binaries/src/ViennaRNA/doc/html/cofold_8h_source.html

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  68 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h</h1><a href="cofold_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__</span>
  69 <a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_COFOLD_H__</span>
  70 <a name="l00003"></a>00003 <span class="preprocessor"></span>
  71 <a name="l00004"></a>00004 <span class="preprocessor">#include &quot;<a class="code" href="data__structures_8h.html" title="All datastructures and typedefs shared among the Vienna RNA Package can be found...">data_structures.h</a>&quot;</span>
  72 <a name="l00005"></a>00005
  73 <a name="l00006"></a>00006 <span class="preprocessor">#ifdef __GNUC__</span>
  74 <a name="l00007"></a>00007 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func __attribute__ ((deprecated))</span>
  75 <a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#else</span>
  76 <a name="l00009"></a>00009 <span class="preprocessor"></span><span class="preprocessor">#define DEPRECATED(func) func</span>
  77 <a name="l00010"></a>00010 <span class="preprocessor"></span><span class="preprocessor">#endif</span>
  78 <a name="l00011"></a>00011 <span class="preprocessor"></span>
  79 <a name="l00065"></a>00065 <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
  80 <a name="l00066"></a>00066               <span class="keywordtype">char</span> *structure);
  81 <a name="l00067"></a>00067
  82 <a name="l00072"></a>00072 <span class="keywordtype">float</span> <a class="code" href="group__mfe__cofold.html#gafe430060533f14b11fc611f60b3f1f6f" title="Compute the minimum free energy of two interacting RNA molecules.">cofold_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
  83 <a name="l00073"></a>00073                   <span class="keywordtype">char</span> *structure,
  84 <a name="l00074"></a>00074                   <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters,
  85 <a name="l00075"></a>00075                   <span class="keywordtype">int</span> is_constrained);
  86 <a name="l00076"></a>00076
  87 <a name="l00080"></a>00080 <span class="keywordtype">void</span>      <a class="code" href="group__mfe__cofold.html#gaafb33d7473eb9af9d1b168ca8761c41a" title="Free memory occupied by cofold().">free_co_arrays</a>(<span class="keywordtype">void</span>);
  88 <a name="l00081"></a>00081
  89 <a name="l00085"></a>00085 <span class="keywordtype">void</span>      <a class="code" href="group__mfe__cofold.html#ga4fcbf34e77b99bfbb2333d2ab0c41a57" title="Recalculate parameters.">update_cofold_params</a>(<span class="keywordtype">void</span>);
  90 <a name="l00086"></a>00086
  91 <a name="l00087"></a>00087 <span class="keywordtype">void</span>      update_cofold_params_par(<a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);
  92 <a name="l00088"></a>00088
  93 <a name="l00089"></a>00089
  94 <a name="l00105"></a>00105 <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5f5bf4df35d0554f6ace9579f8744c48" title="Export the arrays of partition function cofold (with gquadruplex support).">export_cofold_arrays_gq</a>( <span class="keywordtype">int</span> **f5_p,
  95 <a name="l00106"></a>00106                               <span class="keywordtype">int</span> **c_p,
  96 <a name="l00107"></a>00107                               <span class="keywordtype">int</span> **fML_p,
  97 <a name="l00108"></a>00108                               <span class="keywordtype">int</span> **fM1_p,
  98 <a name="l00109"></a>00109                               <span class="keywordtype">int</span> **fc_p,
  99 <a name="l00110"></a>00110                               <span class="keywordtype">int</span> **ggg_p,
 100 <a name="l00111"></a>00111                               <span class="keywordtype">int</span> **indx_p,
 101 <a name="l00112"></a>00112                               <span class="keywordtype">char</span> **ptype_p);
 102 <a name="l00113"></a>00113
 103 <a name="l00128"></a>00128 <span class="keywordtype">void</span> <a class="code" href="group__mfe__cofold.html#ga5cb6b59983f1f74ccc00b9b9c4e84482" title="Export the arrays of partition function cofold.">export_cofold_arrays</a>(<span class="keywordtype">int</span> **f5_p,
 104 <a name="l00129"></a>00129                           <span class="keywordtype">int</span> **c_p,
 105 <a name="l00130"></a>00130                           <span class="keywordtype">int</span> **fML_p,
 106 <a name="l00131"></a>00131                           <span class="keywordtype">int</span> **fM1_p,
 107 <a name="l00132"></a>00132                           <span class="keywordtype">int</span> **fc_p,
 108 <a name="l00133"></a>00133                           <span class="keywordtype">int</span> **indx_p,
 109 <a name="l00134"></a>00134                           <span class="keywordtype">char</span> **ptype_p);
 110 <a name="l00135"></a>00135
 111 <a name="l00136"></a>00136
 112 <a name="l00153"></a>00153 <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a>  *<a class="code" href="group__subopt__zuker.html#ga0d5104e3ecf119d8eabd40aa5fe47f90" title="Compute Zuker type suboptimal structures.">zukersubopt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>);
 113 <a name="l00154"></a>00154
 114 <a name="l00161"></a>00161 <a class="code" href="structSOLUTION.html" title="Solution element from subopt.c.">SOLUTION</a>  *<a class="code" href="group__subopt__zuker.html#ga6d98a9450d1affadf144ac79f543da8c" title="Compute Zuker type suboptimal structures.">zukersubopt_par</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,
 115 <a name="l00162"></a>00162                             <a class="code" href="structparamT.html" title="The datastructure that contains temperature scaled energy parameters.">paramT</a> *parameters);
 116 <a name="l00163"></a>00163
 117 <a name="l00172"></a>00172 <span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#a4958b517c613e4d2afd5bce6c1060a79" title="get_monomer_free_energies">get_monomere_mfes</a>( <span class="keywordtype">float</span> *e1,
 118 <a name="l00173"></a>00173                         <span class="keywordtype">float</span> *e2);
 119 <a name="l00174"></a>00174
 120 <a name="l00175"></a>00175
 121 <a name="l00180"></a>00180 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="cofold_8h.html#afee0c32208aa2ac97338b6e3fbad7fa5">initialize_cofold</a>(<span class="keywordtype">int</span> length));
 122 <a name="l00181"></a>00181
 123 <a name="l00182"></a>00182 <span class="preprocessor">#endif</span>
 124 </pre></div></div>
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