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-<div class="title">part_func_co.h File Reference<div class="ingroups"><a class="el" href="group__pf__cofold.html">Partition Function for two hybridized Sequences</a></div></div> </div>
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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_co.h File Reference</h1>
<p>Partition function for two RNA sequences.
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<p><a href="part__func__co_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:gaa86a5f998789ed71813d23d7307a791b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b">co_pf_fold</a> (char *sequence, char *structure)</td></tr>
-<tr class="memdesc:gaa86a5f998789ed71813d23d7307a791b"><td class="mdescLeft"> </td><td class="mdescRight">Calculate partition function and base pair probabilities. <a href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b"></a><br/></td></tr>
-<tr class="memitem:gabd873b450832ab5f21101fc5ab354d21"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21">co_pf_fold_par</a> (char *sequence, char *structure, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained)</td></tr>
-<tr class="memdesc:gabd873b450832ab5f21101fc5ab354d21"><td class="mdescLeft"> </td><td class="mdescRight">Calculate partition function and base pair probabilities. <a href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21"></a><br/></td></tr>
-<tr class="memitem:ga11f0252c1d2c4697253ff4b5bd392d3c"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c">export_co_bppm</a> (void)</td></tr>
-<tr class="memdesc:ga11f0252c1d2c4697253ff4b5bd392d3c"><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability array. <a href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c"></a><br/></td></tr>
-<tr class="memitem:gade3ce34ae8214811374b1d28a40dc247"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gade3ce34ae8214811374b1d28a40dc247"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247">free_co_pf_arrays</a> (void)</td></tr>
-<tr class="memdesc:gade3ce34ae8214811374b1d28a40dc247"><td class="mdescLeft"> </td><td class="mdescRight">Free the memory occupied by <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold()</a> <br/></td></tr>
-<tr class="memitem:ga6e0f36c1f9b7d9dd4bfbad914c1119e5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5">update_co_pf_params</a> (int length)</td></tr>
-<tr class="memdesc:ga6e0f36c1f9b7d9dd4bfbad914c1119e5"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5"></a><br/></td></tr>
-<tr class="memitem:ga117d880df45bef444d5e2785ffa40a53"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53">update_co_pf_params_par</a> (int length, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
-<tr class="memdesc:ga117d880df45bef444d5e2785ffa40a53"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53"></a><br/></td></tr>
-<tr class="memitem:ga15ae04ac5ab84e876dcf0093120cb617"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617">compute_probabilities</a> (double FAB, double FEA, double FEB, struct <a class="el" href="structplist.html">plist</a> *prAB, struct <a class="el" href="structplist.html">plist</a> *prA, struct <a class="el" href="structplist.html">plist</a> *prB, int Alength)</td></tr>
-<tr class="memdesc:ga15ae04ac5ab84e876dcf0093120cb617"><td class="mdescLeft"> </td><td class="mdescRight">Compute Boltzmann probabilities of dimerization without homodimers. <a href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617"></a><br/></td></tr>
-<tr class="memitem:ga5545cb936ac4ff93c7d699d46e72e8c7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structConcEnt.html">ConcEnt</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7">get_concentrations</a> (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)</td></tr>
-<tr class="memdesc:ga5545cb936ac4ff93c7d699d46e72e8c7"><td class="mdescLeft"> </td><td class="mdescRight">Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. <a href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7"></a><br/></td></tr>
-<tr class="memitem:a334de3c96e2186abfbdc0eaea6d08b14"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structplist.html">plist</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a> (struct <a class="el" href="structplist.html">plist</a> *pl, int length, double cut_off)</td></tr>
-<tr class="memitem:aa12dda9dd6179cdd22bcce87c0682c07"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a> (int length)</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:gaff27888c4088cc1f60fd59cbd589474c"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaff27888c4088cc1f60fd59cbd589474c"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c">mirnatog</a></td></tr>
-<tr class="memdesc:gaff27888c4088cc1f60fd59cbd589474c"><td class="mdescLeft"> </td><td class="mdescRight">Toggles no intrabp in 2nd mol. <br/></td></tr>
-<tr class="memitem:gac2d1851a710a8561390861155ca988fe"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gac2d1851a710a8561390861155ca988fe"></a>
-double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe">F_monomer</a> [2]</td></tr>
-<tr class="memdesc:gac2d1851a710a8561390861155ca988fe"><td class="mdescLeft"> </td><td class="mdescRight">Free energies of the two monomers. <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="structcofoldF.html">cofoldF</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b">co_pf_fold</a> (char *sequence, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate partition function and base pair probabilities. <a href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21">co_pf_fold_par</a> (char *sequence, char *structure, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate partition function and base pair probabilities. <a href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c">export_co_bppm</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability array. <a href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gade3ce34ae8214811374b1d28a40dc247"></a><!-- doxytag: member="part_func_co.h::free_co_pf_arrays" ref="gade3ce34ae8214811374b1d28a40dc247" args="(void)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247">free_co_pf_arrays</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free the memory occupied by <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold()</a>. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5">update_co_pf_params</a> (int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53">update_co_pf_params_par</a> (int length, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617">compute_probabilities</a> (double FAB, double FEA, double FEB, struct <a class="el" href="structplist.html">plist</a> *prAB, struct <a class="el" href="structplist.html">plist</a> *prA, struct <a class="el" href="structplist.html">plist</a> *prB, int Alength)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute Boltzmann probabilities of dimerization without homodimers. <a href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structConcEnt.html">ConcEnt</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7">get_concentrations</a> (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. <a href="group__pf__cofold.html#ga5545cb936ac4ff93c7d699d46e72e8c7"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structplist.html">plist</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html#a334de3c96e2186abfbdc0eaea6d08b14">get_plist</a> (struct <a class="el" href="structplist.html">plist</a> *pl, int length, double cut_off)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html#aa12dda9dd6179cdd22bcce87c0682c07">init_co_pf_fold</a> (int length)</td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaff27888c4088cc1f60fd59cbd589474c"></a><!-- doxytag: member="part_func_co.h::mirnatog" ref="gaff27888c4088cc1f60fd59cbd589474c" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c">mirnatog</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Toggles no intrabp in 2nd mol. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gac2d1851a710a8561390861155ca988fe"></a><!-- doxytag: member="part_func_co.h::F_monomer" ref="gac2d1851a710a8561390861155ca988fe" args="[2]" -->
+double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe">F_monomer</a> [2]</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free energies of the two monomers. <br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Partition function for two RNA sequences. </p>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Partition function for two RNA sequences. </p>
<p>As for folding one RNA molecule, this computes the partition function of all possible structures and the base pair probabilities. Uses the same global <a class="el" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a> variable to avoid overflows.</p>
<p>To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed.</p>
<p>After computing the partition functions of all possible dimeres one can compute the probabilities of base pairs, the concentrations out of start concentrations and sofar and soaway.</p>
<p>Dimer formation is inherently concentration dependent. Given the free energies of the monomers A and B and dimers AB, AA, and BB one can compute the equilibrium concentrations, given input concentrations of A and B, see e.g. Dimitrov & Zuker (2004) </p>
-</div><hr/><h2>Function Documentation</h2>
-<a class="anchor" id="a334de3c96e2186abfbdc0eaea6d08b14"></a>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a334de3c96e2186abfbdc0eaea6d08b14"></a><!-- doxytag: member="part_func_co.h::get_plist" ref="a334de3c96e2186abfbdc0eaea6d08b14" args="(struct plist *pl, int length, double cut_off)" -->
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<td class="memname"><a class="el" href="structplist.html">plist</a>* get_plist </td>
<td>(</td>
- <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> * </td>
- <td class="paramname"><em>pl</em>, </td>
+ <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> * </td>
+ <td class="paramname"> <em>pl</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">double </td>
- <td class="paramname"><em>cut_off</em> </td>
+ <td class="paramtype">double </td>
+ <td class="paramname"> <em>cut_off</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
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-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>DO NOT USE THIS FUNCTION ANYMORE </p>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000016">Deprecated:</a></b></dt><dd>{ This function is deprecated and will be removed soon!} use <a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr()</a> instead! </dd></dl>
</div>
</div>
-<a class="anchor" id="aa12dda9dd6179cdd22bcce87c0682c07"></a>
+<a class="anchor" id="aa12dda9dd6179cdd22bcce87c0682c07"></a><!-- doxytag: member="part_func_co.h::init_co_pf_fold" ref="aa12dda9dd6179cdd22bcce87c0682c07" args="(int length)" -->
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<td class="memname">void init_co_pf_fold </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em></td><td>)</td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em></td>
+ <td> ) </td>
<td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>DO NOT USE THIS FUNCTION ANYMORE </p>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000017">Deprecated:</a></b></dt><dd>{ This function is deprecated and will be removed soon!} </dd></dl>
</div>
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