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-<div class="title">2Dpfold.h File Reference<div class="ingroups"><a class="el" href="group__kl__neighborhood__pf.html">Calculate Partition Functions of a Distance Based Partitioning</a></div></div> </div>
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<p><a href="2Dpfold_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:ga1aca740e2a75ab2b2951538266e53d64"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64">get_TwoDpfold_variables</a> (const char *seq, const char *structure1, char *structure2, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
-<tr class="memdesc:ga1aca740e2a75ab2b2951538266e53d64"><td class="mdescLeft"> </td><td class="mdescRight">Get a datastructure containing all necessary attributes and global folding switches. <a href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64"></a><br/></td></tr>
-<tr class="memitem:gacc2f66da7ee62096cab629fce7112216"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216">get_TwoDpfold_variables_from_MFE</a> (<a class="el" href="structTwoDfold__vars.html">TwoDfold_vars</a> *mfe_vars)</td></tr>
-<tr class="memdesc:gacc2f66da7ee62096cab629fce7112216"><td class="mdescLeft"> </td><td class="mdescRight">Get the datastructure containing all necessary attributes and global folding switches from a pre-filled mfe-datastructure. <a href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216"></a><br/></td></tr>
-<tr class="memitem:gafe994291458ee2ac34d3eb825ef62a15"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15">destroy_TwoDpfold_variables</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars)</td></tr>
-<tr class="memdesc:gafe994291458ee2ac34d3eb825ef62a15"><td class="mdescLeft"> </td><td class="mdescRight">Free all memory occupied by a <a class="el" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> datastructure. <a href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15"></a><br/></td></tr>
-<tr class="memitem:ga3e1cd3b24eb635c65181182cbb4ae3eb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structTwoDpfold__solution.html">TwoDpfold_solution</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb">TwoDpfoldList</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int maxDistance1, int maxDistance2)</td></tr>
-<tr class="memdesc:ga3e1cd3b24eb635c65181182cbb4ae3eb"><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function for all distance classes. <a href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb"></a><br/></td></tr>
-<tr class="memitem:gae251288f50dd4ae7d315af0085775f71"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71">TwoDpfold_pbacktrack</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int d1, int d2)</td></tr>
-<tr class="memdesc:gae251288f50dd4ae7d315af0085775f71"><td class="mdescLeft"> </td><td class="mdescRight">Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. <a href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71"></a><br/></td></tr>
-<tr class="memitem:ga13430ac6a7f90df426774f131647d2c7"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7">TwoDpfold_pbacktrack5</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int d1, int d2, unsigned int length)</td></tr>
-<tr class="memdesc:ga13430ac6a7f90df426774f131647d2c7"><td class="mdescLeft"> </td><td class="mdescRight">Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. <a href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7"></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"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64">get_TwoDpfold_variables</a> (const char *seq, const char *structure1, char *structure2, int <a class="el" href="fold__vars_8h.html#af9202a1a09f5828dc731e2d9a10fa111">circ</a>)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get a datastructure containing all necessary attributes and global folding switches. <a href="group__kl__neighborhood__pf.html#ga1aca740e2a75ab2b2951538266e53d64"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216">get_TwoDpfold_variables_from_MFE</a> (<a class="el" href="structTwoDfold__vars.html">TwoDfold_vars</a> *mfe_vars)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the datastructure containing all necessary attributes and global folding switches from a pre-filled mfe-datastructure. <a href="group__kl__neighborhood__pf.html#gacc2f66da7ee62096cab629fce7112216"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15">destroy_TwoDpfold_variables</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free all memory occupied by a <a class="el" href="structTwoDpfold__vars.html" title="Variables compound for 2Dfold partition function folding.">TwoDpfold_vars</a> datastructure. <a href="group__kl__neighborhood__pf.html#gafe994291458ee2ac34d3eb825ef62a15"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structTwoDpfold__solution.html">TwoDpfold_solution</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb">TwoDpfoldList</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int maxDistance1, int maxDistance2)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function for all distance classes. <a href="group__kl__neighborhood__pf.html#ga3e1cd3b24eb635c65181182cbb4ae3eb"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71">TwoDpfold_pbacktrack</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int d1, int d2)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. <a href="group__kl__neighborhood__stochbt.html#gae251288f50dd4ae7d315af0085775f71"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7">TwoDpfold_pbacktrack5</a> (<a class="el" href="structTwoDpfold__vars.html">TwoDpfold_vars</a> *vars, int d1, int d2, unsigned int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. <a href="group__kl__neighborhood__stochbt.html#ga13430ac6a7f90df426774f131647d2c7"></a><br/></td></tr>
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