binaries/src/ViennaRNA/doc/latex/part__func_8h_source.tex

   1 \hypertarget{part__func_8h}{\section{part\-\_\-func.\-h}
   2 \label{part__func_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_}
   7 00002 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H\_\_}
   8 00003 \textcolor{preprocessor}{}
   9 00004 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
  10 00005
  11 00006 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
  12 00007 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
  13 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
  14 00009 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
  15 00010 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  16 00011 \textcolor{preprocessor}{}
  17 00012
  18 00041 \textcolor{keyword}{extern}  \textcolor{keywordtype}{int} \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\_back};
  19 00042
  20 00043 \textcolor{comment}{/*}
  21 00044 \textcolor{comment}{#################################################}
  22 00045 \textcolor{comment}{# PARTITION FUNCTION COMPUTATION                #}
  23 00046 \textcolor{comment}{#################################################}
  24 00047 \textcolor{comment}{*/}
  25 00048
  26 00087 \textcolor{keywordtype}{float}   \hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\_fold\_par}(  \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  27 00088                       \textcolor{keywordtype}{char} *structure,
  28 00089                       \hyperlink{structpf__paramT}{pf\_paramT} *parameters,
  29 00090                       \textcolor{keywordtype}{int} calculate\_bppm,
  30 00091                       \textcolor{keywordtype}{int} is\_constrained,
  31 00092                       \textcolor{keywordtype}{int} is\_circular);
  32 00093
  33 00133 \textcolor{keywordtype}{float}   \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  34 00134                 \textcolor{keywordtype}{char} *structure);
  35 00135
  36 00161 \textcolor{keywordtype}{float}   \hyperlink{group__pf__fold_ga819ce5fca8984004ac81c4a3b04cb735}{pf\_circ\_fold}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,
  37 00162                       \textcolor{keywordtype}{char} *structure);
  38 00163
  39 00173 \textcolor{keywordtype}{char}    *\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack}(\textcolor{keywordtype}{char} *sequence);
  40 00174
  41 00186 \textcolor{keywordtype}{char}    *\hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_circ}(\textcolor{keywordtype}{char} *sequence);
  42 00187
  43 00203 \textcolor{keywordtype}{void}  \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}(\textcolor{keywordtype}{void});
  44 00204
  45 00214 \textcolor{keywordtype}{void}  \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\_pf\_params}(\textcolor{keywordtype}{int} length);
  46 00215
  47 00222 \textcolor{keywordtype}{void} \hyperlink{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{update\_pf\_params\_par}(\textcolor{keywordtype}{int} length, \hyperlink{structpf__paramT}{pf\_paramT} *parameters);
  48 00223
  49 00240 FLT\_OR\_DBL  *\hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}(\textcolor{keywordtype}{void});
  50 00241
  51 00242 \textcolor{comment}{/*}
  52 00243 \textcolor{comment}{#################################################}
  53 00244 \textcolor{comment}{# OTHER PARTITION FUNCTION RELATED DECLARATIONS #}
  54 00245 \textcolor{comment}{#################################################}
  55 00246 \textcolor{comment}{*/}
  56 00247
  57 00265 \textcolor{keywordtype}{void}  \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\_plist\_from\_pr}( \hyperlink{structplist}{plist} **pl,
  58 00266                             FLT\_OR\_DBL *probs,
  59 00267                             \textcolor{keywordtype}{int} length,
  60 00268                             \textcolor{keywordtype}{double} cutoff);
  61 00269
  62 00270 \textcolor{comment}{/* this doesn't work if free\_pf\_arrays() is called before */}
  63 00271 \textcolor{keywordtype}{void} assign\_plist\_gquad\_from\_pr(\hyperlink{structplist}{plist} **pl,
  64 00272                                 \textcolor{keywordtype}{int} length,
  65 00273                                 \textcolor{keywordtype}{double} cut\_off);
  66 00274
  67 00275 \textcolor{keywordtype}{char} *get\_centroid\_struct\_gquad\_pr(\textcolor{keywordtype}{int} length,
  68 00276                                   \textcolor{keywordtype}{double} *dist);
  69 00277
  70 00293 \textcolor{keywordtype}{int} \hyperlink{group__pf__fold_ga18607e79e106cad827f482eedd2f632e}{get\_pf\_arrays}(\textcolor{keywordtype}{short} **S\_p,
  71 00294                   \textcolor{keywordtype}{short} **S1\_p,
  72 00295                   \textcolor{keywordtype}{char} **ptype\_p,
  73 00296                   FLT\_OR\_DBL **qb\_p,
  74 00297                   FLT\_OR\_DBL **qm\_p,
  75 00298                   FLT\_OR\_DBL **q1k\_p,
  76 00299                   FLT\_OR\_DBL **qln\_p);
  77 00300
  78 00304 \textcolor{keywordtype}{double} \hyperlink{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{get\_subseq\_F}(\textcolor{keywordtype}{int} i, \textcolor{keywordtype}{int} j);
  79 00305
  80 00322 \textcolor{keywordtype}{char}  *\hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\_centroid\_struct\_pl}(\textcolor{keywordtype}{int} length,
  81 00323                               \textcolor{keywordtype}{double} *dist,
  82 00324                               \hyperlink{structplist}{plist} *pl);
  83 00325
  84 00342 \textcolor{keywordtype}{char}  *\hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\_centroid\_struct\_pr}(\textcolor{keywordtype}{int} length,
  85 00343                               \textcolor{keywordtype}{double} *dist,
  86 00344                               FLT\_OR\_DBL *pr);
  87 00345
  88 00358 \textcolor{keywordtype}{double}  \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\_bp\_distance}(\textcolor{keywordtype}{int} length);
  89 00359
  90 00377 \textcolor{keywordtype}{double}  \hyperlink{group__pf__fold_ga72d84525f0afd3a9d60d830a2f501fa5}{mean\_bp\_distance\_pr}(\textcolor{keywordtype}{int} length,
  91 00378                             FLT\_OR\_DBL *pr);
  92 00379
  93 00383 \textcolor{keywordtype}{void}  \hyperlink{part__func_8h_a1f562d463c14d4703d9656056200eb38}{bppm\_to\_structure}(\textcolor{keywordtype}{char} *structure,
  94 00384                         FLT\_OR\_DBL *pr,
  95 00385                         \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
  96 00386
  97 00387 \hyperlink{structplist}{plist} *stackProb(\textcolor{keywordtype}{double} cutoff);
  98 00388
  99 00392 \textcolor{keywordtype}{char}    \hyperlink{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{bppm\_symbol}(\textcolor{keyword}{const} \textcolor{keywordtype}{float} *x);
 100 00393
 101 00394
 102 00395 \textcolor{comment}{/*}
 103 00396 \textcolor{comment}{#################################################}
 104 00397 \textcolor{comment}{# DEPRECATED FUNCTIONS                          #}
 105 00398 \textcolor{comment}{#################################################}
 106 00399 \textcolor{comment}{*/}
 107 00400
 108 00406 DEPRECATED(\textcolor{keywordtype}{void} \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\_pf\_fold}(\textcolor{keywordtype}{int} length));
 109 00407
 110 00412 DEPRECATED(\textcolor{keywordtype}{char} *\hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid}(\textcolor{keywordtype}{int} length,
 111 00413                           \textcolor{keywordtype}{double} *dist));     \textcolor{comment}{/* mean pair distance of ensemble */}
 112 00414
 113 00420 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\_bp\_dist}(\textcolor{keywordtype}{int} length));
 114 00421
 115 00425 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy}(\textcolor{keywordtype}{int} u1,
 116 00426                                 \textcolor{keywordtype}{int} u2,
 117 00427                                 \textcolor{keywordtype}{int} type,
 118 00428                                 \textcolor{keywordtype}{int} type2,
 119 00429                                 \textcolor{keywordtype}{short} si1,
 120 00430                                 \textcolor{keywordtype}{short} sj1,
 121 00431                                 \textcolor{keywordtype}{short} sp1,
 122 00432                                 \textcolor{keywordtype}{short} sq1));
 123 00433
 124 00437 DEPRECATED(\textcolor{keywordtype}{double} \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy}( \textcolor{keywordtype}{int} u,
 125 00438                                     \textcolor{keywordtype}{int} type,
 126 00439                                     \textcolor{keywordtype}{short} si1,
 127 00440                                     \textcolor{keywordtype}{short} sj1,
 128 00441                                     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}));
 129 00442
 130 00443 \textcolor{preprocessor}{#endif}
 131 \end{DoxyCode}