binaries/src/ViennaRNA/doc/html/group__pf__cofold.html

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  63 <div class="title">Partition Function for two hybridized Sequences</div>  </div>
  64 <div class="ingroups"><a class="el" href="group__cofold.html">Calculate Secondary Structures of two RNAs upon Dimerization</a> &#124; <a class="el" href="group__pf__fold.html">Calculating Partition Functions and Pair Probabilities</a></div></div><!--header-->
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  66
  67 <p>Partition Function Cofolding.
  68 <a href="#details">More...</a></p>
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  81 Files</h2></td></tr>
  82 <tr class="memitem:part__func__co_8h"><td class="memItemLeft" align="right" valign="top">file &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="part__func__co_8h.html">part_func_co.h</a></td></tr>
  83 <tr class="memdesc:part__func__co_8h"><td class="mdescLeft">&#160;</td><td class="mdescRight">Partition function for two RNA sequences. <br/></td></tr>
  84 </table><table class="memberdecls">
  85 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  86 Functions</h2></td></tr>
  87 <tr class="memitem:gaa86a5f998789ed71813d23d7307a791b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a>&#160;</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>
  88 <tr class="memdesc:gaa86a5f998789ed71813d23d7307a791b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate partition function and base pair probabilities.  <a href="#gaa86a5f998789ed71813d23d7307a791b"></a><br/></td></tr>
  89 <tr class="memitem:gabd873b450832ab5f21101fc5ab354d21"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structcofoldF.html">cofoldF</a>&#160;</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>
  90 <tr class="memdesc:gabd873b450832ab5f21101fc5ab354d21"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate partition function and base pair probabilities.  <a href="#gabd873b450832ab5f21101fc5ab354d21"></a><br/></td></tr>
  91 <tr class="memitem:ga11f0252c1d2c4697253ff4b5bd392d3c"><td class="memItemLeft" align="right" valign="top">double *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga11f0252c1d2c4697253ff4b5bd392d3c">export_co_bppm</a> (void)</td></tr>
  92 <tr class="memdesc:ga11f0252c1d2c4697253ff4b5bd392d3c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get a pointer to the base pair probability array.  <a href="#ga11f0252c1d2c4697253ff4b5bd392d3c"></a><br/></td></tr>
  93 <tr class="memitem:gade3ce34ae8214811374b1d28a40dc247"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gade3ce34ae8214811374b1d28a40dc247"></a>
  94 void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gade3ce34ae8214811374b1d28a40dc247">free_co_pf_arrays</a> (void)</td></tr>
  95 <tr class="memdesc:gade3ce34ae8214811374b1d28a40dc247"><td class="mdescLeft">&#160;</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>
  96 <tr class="memitem:ga6e0f36c1f9b7d9dd4bfbad914c1119e5"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5">update_co_pf_params</a> (int length)</td></tr>
  97 <tr class="memdesc:ga6e0f36c1f9b7d9dd4bfbad914c1119e5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Recalculate energy parameters.  <a href="#ga6e0f36c1f9b7d9dd4bfbad914c1119e5"></a><br/></td></tr>
  98 <tr class="memitem:ga117d880df45bef444d5e2785ffa40a53"><td class="memItemLeft" align="right" valign="top">void&#160;</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>
  99 <tr class="memdesc:ga117d880df45bef444d5e2785ffa40a53"><td class="mdescLeft">&#160;</td><td class="mdescRight">Recalculate energy parameters.  <a href="#ga117d880df45bef444d5e2785ffa40a53"></a><br/></td></tr>
 100 <tr class="memitem:ga15ae04ac5ab84e876dcf0093120cb617"><td class="memItemLeft" align="right" valign="top">void&#160;</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>
 101 <tr class="memdesc:ga15ae04ac5ab84e876dcf0093120cb617"><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute Boltzmann probabilities of dimerization without homodimers.  <a href="#ga15ae04ac5ab84e876dcf0093120cb617"></a><br/></td></tr>
 102 <tr class="memitem:ga5545cb936ac4ff93c7d699d46e72e8c7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structConcEnt.html">ConcEnt</a> *&#160;</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>
 103 <tr class="memdesc:ga5545cb936ac4ff93c7d699d46e72e8c7"><td class="mdescLeft">&#160;</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="#ga5545cb936ac4ff93c7d699d46e72e8c7"></a><br/></td></tr>
 104 </table><table class="memberdecls">
 105 <tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
 106 Variables</h2></td></tr>
 107 <tr class="memitem:gaff27888c4088cc1f60fd59cbd589474c"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gaff27888c4088cc1f60fd59cbd589474c"></a>
 108 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gaff27888c4088cc1f60fd59cbd589474c">mirnatog</a></td></tr>
 109 <tr class="memdesc:gaff27888c4088cc1f60fd59cbd589474c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Toggles no intrabp in 2nd mol. <br/></td></tr>
 110 <tr class="memitem:gac2d1851a710a8561390861155ca988fe"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="gac2d1851a710a8561390861155ca988fe"></a>
 111 double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html#gac2d1851a710a8561390861155ca988fe">F_monomer</a> [2]</td></tr>
 112 <tr class="memdesc:gac2d1851a710a8561390861155ca988fe"><td class="mdescLeft">&#160;</td><td class="mdescRight">Free energies of the two monomers. <br/></td></tr>
 113 </table>
 114 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
 115 <p>Partition Function Cofolding. </p>
 116 <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. See <a class="el" href="citelist.html#CITEREF_bernhart:2006">[1]</a> for further details. </p>
 117 <hr/><h2>Function Documentation</h2>
 118 <a class="anchor" id="gaa86a5f998789ed71813d23d7307a791b"></a>
 119 <div class="memitem">
 120 <div class="memproto">
 121       <table class="memname">
 122         <tr>
 123           <td class="memname"><a class="el" href="structcofoldF.html">cofoldF</a> co_pf_fold </td>
 124           <td>(</td>
 125           <td class="paramtype">char *&#160;</td>
 126           <td class="paramname"><em>sequence</em>, </td>
 127         </tr>
 128         <tr>
 129           <td class="paramkey"></td>
 130           <td></td>
 131           <td class="paramtype">char *&#160;</td>
 132           <td class="paramname"><em>structure</em>&#160;</td>
 133         </tr>
 134         <tr>
 135           <td></td>
 136           <td>)</td>
 137           <td></td><td></td>
 138         </tr>
 139       </table>
 140 </div><div class="memdoc">
 141
 142 <p>Calculate partition function and base pair probabilities. </p>
 143 <p>This is the cofold partition function folding. The second molecule starts at the <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule within the concat...">cut_point</a> nucleotide.</p>
 144 <dl class="section note"><dt>Note:</dt><dd>OpenMP: Since this function relies on the global parameters <a class="el" href="fold__vars_8h.html#ad512b5dd4dbec60faccfe137bb474489" title="do backtracking, i.e. compute secondary structures or base pair probabilities">do_backtrack</a>, <a class="el" href="fold__vars_8h.html#a72b511ed1201f7e23ec437e468790d74" title="Switch the energy model for dangling end contributions (0, 1, 2, 3)">dangles</a>, <a class="el" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a> and <a class="el" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a> it is not threadsafe according to concurrent changes in these variables! Use <a class="el" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21" title="Calculate partition function and base pair probabilities.">co_pf_fold_par()</a> instead to circumvent this issue.</dd></dl>
 145 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__pf__cofold.html#gabd873b450832ab5f21101fc5ab354d21" title="Calculate partition function and base pair probabilities.">co_pf_fold_par()</a></dd></dl>
 146 <dl class="params"><dt>Parameters:</dt><dd>
 147   <table class="params">
 148     <tr><td class="paramname">sequence</td><td>Concatenated RNA sequences </td></tr>
 149     <tr><td class="paramname">structure</td><td>Will hold the structure or constraints </td></tr>
 150   </table>
 151   </dd>
 152 </dl>
 153 <dl class="section return"><dt>Returns:</dt><dd><a class="el" href="structcofoldF.html">cofoldF</a> structure containing a set of energies needed for concentration computations. </dd></dl>
 154
 155 </div>
 156 </div>
 157 <a class="anchor" id="gabd873b450832ab5f21101fc5ab354d21"></a>
 158 <div class="memitem">
 159 <div class="memproto">
 160       <table class="memname">
 161         <tr>
 162           <td class="memname"><a class="el" href="structcofoldF.html">cofoldF</a> co_pf_fold_par </td>
 163           <td>(</td>
 164           <td class="paramtype">char *&#160;</td>
 165           <td class="paramname"><em>sequence</em>, </td>
 166         </tr>
 167         <tr>
 168           <td class="paramkey"></td>
 169           <td></td>
 170           <td class="paramtype">char *&#160;</td>
 171           <td class="paramname"><em>structure</em>, </td>
 172         </tr>
 173         <tr>
 174           <td class="paramkey"></td>
 175           <td></td>
 176           <td class="paramtype"><a class="el" href="structpf__paramT.html">pf_paramT</a> *&#160;</td>
 177           <td class="paramname"><em>parameters</em>, </td>
 178         </tr>
 179         <tr>
 180           <td class="paramkey"></td>
 181           <td></td>
 182           <td class="paramtype">int&#160;</td>
 183           <td class="paramname"><em>calculate_bppm</em>, </td>
 184         </tr>
 185         <tr>
 186           <td class="paramkey"></td>
 187           <td></td>
 188           <td class="paramtype">int&#160;</td>
 189           <td class="paramname"><em>is_constrained</em>&#160;</td>
 190         </tr>
 191         <tr>
 192           <td></td>
 193           <td>)</td>
 194           <td></td><td></td>
 195         </tr>
 196       </table>
 197 </div><div class="memdoc">
 198
 199 <p>Calculate partition function and base pair probabilities. </p>
 200 <p>This is the cofold partition function folding. The second molecule starts at the <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule within the concat...">cut_point</a> nucleotide.</p>
 201 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent th...">get_boltzmann_factors()</a>, <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold()</a></dd></dl>
 202 <dl class="params"><dt>Parameters:</dt><dd>
 203   <table class="params">
 204     <tr><td class="paramname">sequence</td><td>Concatenated RNA sequences </td></tr>
 205     <tr><td class="paramname">structure</td><td>Pointer to the structure constraint </td></tr>
 206     <tr><td class="paramname">parameters</td><td>Data structure containing the precalculated Boltzmann factors </td></tr>
 207     <tr><td class="paramname">calculate_bppm</td><td>Switch to turn Base pair probability calculations on/off (0==off) </td></tr>
 208     <tr><td class="paramname">is_constrained</td><td>Switch to indicate that a structure contraint is passed via the structure argument (0==off) </td></tr>
 209   </table>
 210   </dd>
 211 </dl>
 212 <dl class="section return"><dt>Returns:</dt><dd><a class="el" href="structcofoldF.html">cofoldF</a> structure containing a set of energies needed for concentration computations. </dd></dl>
 213
 214 </div>
 215 </div>
 216 <a class="anchor" id="ga11f0252c1d2c4697253ff4b5bd392d3c"></a>
 217 <div class="memitem">
 218 <div class="memproto">
 219       <table class="memname">
 220         <tr>
 221           <td class="memname">double* export_co_bppm </td>
 222           <td>(</td>
 223           <td class="paramtype">void&#160;</td>
 224           <td class="paramname"></td><td>)</td>
 225           <td></td>
 226         </tr>
 227       </table>
 228 </div><div class="memdoc">
 229
 230 <p>Get a pointer to the base pair probability array. </p>
 231 <p>Accessing the base pair probabilities for a pair (i,j) is achieved by </p>
 232 <pre class="fragment">FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; </pre><dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397" title="Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...">get_iindx()</a> </dd></dl>
 233 <dl class="section return"><dt>Returns:</dt><dd>A pointer to the base pair probability array </dd></dl>
 234
 235 </div>
 236 </div>
 237 <a class="anchor" id="ga6e0f36c1f9b7d9dd4bfbad914c1119e5"></a>
 238 <div class="memitem">
 239 <div class="memproto">
 240       <table class="memname">
 241         <tr>
 242           <td class="memname">void update_co_pf_params </td>
 243           <td>(</td>
 244           <td class="paramtype">int&#160;</td>
 245           <td class="paramname"><em>length</em></td><td>)</td>
 246           <td></td>
 247         </tr>
 248       </table>
 249 </div><div class="memdoc">
 250
 251 <p>Recalculate energy parameters. </p>
 252 <p>This function recalculates all energy parameters given the current model settings.</p>
 253 <dl class="section note"><dt>Note:</dt><dd>This function relies on the global variables <a class="el" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a>, <a class="el" href="fold__vars_8h.html#a72b511ed1201f7e23ec437e468790d74" title="Switch the energy model for dangling end contributions (0, 1, 2, 3)">dangles</a> and <a class="el" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a>. Thus it might not be threadsafe in certain situations. Use <a class="el" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53" title="Recalculate energy parameters.">update_co_pf_params_par()</a> instead.</dd></dl>
 254 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent th...">get_boltzmann_factors()</a>, <a class="el" href="group__pf__cofold.html#ga117d880df45bef444d5e2785ffa40a53" title="Recalculate energy parameters.">update_co_pf_params_par()</a></dd></dl>
 255 <dl class="params"><dt>Parameters:</dt><dd>
 256   <table class="params">
 257     <tr><td class="paramname">length</td><td>Length of the current RNA sequence </td></tr>
 258   </table>
 259   </dd>
 260 </dl>
 261
 262 </div>
 263 </div>
 264 <a class="anchor" id="ga117d880df45bef444d5e2785ffa40a53"></a>
 265 <div class="memitem">
 266 <div class="memproto">
 267       <table class="memname">
 268         <tr>
 269           <td class="memname">void update_co_pf_params_par </td>
 270           <td>(</td>
 271           <td class="paramtype">int&#160;</td>
 272           <td class="paramname"><em>length</em>, </td>
 273         </tr>
 274         <tr>
 275           <td class="paramkey"></td>
 276           <td></td>
 277           <td class="paramtype"><a class="el" href="structpf__paramT.html">pf_paramT</a> *&#160;</td>
 278           <td class="paramname"><em>parameters</em>&#160;</td>
 279         </tr>
 280         <tr>
 281           <td></td>
 282           <td>)</td>
 283           <td></td><td></td>
 284         </tr>
 285       </table>
 286 </div><div class="memdoc">
 287
 288 <p>Recalculate energy parameters. </p>
 289 <p>This function recalculates all energy parameters given the current model settings. It's second argument can either be NULL or a data structure containing the precomputed Boltzmann factors. In the first scenario, the necessary data structure will be created automatically according to the current global model settings, i.e. this mode might not be threadsafe. However, if the provided data structure is not NULL, threadsafety for the model parameters <a class="el" href="fold__vars_8h.html#a72b511ed1201f7e23ec437e468790d74" title="Switch the energy model for dangling end contributions (0, 1, 2, 3)">dangles</a>, <a class="el" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a> and <a class="el" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a> is regained, since their values are taken from this data structure during subsequent calculations.</p>
 290 <dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__energy__parameters.html#ga6fc2f3eef5a3024d44963ac59a42e39d" title="Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent th...">get_boltzmann_factors()</a>, <a class="el" href="group__pf__cofold.html#ga6e0f36c1f9b7d9dd4bfbad914c1119e5" title="Recalculate energy parameters.">update_co_pf_params()</a></dd></dl>
 291 <dl class="params"><dt>Parameters:</dt><dd>
 292   <table class="params">
 293     <tr><td class="paramname">length</td><td>Length of the current RNA sequence </td></tr>
 294     <tr><td class="paramname">parameters</td><td>data structure containing the precomputed Boltzmann factors </td></tr>
 295   </table>
 296   </dd>
 297 </dl>
 298
 299 </div>
 300 </div>
 301 <a class="anchor" id="ga15ae04ac5ab84e876dcf0093120cb617"></a>
 302 <div class="memitem">
 303 <div class="memproto">
 304       <table class="memname">
 305         <tr>
 306           <td class="memname">void compute_probabilities </td>
 307           <td>(</td>
 308           <td class="paramtype">double&#160;</td>
 309           <td class="paramname"><em>FAB</em>, </td>
 310         </tr>
 311         <tr>
 312           <td class="paramkey"></td>
 313           <td></td>
 314           <td class="paramtype">double&#160;</td>
 315           <td class="paramname"><em>FEA</em>, </td>
 316         </tr>
 317         <tr>
 318           <td class="paramkey"></td>
 319           <td></td>
 320           <td class="paramtype">double&#160;</td>
 321           <td class="paramname"><em>FEB</em>, </td>
 322         </tr>
 323         <tr>
 324           <td class="paramkey"></td>
 325           <td></td>
 326           <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> *&#160;</td>
 327           <td class="paramname"><em>prAB</em>, </td>
 328         </tr>
 329         <tr>
 330           <td class="paramkey"></td>
 331           <td></td>
 332           <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> *&#160;</td>
 333           <td class="paramname"><em>prA</em>, </td>
 334         </tr>
 335         <tr>
 336           <td class="paramkey"></td>
 337           <td></td>
 338           <td class="paramtype">struct <a class="el" href="structplist.html">plist</a> *&#160;</td>
 339           <td class="paramname"><em>prB</em>, </td>
 340         </tr>
 341         <tr>
 342           <td class="paramkey"></td>
 343           <td></td>
 344           <td class="paramtype">int&#160;</td>
 345           <td class="paramname"><em>Alength</em>&#160;</td>
 346         </tr>
 347         <tr>
 348           <td></td>
 349           <td>)</td>
 350           <td></td><td></td>
 351         </tr>
 352       </table>
 353 </div><div class="memdoc">
 354
 355 <p>Compute Boltzmann probabilities of dimerization without homodimers. </p>
 356 <p>Given the pair probabilities and free energies (in the null model) for a dimer AB and the two constituent monomers A and B, compute the conditional pair probabilities given that a dimer AB actually forms. Null model pair probabilities are given as a list as produced by <a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019" title="Create a plist from a probability matrix.">assign_plist_from_pr()</a>, the dimer probabilities 'prAB' are modified in place.</p>
 357 <dl class="params"><dt>Parameters:</dt><dd>
 358   <table class="params">
 359     <tr><td class="paramname">FAB</td><td>free energy of dimer AB </td></tr>
 360     <tr><td class="paramname">FEA</td><td>free energy of monomer A </td></tr>
 361     <tr><td class="paramname">FEB</td><td>free energy of monomer B </td></tr>
 362     <tr><td class="paramname">prAB</td><td>pair probabilities for dimer </td></tr>
 363     <tr><td class="paramname">prA</td><td>pair probabilities monomer </td></tr>
 364     <tr><td class="paramname">prB</td><td>pair probabilities monomer </td></tr>
 365     <tr><td class="paramname">Alength</td><td>Length of molecule A </td></tr>
 366   </table>
 367   </dd>
 368 </dl>
 369
 370 </div>
 371 </div>
 372 <a class="anchor" id="ga5545cb936ac4ff93c7d699d46e72e8c7"></a>
 373 <div class="memitem">
 374 <div class="memproto">
 375       <table class="memname">
 376         <tr>
 377           <td class="memname"><a class="el" href="structConcEnt.html">ConcEnt</a>* get_concentrations </td>
 378           <td>(</td>
 379           <td class="paramtype">double&#160;</td>
 380           <td class="paramname"><em>FEAB</em>, </td>
 381         </tr>
 382         <tr>
 383           <td class="paramkey"></td>
 384           <td></td>
 385           <td class="paramtype">double&#160;</td>
 386           <td class="paramname"><em>FEAA</em>, </td>
 387         </tr>
 388         <tr>
 389           <td class="paramkey"></td>
 390           <td></td>
 391           <td class="paramtype">double&#160;</td>
 392           <td class="paramname"><em>FEBB</em>, </td>
 393         </tr>
 394         <tr>
 395           <td class="paramkey"></td>
 396           <td></td>
 397           <td class="paramtype">double&#160;</td>
 398           <td class="paramname"><em>FEA</em>, </td>
 399         </tr>
 400         <tr>
 401           <td class="paramkey"></td>
 402           <td></td>
 403           <td class="paramtype">double&#160;</td>
 404           <td class="paramname"><em>FEB</em>, </td>
 405         </tr>
 406         <tr>
 407           <td class="paramkey"></td>
 408           <td></td>
 409           <td class="paramtype">double *&#160;</td>
 410           <td class="paramname"><em>startconc</em>&#160;</td>
 411         </tr>
 412         <tr>
 413           <td></td>
 414           <td>)</td>
 415           <td></td><td></td>
 416         </tr>
 417       </table>
 418 </div><div class="memdoc">
 419
 420 <p>Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. </p>
 421 <p>This function takes an array 'startconc' of input concentrations with alternating entries for the initial concentrations of molecules A and B (terminated by two zeroes), then computes the resulting equilibrium concentrations from the free energies for the dimers. Dimer free energies should be the dimer-only free energies, i.e. the FcAB entries from the <a class="el" href="structcofoldF.html">cofoldF</a> struct.</p>
 422 <dl class="params"><dt>Parameters:</dt><dd>
 423   <table class="params">
 424     <tr><td class="paramname">FEAB</td><td>Free energy of AB dimer (FcAB entry) </td></tr>
 425     <tr><td class="paramname">FEAA</td><td>Free energy of AA dimer (FcAB entry) </td></tr>
 426     <tr><td class="paramname">FEBB</td><td>Free energy of BB dimer (FcAB entry) </td></tr>
 427     <tr><td class="paramname">FEA</td><td>Free energy of monomer A </td></tr>
 428     <tr><td class="paramname">FEB</td><td>Free energy of monomer B </td></tr>
 429     <tr><td class="paramname">startconc</td><td>List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0] </td></tr>
 430   </table>
 431   </dd>
 432 </dl>
 433 <dl class="section return"><dt>Returns:</dt><dd><a class="el" href="structConcEnt.html">ConcEnt</a> array containing the equilibrium energies and start concentrations </dd></dl>
 434
 435 </div>
 436 </div>
 437 </div><!-- contents -->
 438 </div><!-- doc-content -->
 439 <!-- start footer part -->
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 441   <ul>
 442     <li class="footer">Generated on Wed Jul 24 2013 13:38:59 for RNAlib-2.1.2 by
 443     <a href="http://www.doxygen.org/index.html">
 444     <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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