binaries/src/ViennaRNA/doc/html/part__func_8h_source.html

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  68 <h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func.h</h1><a href="part__func_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_PART_FUNC_H__</span>
  69 <a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_PART_FUNC_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="l00012"></a>00012
  80 <a name="l00041"></a>00041 <span class="keyword">extern</span>  <span class="keywordtype">int</span> <a class="code" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a" title="Flag indicating that auxilary arrays are needed throughout the computations. This...">st_back</a>;
  81 <a name="l00042"></a>00042
  82 <a name="l00043"></a>00043 <span class="comment">/*</span>
  83 <a name="l00044"></a>00044 <span class="comment">#################################################</span>
  84 <a name="l00045"></a>00045 <span class="comment"># PARTITION FUNCTION COMPUTATION                #</span>
  85 <a name="l00046"></a>00046 <span class="comment">#################################################</span>
  86 <a name="l00047"></a>00047 <span class="comment">*/</span>
  87 <a name="l00048"></a>00048
  88 <a name="l00087"></a>00087 <span class="keywordtype">float</span>   <a class="code" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823" title="Compute the partition function  for a given RNA sequence.">pf_fold_par</a>(  <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
  89 <a name="l00088"></a>00088                       <span class="keywordtype">char</span> *structure,
  90 <a name="l00089"></a>00089                       <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters,
  91 <a name="l00090"></a>00090                       <span class="keywordtype">int</span> calculate_bppm,
  92 <a name="l00091"></a>00091                       <span class="keywordtype">int</span> is_constrained,
  93 <a name="l00092"></a>00092                       <span class="keywordtype">int</span> is_circular);
  94 <a name="l00093"></a>00093
  95 <a name="l00133"></a>00133 <span class="keywordtype">float</span>   <a class="code" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function  of an RNA sequence.">pf_fold</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
  96 <a name="l00134"></a>00134                 <span class="keywordtype">char</span> *structure);
  97 <a name="l00135"></a>00135
  98 <a name="l00161"></a>00161 <span class="keywordtype">float</span>   <a class="code" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735" title="Compute the partition function of a circular RNA sequence.">pf_circ_fold</a>( <span class="keyword">const</span> <span class="keywordtype">char</span> *sequence,
  99 <a name="l00162"></a>00162                       <span class="keywordtype">char</span> *structure);
 100 <a name="l00163"></a>00163
 101 <a name="l00173"></a>00173 <span class="keywordtype">char</span>    *<a class="code" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03" title="Sample a secondary structure from the Boltzmann ensemble according its probability...">pbacktrack</a>(<span class="keywordtype">char</span> *sequence);
 102 <a name="l00174"></a>00174
 103 <a name="l00186"></a>00186 <span class="keywordtype">char</span>    *<a class="code" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff" title="Sample a secondary structure of a circular RNA from the Boltzmann ensemble according...">pbacktrack_circ</a>(<span class="keywordtype">char</span> *sequence);
 104 <a name="l00187"></a>00187
 105 <a name="l00203"></a>00203 <span class="keywordtype">void</span>  <a class="code" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd" title="Free arrays for the partition function recursions.">free_pf_arrays</a>(<span class="keywordtype">void</span>);
 106 <a name="l00204"></a>00204
 107 <a name="l00214"></a>00214 <span class="keywordtype">void</span>  <a class="code" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28" title="Recalculate energy parameters.">update_pf_params</a>(<span class="keywordtype">int</span> length);
 108 <a name="l00215"></a>00215
 109 <a name="l00222"></a>00222 <span class="keywordtype">void</span> <a class="code" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc" title="Recalculate energy parameters.">update_pf_params_par</a>(<span class="keywordtype">int</span> length, <a class="code" href="structpf__paramT.html" title="The datastructure that contains temperature scaled Boltzmann weights of the energy...">pf_paramT</a> *parameters);
 110 <a name="l00223"></a>00223
 111 <a name="l00240"></a>00240 FLT_OR_DBL  *<a class="code" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115" title="Get a pointer to the base pair probability arrayAccessing the base pair probabilities...">export_bppm</a>(<span class="keywordtype">void</span>);
 112 <a name="l00241"></a>00241
 113 <a name="l00242"></a>00242 <span class="comment">/*</span>
 114 <a name="l00243"></a>00243 <span class="comment">#################################################</span>
 115 <a name="l00244"></a>00244 <span class="comment"># OTHER PARTITION FUNCTION RELATED DECLARATIONS #</span>
 116 <a name="l00245"></a>00245 <span class="comment">#################################################</span>
 117 <a name="l00246"></a>00246 <span class="comment">*/</span>
 118 <a name="l00247"></a>00247
 119 <a name="l00265"></a>00265 <span class="keywordtype">void</span>  <a class="code" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019" title="Create a plist from a probability matrix.">assign_plist_from_pr</a>( <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **pl,
 120 <a name="l00266"></a>00266                             FLT_OR_DBL *probs,
 121 <a name="l00267"></a>00267                             <span class="keywordtype">int</span> length,
 122 <a name="l00268"></a>00268                             <span class="keywordtype">double</span> cutoff);
 123 <a name="l00269"></a>00269
 124 <a name="l00270"></a>00270 <span class="comment">/* this doesn&apos;t work if free_pf_arrays() is called before */</span>
 125 <a name="l00271"></a>00271 <span class="keywordtype">void</span> assign_plist_gquad_from_pr(<a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> **pl,
 126 <a name="l00272"></a>00272                                 <span class="keywordtype">int</span> length,
 127 <a name="l00273"></a>00273                                 <span class="keywordtype">double</span> cut_off);
 128 <a name="l00274"></a>00274
 129 <a name="l00275"></a>00275 <span class="keywordtype">char</span> *get_centroid_struct_gquad_pr(<span class="keywordtype">int</span> length,
 130 <a name="l00276"></a>00276                                   <span class="keywordtype">double</span> *dist);
 131 <a name="l00277"></a>00277
 132 <a name="l00293"></a>00293 <span class="keywordtype">int</span> <a class="code" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e" title="Get the pointers to (almost) all relavant computation arrays used in partition function...">get_pf_arrays</a>(<span class="keywordtype">short</span> **S_p,
 133 <a name="l00294"></a>00294                   <span class="keywordtype">short</span> **S1_p,
 134 <a name="l00295"></a>00295                   <span class="keywordtype">char</span> **ptype_p,
 135 <a name="l00296"></a>00296                   FLT_OR_DBL **qb_p,
 136 <a name="l00297"></a>00297                   FLT_OR_DBL **qm_p,
 137 <a name="l00298"></a>00298                   FLT_OR_DBL **q1k_p,
 138 <a name="l00299"></a>00299                   FLT_OR_DBL **qln_p);
 139 <a name="l00300"></a>00300
 140 <a name="l00304"></a>00304 <span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e" title="Get the free energy of a subsequence from the q[] array.">get_subseq_F</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j);
 141 <a name="l00305"></a>00305
 142 <a name="l00322"></a>00322 <span class="keywordtype">char</span>  *<a class="code" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6" title="Get the centroid structure of the ensemble.">get_centroid_struct_pl</a>(<span class="keywordtype">int</span> length,
 143 <a name="l00323"></a>00323                               <span class="keywordtype">double</span> *dist,
 144 <a name="l00324"></a>00324                               <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> *pl);
 145 <a name="l00325"></a>00325
 146 <a name="l00342"></a>00342 <span class="keywordtype">char</span>  *<a class="code" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38" title="Get the centroid structure of the ensemble.">get_centroid_struct_pr</a>(<span class="keywordtype">int</span> length,
 147 <a name="l00343"></a>00343                               <span class="keywordtype">double</span> *dist,
 148 <a name="l00344"></a>00344                               FLT_OR_DBL *pr);
 149 <a name="l00345"></a>00345
 150 <a name="l00358"></a>00358 <span class="keywordtype">double</span>  <a class="code" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d" title="Get the mean base pair distance of the last partition function computation.">mean_bp_distance</a>(<span class="keywordtype">int</span> length);
 151 <a name="l00359"></a>00359
 152 <a name="l00377"></a>00377 <span class="keywordtype">double</span>  <a class="code" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5" title="Get the mean base pair distance in the thermodynamic ensemble.">mean_bp_distance_pr</a>(<span class="keywordtype">int</span> length,
 153 <a name="l00378"></a>00378                             FLT_OR_DBL *pr);
 154 <a name="l00379"></a>00379
 155 <a name="l00383"></a>00383 <span class="keywordtype">void</span>  <a class="code" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38" title="Create a dot-bracket like structure string from base pair probability matrix.">bppm_to_structure</a>(<span class="keywordtype">char</span> *structure,
 156 <a name="l00384"></a>00384                         FLT_OR_DBL *pr,
 157 <a name="l00385"></a>00385                         <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length);
 158 <a name="l00386"></a>00386
 159 <a name="l00387"></a>00387 <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> *stackProb(<span class="keywordtype">double</span> cutoff);
 160 <a name="l00388"></a>00388
 161 <a name="l00392"></a>00392 <span class="keywordtype">char</span>    <a class="code" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d" title="Get a pseudo dot bracket notation for a given probability information.">bppm_symbol</a>(<span class="keyword">const</span> <span class="keywordtype">float</span> *x);
 162 <a name="l00393"></a>00393
 163 <a name="l00394"></a>00394
 164 <a name="l00395"></a>00395 <span class="comment">/*</span>
 165 <a name="l00396"></a>00396 <span class="comment">#################################################</span>
 166 <a name="l00397"></a>00397 <span class="comment"># DEPRECATED FUNCTIONS                          #</span>
 167 <a name="l00398"></a>00398 <span class="comment">#################################################</span>
 168 <a name="l00399"></a>00399 <span class="comment">*/</span>
 169 <a name="l00400"></a>00400
 170 <a name="l00406"></a>00406 DEPRECATED(<span class="keywordtype">void</span> <a class="code" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af" title="Allocate space for pf_fold().">init_pf_fold</a>(<span class="keywordtype">int</span> length));
 171 <a name="l00407"></a>00407
 172 <a name="l00412"></a>00412 DEPRECATED(<span class="keywordtype">char</span> *<a class="code" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a>(<span class="keywordtype">int</span> length,
 173 <a name="l00413"></a>00413                           <span class="keywordtype">double</span> *dist));     <span class="comment">/* mean pair distance of ensemble */</span>
 174 <a name="l00414"></a>00414
 175 <a name="l00420"></a>00420 DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a>(<span class="keywordtype">int</span> length));
 176 <a name="l00421"></a>00421
 177 <a name="l00425"></a>00425 DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a>(<span class="keywordtype">int</span> u1,
 178 <a name="l00426"></a>00426                                 <span class="keywordtype">int</span> u2,
 179 <a name="l00427"></a>00427                                 <span class="keywordtype">int</span> type,
 180 <a name="l00428"></a>00428                                 <span class="keywordtype">int</span> type2,
 181 <a name="l00429"></a>00429                                 <span class="keywordtype">short</span> si1,
 182 <a name="l00430"></a>00430                                 <span class="keywordtype">short</span> sj1,
 183 <a name="l00431"></a>00431                                 <span class="keywordtype">short</span> sp1,
 184 <a name="l00432"></a>00432                                 <span class="keywordtype">short</span> sq1));
 185 <a name="l00433"></a>00433
 186 <a name="l00437"></a>00437 DEPRECATED(<span class="keywordtype">double</span> <a class="code" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a>( <span class="keywordtype">int</span> u,
 187 <a name="l00438"></a>00438                                     <span class="keywordtype">int</span> type,
 188 <a name="l00439"></a>00439                                     <span class="keywordtype">short</span> si1,
 189 <a name="l00440"></a>00440                                     <span class="keywordtype">short</span> sj1,
 190 <a name="l00441"></a>00441                                     <span class="keyword">const</span> <span class="keywordtype">char</span> *<span class="keywordtype">string</span>));
 191 <a name="l00442"></a>00442
 192 <a name="l00443"></a>00443 <span class="preprocessor">#endif</span>
 193 </pre></div></div>
 194 <hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by&nbsp;
 195 <a href="http://www.doxygen.org/index.html">
 196 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 197 </body>
 198 </html>