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-<div class="title">TwoDpfold_vars Struct Reference</div> </div>
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+<h1>TwoDpfold_vars Struct Reference</h1><!-- doxytag: class="TwoDpfold_vars" -->
<p>Variables compound for 2Dfold partition function folding.
- <a href="structTwoDpfold__vars.html#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 TwoDpfold_vars:</div>
-<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
-</div>
-<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<a href="#_details">More...</a></p>
+<div class="dynheader">
+Collaboration diagram for TwoDpfold_vars:</div>
+<div class="dynsection">
<div class="center"><img src="structTwoDpfold__vars__coll__graph.png" border="0" usemap="#TwoDpfold__vars_coll__map" alt="Collaboration graph"/></div>
<map name="TwoDpfold__vars_coll__map" id="TwoDpfold__vars_coll__map">
-<area shape="rect" id="node2" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy parameters..." alt="" coords="19,96,109,123"/><area shape="rect" id="node4" href="structmodel__detailsT.html" title="The data structure that contains the complete model details used throughout the calculations." alt="" coords="5,5,123,32"/></map>
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<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="pub-attribs"></a>
-Data Fields</h2></td></tr>
-<tr class="memitem:a67f37b8901b8d0a049c216d4c6241b07"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a67f37b8901b8d0a049c216d4c6241b07"></a>
-char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a67f37b8901b8d0a049c216d4c6241b07">ptype</a></td></tr>
-<tr class="memdesc:a67f37b8901b8d0a049c216d4c6241b07"><td class="mdescLeft"> </td><td class="mdescRight">Precomputed array of pair types. <br/></td></tr>
-<tr class="memitem:a32c15a1e31856588259556c9020f32c6"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a32c15a1e31856588259556c9020f32c6"></a>
-char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a32c15a1e31856588259556c9020f32c6">sequence</a></td></tr>
-<tr class="memdesc:a32c15a1e31856588259556c9020f32c6"><td class="mdescLeft"> </td><td class="mdescRight">The input sequence. <br/></td></tr>
-<tr class="memitem:a240311ae1e8e121441651d6101e187ac"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a240311ae1e8e121441651d6101e187ac"></a>
-short * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a240311ae1e8e121441651d6101e187ac">S1</a></td></tr>
-<tr class="memdesc:a240311ae1e8e121441651d6101e187ac"><td class="mdescLeft"> </td><td class="mdescRight">The input sequences in numeric form. <br/></td></tr>
-<tr class="memitem:a7292b6cbc1ee5bacf55e842f316c4bef"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a7292b6cbc1ee5bacf55e842f316c4bef"></a>
-unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a7292b6cbc1ee5bacf55e842f316c4bef">maxD1</a></td></tr>
-<tr class="memdesc:a7292b6cbc1ee5bacf55e842f316c4bef"><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to first reference. <br/></td></tr>
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-unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a8900622d91454d2d037242e290e42834">maxD2</a></td></tr>
-<tr class="memdesc:a8900622d91454d2d037242e290e42834"><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to second reference. <br/></td></tr>
-<tr class="memitem:ac2d3e6abf0cb0e1df363904fc938076e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ac2d3e6abf0cb0e1df363904fc938076e"></a>
-int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#ac2d3e6abf0cb0e1df363904fc938076e">my_iindx</a></td></tr>
-<tr class="memdesc:ac2d3e6abf0cb0e1df363904fc938076e"><td class="mdescLeft"> </td><td class="mdescRight">Index for moving in quadratic distancy dimensions. <br/></td></tr>
-<tr class="memitem:a0699e194a797532c91b284ab10272384"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a0699e194a797532c91b284ab10272384"></a>
-int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a0699e194a797532c91b284ab10272384">jindx</a></td></tr>
-<tr class="memdesc:a0699e194a797532c91b284ab10272384"><td class="mdescLeft"> </td><td class="mdescRight">Index for moving in the triangular matrix qm1. <br/></td></tr>
-<tr class="memitem:aea15706d27b6b0fc19f5773919f43a8a"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aea15706d27b6b0fc19f5773919f43a8a"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#aea15706d27b6b0fc19f5773919f43a8a">referenceBPs1</a></td></tr>
-<tr class="memdesc:aea15706d27b6b0fc19f5773919f43a8a"><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure1 in interval [i,j]. <br/></td></tr>
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-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a1221396d712bf76b7f35297f2ab35a9f">referenceBPs2</a></td></tr>
-<tr class="memdesc:a1221396d712bf76b7f35297f2ab35a9f"><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure2 in interval [i,j]. <br/></td></tr>
-<tr class="memitem:accef8eaa05fa57ca33aa22cbc7b7aaff"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="accef8eaa05fa57ca33aa22cbc7b7aaff"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#accef8eaa05fa57ca33aa22cbc7b7aaff">bpdist</a></td></tr>
-<tr class="memdesc:accef8eaa05fa57ca33aa22cbc7b7aaff"><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j]. <br/></td></tr>
-<tr class="memitem:a7c9e9af6224d4696118e05835441863d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a7c9e9af6224d4696118e05835441863d"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a7c9e9af6224d4696118e05835441863d">mm1</a></td></tr>
-<tr class="memdesc:a7c9e9af6224d4696118e05835441863d"><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 1 disallowed. <br/></td></tr>
-<tr class="memitem:affb913470783f9edb12a0bfc22466269"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="affb913470783f9edb12a0bfc22466269"></a>
-unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#affb913470783f9edb12a0bfc22466269">mm2</a></td></tr>
-<tr class="memdesc:affb913470783f9edb12a0bfc22466269"><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 2 disallowed. <br/></td></tr>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Data Fields</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a67f37b8901b8d0a049c216d4c6241b07"></a><!-- doxytag: member="TwoDpfold_vars::ptype" ref="a67f37b8901b8d0a049c216d4c6241b07" args="" -->
+char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a67f37b8901b8d0a049c216d4c6241b07">ptype</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Precomputed array of pair types. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a32c15a1e31856588259556c9020f32c6"></a><!-- doxytag: member="TwoDpfold_vars::sequence" ref="a32c15a1e31856588259556c9020f32c6" args="" -->
+char * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a32c15a1e31856588259556c9020f32c6">sequence</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">The input sequence. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a240311ae1e8e121441651d6101e187ac"></a><!-- doxytag: member="TwoDpfold_vars::S1" ref="a240311ae1e8e121441651d6101e187ac" args="" -->
+short * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a240311ae1e8e121441651d6101e187ac">S1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">The input sequences in numeric form. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a7292b6cbc1ee5bacf55e842f316c4bef"></a><!-- doxytag: member="TwoDpfold_vars::maxD1" ref="a7292b6cbc1ee5bacf55e842f316c4bef" args="" -->
+unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a7292b6cbc1ee5bacf55e842f316c4bef">maxD1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to first reference. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a8900622d91454d2d037242e290e42834"></a><!-- doxytag: member="TwoDpfold_vars::maxD2" ref="a8900622d91454d2d037242e290e42834" args="" -->
+unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a8900622d91454d2d037242e290e42834">maxD2</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed base pair distance to second reference. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ac2d3e6abf0cb0e1df363904fc938076e"></a><!-- doxytag: member="TwoDpfold_vars::my_iindx" ref="ac2d3e6abf0cb0e1df363904fc938076e" args="" -->
+int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#ac2d3e6abf0cb0e1df363904fc938076e">my_iindx</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Index for moving in quadratic distancy dimensions. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a0699e194a797532c91b284ab10272384"></a><!-- doxytag: member="TwoDpfold_vars::jindx" ref="a0699e194a797532c91b284ab10272384" args="" -->
+int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a0699e194a797532c91b284ab10272384">jindx</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Index for moving in the triangular matrix qm1. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aea15706d27b6b0fc19f5773919f43a8a"></a><!-- doxytag: member="TwoDpfold_vars::referenceBPs1" ref="aea15706d27b6b0fc19f5773919f43a8a" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#aea15706d27b6b0fc19f5773919f43a8a">referenceBPs1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure1 in interval [i,j]. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a1221396d712bf76b7f35297f2ab35a9f"></a><!-- doxytag: member="TwoDpfold_vars::referenceBPs2" ref="a1221396d712bf76b7f35297f2ab35a9f" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a1221396d712bf76b7f35297f2ab35a9f">referenceBPs2</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing number of basepairs of reference structure2 in interval [i,j]. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="accef8eaa05fa57ca33aa22cbc7b7aaff"></a><!-- doxytag: member="TwoDpfold_vars::bpdist" ref="accef8eaa05fa57ca33aa22cbc7b7aaff" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#accef8eaa05fa57ca33aa22cbc7b7aaff">bpdist</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j]. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a7c9e9af6224d4696118e05835441863d"></a><!-- doxytag: member="TwoDpfold_vars::mm1" ref="a7c9e9af6224d4696118e05835441863d" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#a7c9e9af6224d4696118e05835441863d">mm1</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 1 disallowed. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="affb913470783f9edb12a0bfc22466269"></a><!-- doxytag: member="TwoDpfold_vars::mm2" ref="affb913470783f9edb12a0bfc22466269" args="" -->
+unsigned int * </td><td class="memItemRight" valign="bottom"><a class="el" href="structTwoDpfold__vars.html#affb913470783f9edb12a0bfc22466269">mm2</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Maximum matching matrix, reference struct 2 disallowed. <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Variables compound for 2Dfold partition function folding. </p>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64" title="Get a datastructure containing all necessary attributes and global folding switches.">get_TwoDpfold_variables()</a>, <a class="el" href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216" title="Get the datastructure containing all necessary attributes and global folding switches from a pre-fill...">get_TwoDpfold_variables_from_MFE()</a>, <a class="el" href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15" title="Free all memory occupied by a TwoDpfold_vars datastructure.">destroy_TwoDpfold_variables()</a>, <a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList()</a> </dd></dl>
-</div><hr/>The documentation for this struct was generated from the following file:<ul>
-<li>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/<a class="el" href="data__structures_8h_source.html">data_structures.h</a></li>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Variables compound for 2Dfold partition function folding. </p>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64" title="Get a datastructure containing all necessary attributes and global folding switches...">get_TwoDpfold_variables()</a>, <a class="el" href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216" title="Get the datastructure containing all necessary attributes and global folding switches...">get_TwoDpfold_variables_from_MFE()</a>, <a class="el" href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15" title="Free all memory occupied by a TwoDpfold_vars datastructure.">destroy_TwoDpfold_variables()</a>, <a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb" title="Compute the partition function for all distance classes.">TwoDpfoldList()</a> </dd></dl>
+<hr/>The documentation for this struct was generated from the following file:<ul>
+<li>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/<a class="el" href="data__structures_8h_source.html">data_structures.h</a></li>
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