</h2></td></tr>
-<tr class="memitem:ga567530678f6260a1a649a5beca5da4c5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
-<tr class="memdesc:ga567530678f6260a1a649a5beca5da4c5"><td class="mdescLeft"> </td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>
+</p>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </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>
+<tr><td class="mdescLeft"> </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>
+<tr><td class="memItemLeft" align="right" valign="top">float </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </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>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a><!-- doxytag: member="eval::eos_debug" ref="ga567530678f6260a1a649a5beca5da4c5" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>This module contains all functions and variables related to energy evaluation of sequence/structure pairs. </p>
<hr/><h2>Function Documentation</h2>
-<a class="anchor" id="gaf93986cb3cb29770ec9cca69c9fab8cf"></a>
+<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)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float energy_of_structure </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>string</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>string</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>structure</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>structure</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>verbosity_level</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>verbosity_level</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>Calculate the free energy of an already folded RNA using global model detail settings. </p>
<p>If verbosity level is set to a value >0, energies of structure elements are printed to stdout</p>
-<dl class="section note"><dt>Note:</dt><dd>OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a> for a completely threadsafe implementation.</dd></dl>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a>, <a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_structure()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
- <tr><td class="paramname">structure</td><td>secondary structure in dot-bracket notation </td></tr>
- <tr><td class="paramname">verbosity_level</td><td>a flag to turn verbose output on/off </td></tr>
+<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>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>string</em> </td><td>RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>secondary structure in dot-bracket notation </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em> </td><td>a flag to turn verbose output on/off </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>the free energy of the input structure given the input sequence in kcal/mol </dd></dl>
+<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>
</div>
</div>
-<a class="anchor" id="gab5169ea4f72f250e43811463a33f4e40"></a>
+<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)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">float energy_of_struct_par </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>string</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>string</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>structure</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>structure</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
- <td class="paramname"><em>parameters</em>, </td>
+ <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
+ <td class="paramname"> <em>parameters</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>verbosity_level</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>verbosity_level</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>Calculate the free energy of an already folded RNA. </p>
<p>If verbosity level is set to a value >0, energies of structure elements are printed to stdout</p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_structure()</a>, <a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8" title="Calculate the free energy of an already folded RNA.">energy_of_structure_pt()</a>, <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">string</td><td>RNA sequence in uppercase letters </td></tr>
- <tr><td class="paramname">structure</td><td>Secondary structure in dot-bracket notation </td></tr>
- <tr><td class="paramname">parameters</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
- <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>string</em> </td><td>RNA sequence in uppercase letters </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>Secondary structure in dot-bracket notation </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>parameters</em> </td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em> </td><td>A flag to turn verbose output on/off </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
+<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>
</div>
</div>
-<a class="anchor" id="gaeb14f3664aec67fc03268ac75253f0f8"></a>
+<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)" -->
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<td class="memname">float energy_of_circ_structure </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>string</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>string</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>structure</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>structure</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>verbosity_level</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>verbosity_level</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>Calculate the free energy of an already folded circular RNA. </p>
-<dl class="section note"><dt>Note:</dt><dd>OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See <a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_struct_par()</a> for a completely threadsafe implementation.</dd></dl>
+<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>
<p>If verbosity level is set to a value >0, energies of structure elements are printed to stdout</p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5" title="Calculate the free energy of an already folded circular RNA.">energy_of_circ_struct_par()</a>, <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
- <tr><td class="paramname">structure</td><td>Secondary structure in dot-bracket notation </td></tr>
- <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>string</em> </td><td>RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>Secondary structure in dot-bracket notation </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em> </td><td>A flag to turn verbose output on/off </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
+<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>
</div>
</div>
-<a class="anchor" id="ga75dc765ee4a1177832bc817c94cf88e5"></a>
+<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)" -->
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<div class="memproto">
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<td class="memname">float energy_of_circ_struct_par </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>string</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>string</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>structure</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>structure</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
- <td class="paramname"><em>parameters</em>, </td>
+ <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
+ <td class="paramname"> <em>parameters</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>verbosity_level</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>verbosity_level</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>Calculate the free energy of an already folded circular RNA. </p>
<p>If verbosity level is set to a value >0, energies of structure elements are printed to stdout</p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a>, <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
- <tr><td class="paramname">structure</td><td>Secondary structure in dot-bracket notation </td></tr>
- <tr><td class="paramname">parameters</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
- <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>string</em> </td><td>RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>structure</em> </td><td>Secondary structure in dot-bracket notation </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>parameters</em> </td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em> </td><td>A flag to turn verbose output on/off </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in kcal/mol </dd></dl>
+<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>
</div>
</div>
-<a class="anchor" id="ga8831445966b761417e713360791299d8"></a>
+<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)" -->
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<tr>
<td class="memname">int energy_of_structure_pt </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>string</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>string</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>ptable</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>ptable</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>s</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>s</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>s1</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>s1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>verbosity_level</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>verbosity_level</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>Calculate the free energy of an already folded RNA. </p>
<p>If verbosity level is set to a value >0, energies of structure elements are printed to stdout</p>
-<dl class="section note"><dt>Note:</dt><dd>OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See <a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e" title="Calculate the free energy of an already folded RNA.">energy_of_struct_pt_par()</a> for a completely threadsafe implementation.</dd></dl>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table()</a>, <a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e" title="Calculate the free energy of an already folded RNA.">energy_of_struct_pt_par()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">string</td><td>RNA sequence </td></tr>
- <tr><td class="paramname">ptable</td><td>the pair table of the secondary structure </td></tr>
- <tr><td class="paramname">s</td><td>encoded RNA sequence </td></tr>
- <tr><td class="paramname">s1</td><td>encoded RNA sequence </td></tr>
- <tr><td class="paramname">verbosity_level</td><td>a flag to turn verbose output on/off </td></tr>
+<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>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>string</em> </td><td>RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ptable</em> </td><td>the pair table of the secondary structure </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s</em> </td><td>encoded RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s1</em> </td><td>encoded RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em> </td><td>a flag to turn verbose output on/off </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>the free energy of the input structure given the input sequence in 10kcal/mol </dd></dl>
+<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>
</div>
</div>
-<a class="anchor" id="gada4701dd7519b29da75ceac147601f4e"></a>
+<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)" -->
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<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int energy_of_struct_pt_par </td>
<td>(</td>
- <td class="paramtype">const char * </td>
- <td class="paramname"><em>string</em>, </td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"> <em>string</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>ptable</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>ptable</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>s</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>s</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short * </td>
- <td class="paramname"><em>s1</em>, </td>
+ <td class="paramtype">short * </td>
+ <td class="paramname"> <em>s1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
- <td class="paramname"><em>parameters</em>, </td>
+ <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> * </td>
+ <td class="paramname"> <em>parameters</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>verbosity_level</em> </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>verbosity_level</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>Calculate the free energy of an already folded RNA. </p>
<p>If verbosity level is set to a value >0, energies of structure elements are printed to stdout</p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table()</a>, <a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40" title="Calculate the free energy of an already folded RNA.">energy_of_struct_par()</a>, <a class="el" href="group__energy__parameters.html#gac2f3ca440b7eaf4d999fb27da949fe72" title="Get precomputed energy contributions for all the known loop types.">get_scaled_parameters()</a></dd></dl>
-<dl class="params"><dt>Parameters:</dt><dd>
- <table class="params">
- <tr><td class="paramname">string</td><td>RNA sequence in uppercase letters </td></tr>
- <tr><td class="paramname">ptable</td><td>The pair table of the secondary structure </td></tr>
- <tr><td class="paramname">s</td><td>Encoded RNA sequence </td></tr>
- <tr><td class="paramname">s1</td><td>Encoded RNA sequence </td></tr>
- <tr><td class="paramname">parameters</td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
- <tr><td class="paramname">verbosity_level</td><td>A flag to turn verbose output on/off </td></tr>
+<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>
+<dl><dt><b>Parameters:</b></dt><dd>
+ <table border="0" cellspacing="2" cellpadding="0">
+ <tr><td valign="top"></td><td valign="top"><em>string</em> </td><td>RNA sequence in uppercase letters </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>ptable</em> </td><td>The pair table of the secondary structure </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s</em> </td><td>Encoded RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>s1</em> </td><td>Encoded RNA sequence </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>parameters</em> </td><td>A data structure containing the prescaled energy contributions and the model details. </td></tr>
+ <tr><td valign="top"></td><td valign="top"><em>verbosity_level</em> </td><td>A flag to turn verbose output on/off </td></tr>
</table>
</dd>
</dl>
-<dl class="section return"><dt>Returns:</dt><dd>The free energy of the input structure given the input sequence in 10kcal/mol </dd></dl>
+<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>
</div>
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-</div><!-- doc-content -->
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