binaries/src/ViennaRNA/doc/html/part__func__co_8h.html

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  70 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_co.h File Reference</h1>
  71 <p>Partition function for two RNA sequences.
  72 <a href="#_details">More...</a></p>
  73 <div class="dynheader">
  74 Include dependency graph for part_func_co.h:</div>
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  76 <div class="center"><img src="part__func__co_8h__incl.png" border="0" usemap="#_2homes_2fmmarquesmadeira_2Projects_2jabaws_2binaries_2src_2ViennaRNA_2H_2part__func__co_8h_map" alt=""/></div>
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  78 <area shape="rect" id="node3" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found..." alt="" coords="212,86,335,117"/><area shape="rect" id="node5" href="energy__const_8h.html" title="energy_const.h" alt="" coords="217,166,329,197"/></map>
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  80
  81 <p><a href="part__func__co_8h_source.html">Go to the source code of this file.</a></p>
  82 <table border="0" cellpadding="0" cellspacing="0">
  83 <tr><td colspan="2"><h2>Functions</h2></td></tr>
  84 <tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a>&nbsp;</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>
  85 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate partition function and base pair probabilities.  <a href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b"></a><br/></td></tr>
  86 <tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a>&nbsp;</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>
  87 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Calculate partition function and base pair probabilities.  <a href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21"></a><br/></td></tr>
  88 <tr><td class="memItemLeft" align="right" valign="top">double *&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c">export_co_bppm</a> (void)</td></tr>
  89 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Get a pointer to the base pair probability array.  <a href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c"></a><br/></td></tr>
  90 <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)" -->
  91 void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247">free_co_pf_arrays</a> (void)</td></tr>
  92 <tr><td class="mdescLeft">&nbsp;</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>
  93 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5">update_co_pf_params</a> (int length)</td></tr>
  94 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Recalculate energy parameters.  <a href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5"></a><br/></td></tr>
  95 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</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>
  96 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Recalculate energy parameters.  <a href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53"></a><br/></td></tr>
  97 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</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>
  98 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Compute Boltzmann probabilities of dimerization without homodimers.  <a href="group__pf__cofold.html#ga15ae04ac5ab84e876dcf0093120cb617"></a><br/></td></tr>
  99 <tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structConcEnt.html">ConcEnt</a> *&nbsp;</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>
 100 <tr><td class="mdescLeft">&nbsp;</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>
 101 <tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structplist.html">plist</a> *&nbsp;</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>
 102 <tr><td class="memItemLeft" align="right" valign="top">void&nbsp;</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>
 103 <tr><td colspan="2"><h2>Variables</h2></td></tr>
 104 <tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaff27888c4088cc1f60fd59cbd589474c"></a><!-- doxytag: member="part_func_co.h::mirnatog" ref="gaff27888c4088cc1f60fd59cbd589474c" args="" -->
 105 int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c">mirnatog</a></td></tr>
 106 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Toggles no intrabp in 2nd mol. <br/></td></tr>
 107 <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]" -->
 108 double&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe">F_monomer</a> [2]</td></tr>
 109 <tr><td class="mdescLeft">&nbsp;</td><td class="mdescRight">Free energies of the two monomers. <br/></td></tr>
 110 </table>
 111 <hr/><a name="_details"></a><h2>Detailed Description</h2>
 112 <p>Partition function for two RNA sequences. </p>
 113 <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>
 114 <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>
 115 <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>
 116 <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 &amp; Zuker (2004) </p>
 117 <hr/><h2>Function Documentation</h2>
 118 <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)" -->
 119 <div class="memitem">
 120 <div class="memproto">
 121       <table class="memname">
 122         <tr>
 123           <td class="memname"><a class="el" href="structplist.html">plist</a>* get_plist </td>
 124           <td>(</td>
 125           <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> *&nbsp;</td>
 126           <td class="paramname"> <em>pl</em>, </td>
 127         </tr>
 128         <tr>
 129           <td class="paramkey"></td>
 130           <td></td>
 131           <td class="paramtype">int&nbsp;</td>
 132           <td class="paramname"> <em>length</em>, </td>
 133         </tr>
 134         <tr>
 135           <td class="paramkey"></td>
 136           <td></td>
 137           <td class="paramtype">double&nbsp;</td>
 138           <td class="paramname"> <em>cut_off</em></td><td>&nbsp;</td>
 139         </tr>
 140         <tr>
 141           <td></td>
 142           <td>)</td>
 143           <td></td><td></td><td></td>
 144         </tr>
 145       </table>
 146 </div>
 147 <div class="memdoc">
 148 <p>DO NOT USE THIS FUNCTION ANYMORE </p>
 149 <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>
 150
 151 </div>
 152 </div>
 153 <a class="anchor" id="aa12dda9dd6179cdd22bcce87c0682c07"></a><!-- doxytag: member="part_func_co.h::init_co_pf_fold" ref="aa12dda9dd6179cdd22bcce87c0682c07" args="(int length)" -->
 154 <div class="memitem">
 155 <div class="memproto">
 156       <table class="memname">
 157         <tr>
 158           <td class="memname">void init_co_pf_fold </td>
 159           <td>(</td>
 160           <td class="paramtype">int&nbsp;</td>
 161           <td class="paramname"> <em>length</em></td>
 162           <td>&nbsp;)&nbsp;</td>
 163           <td></td>
 164         </tr>
 165       </table>
 166 </div>
 167 <div class="memdoc">
 168 <p>DO NOT USE THIS FUNCTION ANYMORE </p>
 169 <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>
 170
 171 </div>
 172 </div>
 173 </div>
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