binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag

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   5     <title>ViennaRNA Package core - RNAlib</title>
   6     <filename>main</filename>
   7     <docanchor file="main">mp_intro</docanchor>
   8   </compound>
   9   <compound kind="file">
  10     <name>2Dfold.h</name>
  11     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
  12     <filename>2Dfold_8h</filename>
  13     <member kind="function">
  14       <type>TwoDfold_vars *</type>
  15       <name>get_TwoDfold_variables</name>
  16       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
  17       <anchor>gac9284f132cf0eaa0a2f43590eda05488</anchor>
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  19     </member>
  20     <member kind="function">
  21       <type>void</type>
  22       <name>destroy_TwoDfold_variables</name>
  23       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
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  25       <arglist>(TwoDfold_vars *our_variables)</arglist>
  26     </member>
  27     <member kind="function">
  28       <type>TwoDfold_solution *</type>
  29       <name>TwoDfoldList</name>
  30       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
  31       <anchor>ga47da790166020558d27323aef489703e</anchor>
  32       <arglist>(TwoDfold_vars *vars, int distance1, int distance2)</arglist>
  33     </member>
  34     <member kind="function">
  35       <type>char *</type>
  36       <name>TwoDfold_backtrack_f5</name>
  37       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
  38       <anchor>gaf4dc05bf8fc1ea53acd7aeb798ba80c2</anchor>
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  43     <name>2Dpfold.h</name>
  44     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
  45     <filename>2Dpfold_8h</filename>
  46     <member kind="function">
  47       <type>TwoDpfold_vars *</type>
  48       <name>get_TwoDpfold_variables</name>
  49       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
  50       <anchor>ga1aca740e2a75ab2b2951538266e53d64</anchor>
  51       <arglist>(const char *seq, const char *structure1, char *structure2, int circ)</arglist>
  52     </member>
  53     <member kind="function">
  54       <type>TwoDpfold_vars *</type>
  55       <name>get_TwoDpfold_variables_from_MFE</name>
  56       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
  57       <anchor>gacc2f66da7ee62096cab629fce7112216</anchor>
  58       <arglist>(TwoDfold_vars *mfe_vars)</arglist>
  59     </member>
  60     <member kind="function">
  61       <type>void</type>
  62       <name>destroy_TwoDpfold_variables</name>
  63       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
  64       <anchor>gafe994291458ee2ac34d3eb825ef62a15</anchor>
  65       <arglist>(TwoDpfold_vars *vars)</arglist>
  66     </member>
  67     <member kind="function">
  68       <type>TwoDpfold_solution *</type>
  69       <name>TwoDpfoldList</name>
  70       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
  71       <anchor>ga3e1cd3b24eb635c65181182cbb4ae3eb</anchor>
  72       <arglist>(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)</arglist>
  73     </member>
  74     <member kind="function">
  75       <type>char *</type>
  76       <name>TwoDpfold_pbacktrack</name>
  77       <anchorfile>group__kl__neighborhood__stochbt.html</anchorfile>
  78       <anchor>gae251288f50dd4ae7d315af0085775f71</anchor>
  79       <arglist>(TwoDpfold_vars *vars, int d1, int d2)</arglist>
  80     </member>
  81     <member kind="function">
  82       <type>char *</type>
  83       <name>TwoDpfold_pbacktrack5</name>
  84       <anchorfile>group__kl__neighborhood__stochbt.html</anchorfile>
  85       <anchor>ga13430ac6a7f90df426774f131647d2c7</anchor>
  86       <arglist>(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)</arglist>
  87     </member>
  88   </compound>
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  91     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
  92     <filename>alifold_8h</filename>
  93     <member kind="function">
  94       <type>void</type>
  95       <name>update_alifold_params</name>
  96       <anchorfile>alifold_8h.html</anchorfile>
  97       <anchor>ac484c6bd429bafbd353b91044508d8e9</anchor>
  98       <arglist>(void)</arglist>
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 100     <member kind="function">
 101       <type>float</type>
 102       <name>alifold</name>
 103       <anchorfile>group__consensus__mfe__fold.html</anchorfile>
 104       <anchor>ga4cf00f0659e5f0480335d69e797f05b1</anchor>
 105       <arglist>(const char **strings, char *structure)</arglist>
 106     </member>
 107     <member kind="function">
 108       <type>float</type>
 109       <name>circalifold</name>
 110       <anchorfile>group__consensus__mfe__fold.html</anchorfile>
 111       <anchor>gadbd3b0b1c144cbfb4efe704b2b260f96</anchor>
 112       <arglist>(const char **strings, char *structure)</arglist>
 113     </member>
 114     <member kind="function">
 115       <type>void</type>
 116       <name>free_alifold_arrays</name>
 117       <anchorfile>group__consensus__mfe__fold.html</anchorfile>
 118       <anchor>ga72095e4554b5d577250ea14c42acc49e</anchor>
 119       <arglist>(void)</arglist>
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 121     <member kind="function">
 122       <type>int</type>
 123       <name>get_mpi</name>
 124       <anchorfile>group__consensus__fold.html</anchorfile>
 125       <anchor>gaa2d600be90844094ec145ea14a314d2f</anchor>
 126       <arglist>(char *Alseq[], int n_seq, int length, int *mini)</arglist>
 127     </member>
 128     <member kind="function">
 129       <type>float **</type>
 130       <name>readribosum</name>
 131       <anchorfile>group__consensus__fold.html</anchorfile>
 132       <anchor>ga5e125c9586fcd4e2e1559fe76f7289cc</anchor>
 133       <arglist>(char *name)</arglist>
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 138       <anchorfile>group__consensus__fold.html</anchorfile>
 139       <anchor>ga1c48869c03b49a342bf4cbdd61900081</anchor>
 140       <arglist>(const char **sequences, const char *structure, int n_seq, float *energy)</arglist>
 141     </member>
 142     <member kind="function">
 143       <type>void</type>
 144       <name>encode_ali_sequence</name>
 145       <anchorfile>group__consensus__fold.html</anchorfile>
 146       <anchor>gaa3e40277c837d6f7603afe319884c786</anchor>
 147       <arglist>(const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)</arglist>
 148     </member>
 149     <member kind="function">
 150       <type>void</type>
 151       <name>alloc_sequence_arrays</name>
 152       <anchorfile>group__consensus__fold.html</anchorfile>
 153       <anchor>ga8a560930f7f2582cc3967723a86cfdfa</anchor>
 154       <arglist>(const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)</arglist>
 155     </member>
 156     <member kind="function">
 157       <type>void</type>
 158       <name>free_sequence_arrays</name>
 159       <anchorfile>group__consensus__fold.html</anchorfile>
 160       <anchor>ga298a420a8c879202e2617b3f724fde38</anchor>
 161       <arglist>(unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)</arglist>
 162     </member>
 163     <member kind="function">
 164       <type>float</type>
 165       <name>alipf_fold_par</name>
 166       <anchorfile>group__consensus__pf__fold.html</anchorfile>
 167       <anchor>ga4d2ff54d8210fc7cceeeff389d4dbd1d</anchor>
 168       <arglist>(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
 169     </member>
 170     <member kind="function">
 171       <type>float</type>
 172       <name>alipf_fold</name>
 173       <anchorfile>group__consensus__pf__fold.html</anchorfile>
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 175       <arglist>(const char **sequences, char *structure, plist **pl)</arglist>
 176     </member>
 177     <member kind="function">
 178       <type>float</type>
 179       <name>alipf_circ_fold</name>
 180       <anchorfile>group__consensus__pf__fold.html</anchorfile>
 181       <anchor>ga6b4dde1d43b79ab3753508c46cf50363</anchor>
 182       <arglist>(const char **sequences, char *structure, plist **pl)</arglist>
 183     </member>
 184     <member kind="function">
 185       <type>FLT_OR_DBL *</type>
 186       <name>export_ali_bppm</name>
 187       <anchorfile>group__consensus__pf__fold.html</anchorfile>
 188       <anchor>ga11b6ab8bd9be1821fea352b190a01cab</anchor>
 189       <arglist>(void)</arglist>
 190     </member>
 191     <member kind="function">
 192       <type>char *</type>
 193       <name>alipbacktrack</name>
 194       <anchorfile>group__consensus__stochbt.html</anchorfile>
 195       <anchor>ga0df40248788f0fb17ebdc59d74116d1c</anchor>
 196       <arglist>(double *prob)</arglist>
 197     </member>
 198     <member kind="function">
 199       <type>int</type>
 200       <name>get_alipf_arrays</name>
 201       <anchorfile>group__consensus__fold.html</anchorfile>
 202       <anchor>ga5349960075b1847720a2e9df021e2675</anchor>
 203       <arglist>(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)</arglist>
 204     </member>
 205     <member kind="variable">
 206       <type>double</type>
 207       <name>cv_fact</name>
 208       <anchorfile>group__consensus__fold.html</anchorfile>
 209       <anchor>gaf3cbac6ff5d706d6e414677841ddf94c</anchor>
 210       <arglist></arglist>
 211     </member>
 212     <member kind="variable">
 213       <type>double</type>
 214       <name>nc_fact</name>
 215       <anchorfile>group__consensus__fold.html</anchorfile>
 216       <anchor>ga502948a122a2af5b914355b1f3ea2f61</anchor>
 217       <arglist></arglist>
 218     </member>
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 221     <name>cofold.h</name>
 222     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
 223     <filename>cofold_8h</filename>
 224     <member kind="function">
 225       <type>float</type>
 226       <name>cofold</name>
 227       <anchorfile>group__mfe__cofold.html</anchorfile>
 228       <anchor>gabc8517f22cfe70595ee81fc837910d52</anchor>
 229       <arglist>(const char *sequence, char *structure)</arglist>
 230     </member>
 231     <member kind="function">
 232       <type>float</type>
 233       <name>cofold_par</name>
 234       <anchorfile>group__mfe__cofold.html</anchorfile>
 235       <anchor>gafe430060533f14b11fc611f60b3f1f6f</anchor>
 236       <arglist>(const char *string, char *structure, paramT *parameters, int is_constrained)</arglist>
 237     </member>
 238     <member kind="function">
 239       <type>void</type>
 240       <name>free_co_arrays</name>
 241       <anchorfile>group__mfe__cofold.html</anchorfile>
 242       <anchor>gaafb33d7473eb9af9d1b168ca8761c41a</anchor>
 243       <arglist>(void)</arglist>
 244     </member>
 245     <member kind="function">
 246       <type>void</type>
 247       <name>update_cofold_params</name>
 248       <anchorfile>group__mfe__cofold.html</anchorfile>
 249       <anchor>ga4fcbf34e77b99bfbb2333d2ab0c41a57</anchor>
 250       <arglist>(void)</arglist>
 251     </member>
 252     <member kind="function">
 253       <type>void</type>
 254       <name>export_cofold_arrays_gq</name>
 255       <anchorfile>group__mfe__cofold.html</anchorfile>
 256       <anchor>ga5f5bf4df35d0554f6ace9579f8744c48</anchor>
 257       <arglist>(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)</arglist>
 258     </member>
 259     <member kind="function">
 260       <type>void</type>
 261       <name>export_cofold_arrays</name>
 262       <anchorfile>group__mfe__cofold.html</anchorfile>
 263       <anchor>ga5cb6b59983f1f74ccc00b9b9c4e84482</anchor>
 264       <arglist>(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)</arglist>
 265     </member>
 266     <member kind="function">
 267       <type>SOLUTION *</type>
 268       <name>zukersubopt</name>
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 270       <anchor>ga0d5104e3ecf119d8eabd40aa5fe47f90</anchor>
 271       <arglist>(const char *string)</arglist>
 272     </member>
 273     <member kind="function">
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 277       <anchor>ga6d98a9450d1affadf144ac79f543da8c</anchor>
 278       <arglist>(const char *string, paramT *parameters)</arglist>
 279     </member>
 280     <member kind="function">
 281       <type>void</type>
 282       <name>get_monomere_mfes</name>
 283       <anchorfile>cofold_8h.html</anchorfile>
 284       <anchor>a4958b517c613e4d2afd5bce6c1060a79</anchor>
 285       <arglist>(float *e1, float *e2)</arglist>
 286     </member>
 287     <member kind="function">
 288       <type>void</type>
 289       <name>initialize_cofold</name>
 290       <anchorfile>cofold_8h.html</anchorfile>
 291       <anchor>afee0c32208aa2ac97338b6e3fbad7fa5</anchor>
 292       <arglist>(int length)</arglist>
 293     </member>
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 297     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
 298     <filename>convert__epars_8h</filename>
 299     <member kind="define">
 300       <type>#define</type>
 301       <name>VRNA_CONVERT_OUTPUT_ALL</name>
 302       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 303       <anchor>ga8dc6aee5a806c49b71557152f9616bc4</anchor>
 304       <arglist></arglist>
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 311       <arglist></arglist>
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 314       <type>#define</type>
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 316       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 317       <anchor>gad23522d63f8d4c50d5a5deee9bee3ef2</anchor>
 318       <arglist></arglist>
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 320     <member kind="define">
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 323       <anchorfile>group__energy__parameters__convert.html</anchorfile>
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 325       <arglist></arglist>
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 330       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 331       <anchor>ga4ff223fb1f9c62cd92d9ab811ad03d55</anchor>
 332       <arglist></arglist>
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 334     <member kind="define">
 335       <type>#define</type>
 336       <name>VRNA_CONVERT_OUTPUT_MM_INT_1N</name>
 337       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 338       <anchor>gaf5d3743219f83c6348155cd81e755bbb</anchor>
 339       <arglist></arglist>
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 342       <type>#define</type>
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 344       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 345       <anchor>ga78382ec622ba99e0ac2262317bdd7316</anchor>
 346       <arglist></arglist>
 347     </member>
 348     <member kind="define">
 349       <type>#define</type>
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 351       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 352       <anchor>gae67af9f1cdf7baf2865481282a5d1034</anchor>
 353       <arglist></arglist>
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 358       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 359       <anchor>gaf14ead7ef1fdbe725ade653750fc51e3</anchor>
 360       <arglist></arglist>
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 365       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 366       <anchor>ga036ffd996d8c8a9acf631760dd1da24b</anchor>
 367       <arglist></arglist>
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 372       <anchorfile>group__energy__parameters__convert.html</anchorfile>
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 379       <anchorfile>group__energy__parameters__convert.html</anchorfile>
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 386       <anchorfile>group__energy__parameters__convert.html</anchorfile>
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 389     </member>
 390     <member kind="define">
 391       <type>#define</type>
 392       <name>VRNA_CONVERT_OUTPUT_INT_22</name>
 393       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 394       <anchor>gaa307671e2631cdacad9cbe4c6583b05f</anchor>
 395       <arglist></arglist>
 396     </member>
 397     <member kind="define">
 398       <type>#define</type>
 399       <name>VRNA_CONVERT_OUTPUT_BULGE</name>
 400       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 401       <anchor>ga7092fe0be4de6f02cc0bf08e81af726a</anchor>
 402       <arglist></arglist>
 403     </member>
 404     <member kind="define">
 405       <type>#define</type>
 406       <name>VRNA_CONVERT_OUTPUT_INT</name>
 407       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 408       <anchor>gac5c2289fdf8ff1b980976d1613ff943a</anchor>
 409       <arglist></arglist>
 410     </member>
 411     <member kind="define">
 412       <type>#define</type>
 413       <name>VRNA_CONVERT_OUTPUT_ML</name>
 414       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 415       <anchor>gaf2c8755d64eff3852aa45df9ac80a4fe</anchor>
 416       <arglist></arglist>
 417     </member>
 418     <member kind="define">
 419       <type>#define</type>
 420       <name>VRNA_CONVERT_OUTPUT_MISC</name>
 421       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 422       <anchor>ga46d5b1535ae86060b6317565b7c6b40b</anchor>
 423       <arglist></arglist>
 424     </member>
 425     <member kind="define">
 426       <type>#define</type>
 427       <name>VRNA_CONVERT_OUTPUT_SPECIAL_HP</name>
 428       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 429       <anchor>gaa1ff48a79642d69579d1766561ec6db6</anchor>
 430       <arglist></arglist>
 431     </member>
 432     <member kind="define">
 433       <type>#define</type>
 434       <name>VRNA_CONVERT_OUTPUT_VANILLA</name>
 435       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 436       <anchor>ga0d4e8a836bb4864ab5129c085dbf592d</anchor>
 437       <arglist></arglist>
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 439     <member kind="define">
 440       <type>#define</type>
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 444       <arglist></arglist>
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 446     <member kind="define">
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 450       <anchor>gac86976e9c2a55b3a6481ea60044f6098</anchor>
 451       <arglist></arglist>
 452     </member>
 453     <member kind="function">
 454       <type>void</type>
 455       <name>convert_parameter_file</name>
 456       <anchorfile>group__energy__parameters__convert.html</anchorfile>
 457       <anchor>gafbe538bc4eb2cf2a33326e1010005f8a</anchor>
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 463     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
 464     <filename>data__structures_8h</filename>
 465     <class kind="struct">plist</class>
 466     <class kind="struct">cpair</class>
 467     <class kind="struct">COORDINATE</class>
 468     <class kind="struct">sect</class>
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 470     <class kind="struct">bondTEn</class>
 471     <class kind="struct">model_detailsT</class>
 472     <class kind="struct">paramT</class>
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 474     <class kind="struct">PAIR</class>
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 476     <class kind="struct">SOLUTION</class>
 477     <class kind="struct">cofoldF</class>
 478     <class kind="struct">ConcEnt</class>
 479     <class kind="struct">pairpro</class>
 480     <class kind="struct">pair_info</class>
 481     <class kind="struct">move_t</class>
 482     <class kind="struct">intermediate_t</class>
 483     <class kind="struct">path_t</class>
 484     <class kind="struct">pu_contrib</class>
 485     <class kind="struct">interact</class>
 486     <class kind="struct">pu_out</class>
 487     <class kind="struct">constrain</class>
 488     <class kind="struct">duplexT</class>
 489     <class kind="struct">folden</class>
 490     <class kind="struct">snoopT</class>
 491     <class kind="struct">dupVar</class>
 492     <class kind="struct">TwoDfold_solution</class>
 493     <class kind="struct">TwoDfold_vars</class>
 494     <class kind="struct">TwoDpfold_solution</class>
 495     <class kind="struct">TwoDpfold_vars</class>
 496     <member kind="define">
 497       <type>#define</type>
 498       <name>MAXALPHA</name>
 499       <anchorfile>data__structures_8h.html</anchorfile>
 500       <anchor>a05a5ffe718aa431d97419a12fb082379</anchor>
 501       <arglist></arglist>
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 515     <class kind="struct">Postorder_list</class>
 516     <class kind="struct">Tree</class>
 517     <class kind="struct">swString</class>
 518     <member kind="variable">
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 520       <name>edit_backtrack</name>
 521       <anchorfile>dist__vars_8h.html</anchorfile>
 522       <anchor>aa03194c513af6b860e7b33e370b82bdb</anchor>
 523       <arglist></arglist>
 524     </member>
 525     <member kind="variable">
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 528       <anchorfile>dist__vars_8h.html</anchorfile>
 529       <anchor>ac1605fe3448ad0a0b809c4fb8f6a854a</anchor>
 530       <arglist>[4]</arglist>
 531     </member>
 532     <member kind="variable">
 533       <type>int</type>
 534       <name>cost_matrix</name>
 535       <anchorfile>dist__vars_8h.html</anchorfile>
 536       <anchor>ab65d8ff14c6937612212526a60f59b3c</anchor>
 537       <arglist></arglist>
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 543     <filename>duplex_8h</filename>
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 546     <name>edit_cost.h</name>
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 548     <filename>edit__cost_8h</filename>
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 553     <filename>energy__const_8h</filename>
 554     <member kind="define">
 555       <type>#define</type>
 556       <name>GASCONST</name>
 557       <anchorfile>energy__const_8h.html</anchorfile>
 558       <anchor>ab1e4a8d82f24ed5db01dde5f25269cf1</anchor>
 559       <arglist></arglist>
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 561     <member kind="define">
 562       <type>#define</type>
 563       <name>K0</name>
 564       <anchorfile>energy__const_8h.html</anchorfile>
 565       <anchor>a307c72605e3713972b4f4fb2d53ea20e</anchor>
 566       <arglist></arglist>
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 568     <member kind="define">
 569       <type>#define</type>
 570       <name>INF</name>
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 572       <anchor>a12c2040f25d8e3a7b9e1c2024c618cb6</anchor>
 573       <arglist></arglist>
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 575     <member kind="define">
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 580       <arglist></arglist>
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 582     <member kind="define">
 583       <type>#define</type>
 584       <name>BONUS</name>
 585       <anchorfile>energy__const_8h.html</anchorfile>
 586       <anchor>a96a9822fa134450197dd454b1478a193</anchor>
 587       <arglist></arglist>
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 589     <member kind="define">
 590       <type>#define</type>
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 593       <anchor>a5e75221c779d618eab81e096f37e32ce</anchor>
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 596     <member kind="define">
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 616       <type>int</type>
 617       <name>find_saddle</name>
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 623       <type>path_t *</type>
 624       <name>get_path</name>
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 733       <type>float</type>
 734       <name>energy_of_move</name>
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 779       <arglist>(int length)</arglist>
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 782       <type>float</type>
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 786       <arglist>(const char *string, const char *structure)</arglist>
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 802     <member kind="variable">
 803       <type>int</type>
 804       <name>logML</name>
 805       <anchorfile>fold_8h.html</anchorfile>
 806       <anchor>a80c3c5fd35e7479704cc91d2d0367743</anchor>
 807       <arglist></arglist>
 808     </member>
 809     <member kind="variable">
 810       <type>int</type>
 811       <name>uniq_ML</name>
 812       <anchorfile>fold_8h.html</anchorfile>
 813       <anchor>a6c5655c8b272e3e6cab74dd0f540294f</anchor>
 814       <arglist></arglist>
 815     </member>
 816     <member kind="variable">
 817       <type>int</type>
 818       <name>cut_point</name>
 819       <anchorfile>fold_8h.html</anchorfile>
 820       <anchor>ab9b2c3a37a5516614c06d0ab54b97cda</anchor>
 821       <arglist></arglist>
 822     </member>
 823     <member kind="variable">
 824       <type>int</type>
 825       <name>eos_debug</name>
 826       <anchorfile>group__eval.html</anchorfile>
 827       <anchor>ga567530678f6260a1a649a5beca5da4c5</anchor>
 828       <arglist></arglist>
 829     </member>
 830   </compound>
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 833     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
 834     <filename>fold__vars_8h</filename>
 835     <member kind="function">
 836       <type>void</type>
 837       <name>set_model_details</name>
 838       <anchorfile>fold__vars_8h.html</anchorfile>
 839       <anchor>a4c3257186a796182462f18a5480ac8b3</anchor>
 840       <arglist>(model_detailsT *md)</arglist>
 841     </member>
 842     <member kind="variable">
 843       <type>int</type>
 844       <name>fold_constrained</name>
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 846       <anchor>a0afc287c2464866d94858c39175154af</anchor>
 847       <arglist></arglist>
 848     </member>
 849     <member kind="variable">
 850       <type>int</type>
 851       <name>noLonelyPairs</name>
 852       <anchorfile>fold__vars_8h.html</anchorfile>
 853       <anchor>a097eccaabd6ae8b4fef83cccff85bb5d</anchor>
 854       <arglist></arglist>
 855     </member>
 856     <member kind="variable">
 857       <type>int</type>
 858       <name>dangles</name>
 859       <anchorfile>fold__vars_8h.html</anchorfile>
 860       <anchor>a72b511ed1201f7e23ec437e468790d74</anchor>
 861       <arglist></arglist>
 862     </member>
 863     <member kind="variable">
 864       <type>int</type>
 865       <name>noGU</name>
 866       <anchorfile>fold__vars_8h.html</anchorfile>
 867       <anchor>abf380d09e4f1ab94fc6af57cf0ad5d32</anchor>
 868       <arglist></arglist>
 869     </member>
 870     <member kind="variable">
 871       <type>int</type>
 872       <name>no_closingGU</name>
 873       <anchorfile>fold__vars_8h.html</anchorfile>
 874       <anchor>aa8d1c7b92489179e1eafa562b7bdd259</anchor>
 875       <arglist></arglist>
 876     </member>
 877     <member kind="variable">
 878       <type>int</type>
 879       <name>tetra_loop</name>
 880       <anchorfile>fold__vars_8h.html</anchorfile>
 881       <anchor>a4f6265bdf0ead7ff4628a360adbfd77e</anchor>
 882       <arglist></arglist>
 883     </member>
 884     <member kind="variable">
 885       <type>int</type>
 886       <name>energy_set</name>
 887       <anchorfile>fold__vars_8h.html</anchorfile>
 888       <anchor>afb1ef1166da85092ae8a325e02dcae71</anchor>
 889       <arglist></arglist>
 890     </member>
 891     <member kind="variable">
 892       <type>int</type>
 893       <name>circ</name>
 894       <anchorfile>fold__vars_8h.html</anchorfile>
 895       <anchor>af9202a1a09f5828dc731e2d9a10fa111</anchor>
 896       <arglist></arglist>
 897     </member>
 898     <member kind="variable">
 899       <type>int</type>
 900       <name>csv</name>
 901       <anchorfile>fold__vars_8h.html</anchorfile>
 902       <anchor>af2763d55a74663a5e60652b8880baa5b</anchor>
 903       <arglist></arglist>
 904     </member>
 905     <member kind="variable">
 906       <type>int</type>
 907       <name>oldAliEn</name>
 908       <anchorfile>fold__vars_8h.html</anchorfile>
 909       <anchor>ac408868ba00671cbc7d1d535105af045</anchor>
 910       <arglist></arglist>
 911     </member>
 912     <member kind="variable">
 913       <type>int</type>
 914       <name>ribo</name>
 915       <anchorfile>fold__vars_8h.html</anchorfile>
 916       <anchor>a0656afca1d2853f9ee6591172f5638de</anchor>
 917       <arglist></arglist>
 918     </member>
 919     <member kind="variable">
 920       <type>char *</type>
 921       <name>RibosumFile</name>
 922       <anchorfile>fold__vars_8h.html</anchorfile>
 923       <anchor>a5dbaa0cca2c8c82048a0f0e38e164944</anchor>
 924       <arglist></arglist>
 925     </member>
 926     <member kind="variable">
 927       <type>char *</type>
 928       <name>nonstandards</name>
 929       <anchorfile>fold__vars_8h.html</anchorfile>
 930       <anchor>a2695d91cc535d09c2eae5c3884e2ec64</anchor>
 931       <arglist></arglist>
 932     </member>
 933     <member kind="variable">
 934       <type>double</type>
 935       <name>temperature</name>
 936       <anchorfile>fold__vars_8h.html</anchorfile>
 937       <anchor>ab4b11c8d9c758430960896bc3fe82ead</anchor>
 938       <arglist></arglist>
 939     </member>
 940     <member kind="variable">
 941       <type>int</type>
 942       <name>james_rule</name>
 943       <anchorfile>fold__vars_8h.html</anchorfile>
 944       <anchor>af349001ad3b4d008d0051d935b1b6261</anchor>
 945       <arglist></arglist>
 946     </member>
 947     <member kind="variable">
 948       <type>int</type>
 949       <name>logML</name>
 950       <anchorfile>fold__vars_8h.html</anchorfile>
 951       <anchor>a80c3c5fd35e7479704cc91d2d0367743</anchor>
 952       <arglist></arglist>
 953     </member>
 954     <member kind="variable">
 955       <type>int</type>
 956       <name>cut_point</name>
 957       <anchorfile>fold__vars_8h.html</anchorfile>
 958       <anchor>ab9b2c3a37a5516614c06d0ab54b97cda</anchor>
 959       <arglist></arglist>
 960     </member>
 961     <member kind="variable">
 962       <type>bondT *</type>
 963       <name>base_pair</name>
 964       <anchorfile>fold__vars_8h.html</anchorfile>
 965       <anchor>a0244a629b5ab4f58b77590c3dfd130dc</anchor>
 966       <arglist></arglist>
 967     </member>
 968     <member kind="variable">
 969       <type>double *</type>
 970       <name>pr</name>
 971       <anchorfile>fold__vars_8h.html</anchorfile>
 972       <anchor>a0f5757427fd5f2f79d6fca0081cd5a52</anchor>
 973       <arglist></arglist>
 974     </member>
 975     <member kind="variable">
 976       <type>int *</type>
 977       <name>iindx</name>
 978       <anchorfile>fold__vars_8h.html</anchorfile>
 979       <anchor>a92089ae3a51b5d75a14ce9cc29cc8317</anchor>
 980       <arglist></arglist>
 981     </member>
 982     <member kind="variable">
 983       <type>double</type>
 984       <name>pf_scale</name>
 985       <anchorfile>fold__vars_8h.html</anchorfile>
 986       <anchor>ad3b22044065acc6dee0af68931b52cfd</anchor>
 987       <arglist></arglist>
 988     </member>
 989     <member kind="variable">
 990       <type>int</type>
 991       <name>do_backtrack</name>
 992       <anchorfile>fold__vars_8h.html</anchorfile>
 993       <anchor>ad512b5dd4dbec60faccfe137bb474489</anchor>
 994       <arglist></arglist>
 995     </member>
 996     <member kind="variable">
 997       <type>char</type>
 998       <name>backtrack_type</name>
 999       <anchorfile>fold__vars_8h.html</anchorfile>
1000       <anchor>a83bdb43472a259c71e69fa9f70f420c3</anchor>
1001       <arglist></arglist>
1002     </member>
1003     <member kind="variable">
1004       <type>int</type>
1005       <name>gquad</name>
1006       <anchorfile>fold__vars_8h.html</anchorfile>
1007       <anchor>a25f2bdcdf56e813d288845484a13d704</anchor>
1008       <arglist></arglist>
1009     </member>
1010   </compound>
1011   <compound kind="file">
1012     <name>gquad.h</name>
1013     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1014     <filename>gquad_8h</filename>
1015     <member kind="function">
1016       <type>int *</type>
1017       <name>get_gquad_matrix</name>
1018       <anchorfile>gquad_8h.html</anchorfile>
1019       <anchor>a8b0784c14fa1208d0aebbebdc1318b7a</anchor>
1020       <arglist>(short *S, paramT *P)</arglist>
1021     </member>
1022     <member kind="function">
1023       <type>int</type>
1024       <name>parse_gquad</name>
1025       <anchorfile>gquad_8h.html</anchorfile>
1026       <anchor>ae41763215b9c64d2a7b67f0df8a28078</anchor>
1027       <arglist>(const char *struc, int *L, int l[3])</arglist>
1028     </member>
1029     <member kind="function">
1030       <type>PRIVATE int</type>
1031       <name>backtrack_GQuad_IntLoop</name>
1032       <anchorfile>gquad_8h.html</anchorfile>
1033       <anchor>a54475a8eb898fa1e8af8ab5f5375f3be</anchor>
1034       <arglist>(int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, paramT *P)</arglist>
1035     </member>
1036     <member kind="function">
1037       <type>PRIVATE int</type>
1038       <name>backtrack_GQuad_IntLoop_L</name>
1039       <anchorfile>gquad_8h.html</anchorfile>
1040       <anchor>a118ec7289f1936bd810be7fe50b98212</anchor>
1041       <arglist>(int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, paramT *P)</arglist>
1042     </member>
1043   </compound>
1044   <compound kind="file">
1045     <name>inverse.h</name>
1046     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1047     <filename>inverse_8h</filename>
1048     <member kind="function">
1049       <type>float</type>
1050       <name>inverse_fold</name>
1051       <anchorfile>group__inverse__fold.html</anchorfile>
1052       <anchor>ga7af026de55d4babad879f2c92559cbbc</anchor>
1053       <arglist>(char *start, const char *target)</arglist>
1054     </member>
1055     <member kind="function">
1056       <type>float</type>
1057       <name>inverse_pf_fold</name>
1058       <anchorfile>group__inverse__fold.html</anchorfile>
1059       <anchor>gaeef52ecbf2a2450ad585a344f9826806</anchor>
1060       <arglist>(char *start, const char *target)</arglist>
1061     </member>
1062     <member kind="variable">
1063       <type>char *</type>
1064       <name>symbolset</name>
1065       <anchorfile>group__inverse__fold.html</anchorfile>
1066       <anchor>ga8f791e7740a5a28b9f6fafb4e60301d9</anchor>
1067       <arglist></arglist>
1068     </member>
1069     <member kind="variable">
1070       <type>float</type>
1071       <name>final_cost</name>
1072       <anchorfile>group__inverse__fold.html</anchorfile>
1073       <anchor>ga7f17d3b169af048d32bb185039a9c09c</anchor>
1074       <arglist></arglist>
1075     </member>
1076     <member kind="variable">
1077       <type>int</type>
1078       <name>give_up</name>
1079       <anchorfile>group__inverse__fold.html</anchorfile>
1080       <anchor>ga7ec4ba51f86e1717a1e174264e4a75ce</anchor>
1081       <arglist></arglist>
1082     </member>
1083     <member kind="variable">
1084       <type>int</type>
1085       <name>inv_verbose</name>
1086       <anchorfile>group__inverse__fold.html</anchorfile>
1087       <anchor>gafcfc65fba01b9cca5946726ed9057a63</anchor>
1088       <arglist></arglist>
1089     </member>
1090   </compound>
1091   <compound kind="file">
1092     <name>Lfold.h</name>
1093     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1094     <filename>Lfold_8h</filename>
1095     <member kind="function">
1096       <type>float</type>
1097       <name>Lfold</name>
1098       <anchorfile>group__local__mfe__fold.html</anchorfile>
1099       <anchor>ga16e5a70e60835bb969eaecbe6482f1be</anchor>
1100       <arglist>(const char *string, char *structure, int maxdist)</arglist>
1101     </member>
1102     <member kind="function">
1103       <type>float</type>
1104       <name>Lfoldz</name>
1105       <anchorfile>group__local__mfe__fold.html</anchorfile>
1106       <anchor>gab6d79eecc180f586679f7b85cce5cbe9</anchor>
1107       <arglist>(const char *string, char *structure, int maxdist, int zsc, double min_z)</arglist>
1108     </member>
1109     <member kind="function">
1110       <type>float</type>
1111       <name>aliLfold</name>
1112       <anchorfile>group__local__consensus__fold.html</anchorfile>
1113       <anchor>ga20a173a3cdb83f5d1778e36c1a6b1f2b</anchor>
1114       <arglist>(const char **strings, char *structure, int maxdist)</arglist>
1115     </member>
1116   </compound>
1117   <compound kind="file">
1118     <name>loop_energies.h</name>
1119     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1120     <filename>loop__energies_8h</filename>
1121     <member kind="function">
1122       <type>PRIVATE int</type>
1123       <name>E_IntLoop</name>
1124       <anchorfile>loop__energies_8h.html</anchorfile>
1125       <anchor>a3e5ad89f451254b1fe366d77aa8ff7bd</anchor>
1126       <arglist>(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, paramT *P)</arglist>
1127     </member>
1128     <member kind="function">
1129       <type>PRIVATE int</type>
1130       <name>E_Hairpin</name>
1131       <anchorfile>loop__energies_8h.html</anchorfile>
1132       <anchor>aa362183cf6db89a10cdb0f5c4bd180c6</anchor>
1133       <arglist>(int size, int type, int si1, int sj1, const char *string, paramT *P)</arglist>
1134     </member>
1135     <member kind="function">
1136       <type>PRIVATE int</type>
1137       <name>E_Stem</name>
1138       <anchorfile>loop__energies_8h.html</anchorfile>
1139       <anchor>af5a6594eba9b2622cb47076650c69819</anchor>
1140       <arglist>(int type, int si1, int sj1, int extLoop, paramT *P)</arglist>
1141     </member>
1142     <member kind="function">
1143       <type>PRIVATE double</type>
1144       <name>exp_E_Stem</name>
1145       <anchorfile>loop__energies_8h.html</anchorfile>
1146       <anchor>a76cc24ec96199e04beddad13e7891e21</anchor>
1147       <arglist>(int type, int si1, int sj1, int extLoop, pf_paramT *P)</arglist>
1148     </member>
1149     <member kind="function">
1150       <type>PRIVATE double</type>
1151       <name>exp_E_Hairpin</name>
1152       <anchorfile>loop__energies_8h.html</anchorfile>
1153       <anchor>a0e128184bb097dc2da33706f33b555a6</anchor>
1154       <arglist>(int u, int type, short si1, short sj1, const char *string, pf_paramT *P)</arglist>
1155     </member>
1156     <member kind="function">
1157       <type>PRIVATE double</type>
1158       <name>exp_E_IntLoop</name>
1159       <anchorfile>loop__energies_8h.html</anchorfile>
1160       <anchor>aa5e98e524e2a41e290b942b09544bc9e</anchor>
1161       <arglist>(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, pf_paramT *P)</arglist>
1162     </member>
1163   </compound>
1164   <compound kind="file">
1165     <name>LPfold.h</name>
1166     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1167     <filename>LPfold_8h</filename>
1168     <member kind="function">
1169       <type>void</type>
1170       <name>update_pf_paramsLP</name>
1171       <anchorfile>group__local__pf__fold.html</anchorfile>
1172       <anchor>ga5a019014d37fe6105131dfc2fc447880</anchor>
1173       <arglist>(int length)</arglist>
1174     </member>
1175     <member kind="function">
1176       <type>plist *</type>
1177       <name>pfl_fold</name>
1178       <anchorfile>group__local__pf__fold.html</anchorfile>
1179       <anchor>gaa1ecd401617ebc748a0220026543c777</anchor>
1180       <arglist>(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup)</arglist>
1181     </member>
1182     <member kind="function">
1183       <type>plist *</type>
1184       <name>pfl_fold_par</name>
1185       <anchorfile>group__local__pf__fold.html</anchorfile>
1186       <anchor>gab354507e8028f3e1c52ef96bb1eb9df8</anchor>
1187       <arglist>(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters)</arglist>
1188     </member>
1189     <member kind="function">
1190       <type>void</type>
1191       <name>putoutpU_prob</name>
1192       <anchorfile>group__local__pf__fold.html</anchorfile>
1193       <anchor>ga0bcb751860bbf34e3dfee8c2fbdb3ef3</anchor>
1194       <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
1195     </member>
1196     <member kind="function">
1197       <type>void</type>
1198       <name>putoutpU_prob_bin</name>
1199       <anchorfile>group__local__pf__fold.html</anchorfile>
1200       <anchor>ga9acb00ee10e96b1ca4ea394cd8bcec75</anchor>
1201       <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
1202     </member>
1203     <member kind="function">
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1205       <name>init_pf_foldLP</name>
1206       <anchorfile>LPfold_8h.html</anchorfile>
1207       <anchor>ae85bf55053e9fb295208be322e0fa07a</anchor>
1208       <arglist>(int length)</arglist>
1209     </member>
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1212     <name>MEA.h</name>
1213     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1214     <filename>MEA_8h</filename>
1215     <member kind="function">
1216       <type>float</type>
1217       <name>MEA</name>
1218       <anchorfile>MEA_8h.html</anchorfile>
1219       <anchor>a396ec6144c6a74fcbab4cea6b42d76c3</anchor>
1220       <arglist>(plist *p, char *structure, double gamma)</arglist>
1221     </member>
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1224     <name>mm.h</name>
1225     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1226     <filename>mm_8h</filename>
1227   </compound>
1228   <compound kind="file">
1229     <name>naview.h</name>
1230     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1231     <filename>naview_8h</filename>
1232   </compound>
1233   <compound kind="file">
1234     <name>params.h</name>
1235     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1236     <filename>params_8h</filename>
1237     <member kind="function">
1238       <type>paramT *</type>
1239       <name>scale_parameters</name>
1240       <anchorfile>group__energy__parameters.html</anchorfile>
1241       <anchor>ga527ef619cd8210b84d5d53be1e0e29b6</anchor>
1242       <arglist>(void)</arglist>
1243     </member>
1244     <member kind="function">
1245       <type>paramT *</type>
1246       <name>get_scaled_parameters</name>
1247       <anchorfile>group__energy__parameters.html</anchorfile>
1248       <anchor>gac2f3ca440b7eaf4d999fb27da949fe72</anchor>
1249       <arglist>(double temperature, model_detailsT md)</arglist>
1250     </member>
1251     <member kind="function">
1252       <type>pf_paramT *</type>
1253       <name>get_scaled_pf_parameters</name>
1254       <anchorfile>group__energy__parameters.html</anchorfile>
1255       <anchor>gab85f6b6da051f380371deb0d8921bdba</anchor>
1256       <arglist>(void)</arglist>
1257     </member>
1258     <member kind="function">
1259       <type>pf_paramT *</type>
1260       <name>get_boltzmann_factors</name>
1261       <anchorfile>group__energy__parameters.html</anchorfile>
1262       <anchor>ga6fc2f3eef5a3024d44963ac59a42e39d</anchor>
1263       <arglist>(double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
1264     </member>
1265     <member kind="function">
1266       <type>pf_paramT *</type>
1267       <name>get_boltzmann_factor_copy</name>
1268       <anchorfile>group__energy__parameters.html</anchorfile>
1269       <anchor>gacba212326a051734797e65987260fdd0</anchor>
1270       <arglist>(pf_paramT *parameters)</arglist>
1271     </member>
1272     <member kind="function">
1273       <type>pf_paramT *</type>
1274       <name>get_scaled_alipf_parameters</name>
1275       <anchorfile>group__energy__parameters.html</anchorfile>
1276       <anchor>gaa6a4297a2b91d6f7ae47dd61ca1862a0</anchor>
1277       <arglist>(unsigned int n_seq)</arglist>
1278     </member>
1279     <member kind="function">
1280       <type>pf_paramT *</type>
1281       <name>get_boltzmann_factors_ali</name>
1282       <anchorfile>group__energy__parameters.html</anchorfile>
1283       <anchor>gaf0c74574b40f2778556535bf9d382828</anchor>
1284       <arglist>(unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
1285     </member>
1286   </compound>
1287   <compound kind="file">
1288     <name>part_func.h</name>
1289     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1290     <filename>part__func_8h</filename>
1291     <member kind="function">
1292       <type>float</type>
1293       <name>pf_fold_par</name>
1294       <anchorfile>group__pf__fold.html</anchorfile>
1295       <anchor>ga1839c61275760944b3a007c41d5c0823</anchor>
1296       <arglist>(const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
1297     </member>
1298     <member kind="function">
1299       <type>float</type>
1300       <name>pf_fold</name>
1301       <anchorfile>group__pf__fold.html</anchorfile>
1302       <anchor>gadc3db3d98742427e7001a7fd36ef28c2</anchor>
1303       <arglist>(const char *sequence, char *structure)</arglist>
1304     </member>
1305     <member kind="function">
1306       <type>float</type>
1307       <name>pf_circ_fold</name>
1308       <anchorfile>group__pf__fold.html</anchorfile>
1309       <anchor>ga819ce5fca8984004ac81c4a3b04cb735</anchor>
1310       <arglist>(const char *sequence, char *structure)</arglist>
1311     </member>
1312     <member kind="function">
1313       <type>char *</type>
1314       <name>pbacktrack</name>
1315       <anchorfile>group__subopt__stochbt.html</anchorfile>
1316       <anchor>gac03ca6db186bb3bf0a2a326d7fb3ba03</anchor>
1317       <arglist>(char *sequence)</arglist>
1318     </member>
1319     <member kind="function">
1320       <type>char *</type>
1321       <name>pbacktrack_circ</name>
1322       <anchorfile>group__subopt__stochbt.html</anchorfile>
1323       <anchor>ga00474051204ac9ad576b3e45174d03ff</anchor>
1324       <arglist>(char *sequence)</arglist>
1325     </member>
1326     <member kind="function">
1327       <type>void</type>
1328       <name>free_pf_arrays</name>
1329       <anchorfile>group__pf__fold.html</anchorfile>
1330       <anchor>gae73db3f49a94f0f72e067ecd12681dbd</anchor>
1331       <arglist>(void)</arglist>
1332     </member>
1333     <member kind="function">
1334       <type>void</type>
1335       <name>update_pf_params</name>
1336       <anchorfile>group__pf__fold.html</anchorfile>
1337       <anchor>ga384e927890f9c034ff09fa66da102d28</anchor>
1338       <arglist>(int length)</arglist>
1339     </member>
1340     <member kind="function">
1341       <type>void</type>
1342       <name>update_pf_params_par</name>
1343       <anchorfile>group__pf__fold.html</anchorfile>
1344       <anchor>ga0733527a94de3b79eee3c3c03c99c1bc</anchor>
1345       <arglist>(int length, pf_paramT *parameters)</arglist>
1346     </member>
1347     <member kind="function">
1348       <type>double *</type>
1349       <name>export_bppm</name>
1350       <anchorfile>group__pf__fold.html</anchorfile>
1351       <anchor>ga6d463707d5f64bdc4d21515b7dd9b115</anchor>
1352       <arglist>(void)</arglist>
1353     </member>
1354     <member kind="function">
1355       <type>void</type>
1356       <name>assign_plist_from_pr</name>
1357       <anchorfile>group__pf__fold.html</anchorfile>
1358       <anchor>ga03e15e831a31b1154855ab47edbdb019</anchor>
1359       <arglist>(plist **pl, double *probs, int length, double cutoff)</arglist>
1360     </member>
1361     <member kind="function">
1362       <type>int</type>
1363       <name>get_pf_arrays</name>
1364       <anchorfile>group__pf__fold.html</anchorfile>
1365       <anchor>ga18607e79e106cad827f482eedd2f632e</anchor>
1366       <arglist>(short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)</arglist>
1367     </member>
1368     <member kind="function">
1369       <type>double</type>
1370       <name>get_subseq_F</name>
1371       <anchorfile>part__func_8h.html</anchorfile>
1372       <anchor>a189e2a1ec6cc32c53ea72f7543b0441e</anchor>
1373       <arglist>(int i, int j)</arglist>
1374     </member>
1375     <member kind="function">
1376       <type>char *</type>
1377       <name>get_centroid_struct_pl</name>
1378       <anchorfile>group__centroid__fold.html</anchorfile>
1379       <anchor>ga9aba0ba1433a6d259331e0fe9fc4a9a6</anchor>
1380       <arglist>(int length, double *dist, plist *pl)</arglist>
1381     </member>
1382     <member kind="function">
1383       <type>char *</type>
1384       <name>get_centroid_struct_pr</name>
1385       <anchorfile>group__centroid__fold.html</anchorfile>
1386       <anchor>gacdabece4aa1e20c9eaa97acb4c4dcc38</anchor>
1387       <arglist>(int length, double *dist, double *pr)</arglist>
1388     </member>
1389     <member kind="function">
1390       <type>double</type>
1391       <name>mean_bp_distance</name>
1392       <anchorfile>group__pf__fold.html</anchorfile>
1393       <anchor>ga79cbc375af65f11609feb6b055269e7d</anchor>
1394       <arglist>(int length)</arglist>
1395     </member>
1396     <member kind="function">
1397       <type>double</type>
1398       <name>mean_bp_distance_pr</name>
1399       <anchorfile>group__pf__fold.html</anchorfile>
1400       <anchor>ga72d84525f0afd3a9d60d830a2f501fa5</anchor>
1401       <arglist>(int length, double *pr)</arglist>
1402     </member>
1403     <member kind="function">
1404       <type>void</type>
1405       <name>bppm_to_structure</name>
1406       <anchorfile>part__func_8h.html</anchorfile>
1407       <anchor>a1f562d463c14d4703d9656056200eb38</anchor>
1408       <arglist>(char *structure, double *pr, unsigned int length)</arglist>
1409     </member>
1410     <member kind="function">
1411       <type>char</type>
1412       <name>bppm_symbol</name>
1413       <anchorfile>part__func_8h.html</anchorfile>
1414       <anchor>a49962ad6242b8c628de6ca16bb831c1d</anchor>
1415       <arglist>(const float *x)</arglist>
1416     </member>
1417     <member kind="function">
1418       <type>void</type>
1419       <name>init_pf_fold</name>
1420       <anchorfile>part__func_8h.html</anchorfile>
1421       <anchor>a15176e23eceeff8c7d14eabcfec8a2af</anchor>
1422       <arglist>(int length)</arglist>
1423     </member>
1424     <member kind="function">
1425       <type>char *</type>
1426       <name>centroid</name>
1427       <anchorfile>part__func_8h.html</anchorfile>
1428       <anchor>ae89a63bd83e75a80b2ba36d20b31ce81</anchor>
1429       <arglist>(int length, double *dist)</arglist>
1430     </member>
1431     <member kind="function">
1432       <type>double</type>
1433       <name>mean_bp_dist</name>
1434       <anchorfile>part__func_8h.html</anchorfile>
1435       <anchor>ae9556ba7ded44fe2321b6f67c3fc02a3</anchor>
1436       <arglist>(int length)</arglist>
1437     </member>
1438     <member kind="function">
1439       <type>double</type>
1440       <name>expLoopEnergy</name>
1441       <anchorfile>part__func_8h.html</anchorfile>
1442       <anchor>a68ba6f3a48e08ca131ab54621ce3a2d7</anchor>
1443       <arglist>(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</arglist>
1444     </member>
1445     <member kind="function">
1446       <type>double</type>
1447       <name>expHairpinEnergy</name>
1448       <anchorfile>part__func_8h.html</anchorfile>
1449       <anchor>a7b6ab474cc80accc48010ccfcc59f96b</anchor>
1450       <arglist>(int u, int type, short si1, short sj1, const char *string)</arglist>
1451     </member>
1452     <member kind="variable">
1453       <type>int</type>
1454       <name>st_back</name>
1455       <anchorfile>group__subopt__stochbt.html</anchorfile>
1456       <anchor>gacd79b1a570e6ad9be24cb11fe8cae30a</anchor>
1457       <arglist></arglist>
1458     </member>
1459   </compound>
1460   <compound kind="file">
1461     <name>part_func_co.h</name>
1462     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1463     <filename>part__func__co_8h</filename>
1464     <member kind="function">
1465       <type>cofoldF</type>
1466       <name>co_pf_fold</name>
1467       <anchorfile>group__pf__cofold.html</anchorfile>
1468       <anchor>gaa86a5f998789ed71813d23d7307a791b</anchor>
1469       <arglist>(char *sequence, char *structure)</arglist>
1470     </member>
1471     <member kind="function">
1472       <type>cofoldF</type>
1473       <name>co_pf_fold_par</name>
1474       <anchorfile>group__pf__cofold.html</anchorfile>
1475       <anchor>gabd873b450832ab5f21101fc5ab354d21</anchor>
1476       <arglist>(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)</arglist>
1477     </member>
1478     <member kind="function">
1479       <type>double *</type>
1480       <name>export_co_bppm</name>
1481       <anchorfile>group__pf__cofold.html</anchorfile>
1482       <anchor>ga11f0252c1d2c4697253ff4b5bd392d3c</anchor>
1483       <arglist>(void)</arglist>
1484     </member>
1485     <member kind="function">
1486       <type>void</type>
1487       <name>free_co_pf_arrays</name>
1488       <anchorfile>group__pf__cofold.html</anchorfile>
1489       <anchor>gade3ce34ae8214811374b1d28a40dc247</anchor>
1490       <arglist>(void)</arglist>
1491     </member>
1492     <member kind="function">
1493       <type>void</type>
1494       <name>update_co_pf_params</name>
1495       <anchorfile>group__pf__cofold.html</anchorfile>
1496       <anchor>ga6e0f36c1f9b7d9dd4bfbad914c1119e5</anchor>
1497       <arglist>(int length)</arglist>
1498     </member>
1499     <member kind="function">
1500       <type>void</type>
1501       <name>update_co_pf_params_par</name>
1502       <anchorfile>group__pf__cofold.html</anchorfile>
1503       <anchor>ga117d880df45bef444d5e2785ffa40a53</anchor>
1504       <arglist>(int length, pf_paramT *parameters)</arglist>
1505     </member>
1506     <member kind="function">
1507       <type>void</type>
1508       <name>compute_probabilities</name>
1509       <anchorfile>group__pf__cofold.html</anchorfile>
1510       <anchor>ga15ae04ac5ab84e876dcf0093120cb617</anchor>
1511       <arglist>(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)</arglist>
1512     </member>
1513     <member kind="function">
1514       <type>ConcEnt *</type>
1515       <name>get_concentrations</name>
1516       <anchorfile>group__pf__cofold.html</anchorfile>
1517       <anchor>ga5545cb936ac4ff93c7d699d46e72e8c7</anchor>
1518       <arglist>(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)</arglist>
1519     </member>
1520     <member kind="function">
1521       <type>plist *</type>
1522       <name>get_plist</name>
1523       <anchorfile>part__func__co_8h.html</anchorfile>
1524       <anchor>a334de3c96e2186abfbdc0eaea6d08b14</anchor>
1525       <arglist>(struct plist *pl, int length, double cut_off)</arglist>
1526     </member>
1527     <member kind="function">
1528       <type>void</type>
1529       <name>init_co_pf_fold</name>
1530       <anchorfile>part__func__co_8h.html</anchorfile>
1531       <anchor>aa12dda9dd6179cdd22bcce87c0682c07</anchor>
1532       <arglist>(int length)</arglist>
1533     </member>
1534     <member kind="variable">
1535       <type>int</type>
1536       <name>mirnatog</name>
1537       <anchorfile>group__pf__cofold.html</anchorfile>
1538       <anchor>gaff27888c4088cc1f60fd59cbd589474c</anchor>
1539       <arglist></arglist>
1540     </member>
1541     <member kind="variable">
1542       <type>double</type>
1543       <name>F_monomer</name>
1544       <anchorfile>group__pf__cofold.html</anchorfile>
1545       <anchor>gac2d1851a710a8561390861155ca988fe</anchor>
1546       <arglist>[2]</arglist>
1547     </member>
1548   </compound>
1549   <compound kind="file">
1550     <name>part_func_up.h</name>
1551     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1552     <filename>part__func__up_8h</filename>
1553     <member kind="function">
1554       <type>pu_contrib *</type>
1555       <name>pf_unstru</name>
1556       <anchorfile>group__up__cofold.html</anchorfile>
1557       <anchor>ga5b4ee40e190d2f633cd01cf0d2fe93cf</anchor>
1558       <arglist>(char *sequence, int max_w)</arglist>
1559     </member>
1560     <member kind="function">
1561       <type>interact *</type>
1562       <name>pf_interact</name>
1563       <anchorfile>group__up__cofold.html</anchorfile>
1564       <anchor>ga1aa0aa02bc3a724f87360c03097afd00</anchor>
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1566     </member>
1567     <member kind="function">
1568       <type>void</type>
1569       <name>free_interact</name>
1570       <anchorfile>group__up__cofold.html</anchorfile>
1571       <anchor>gadde308fd5f696dc271b1532aa96fd12f</anchor>
1572       <arglist>(interact *pin)</arglist>
1573     </member>
1574     <member kind="function">
1575       <type>void</type>
1576       <name>free_pu_contrib_struct</name>
1577       <anchorfile>group__up__cofold.html</anchorfile>
1578       <anchor>gac20bd61824981d45ce0dc9934aa56df8</anchor>
1579       <arglist>(pu_contrib *pu)</arglist>
1580     </member>
1581   </compound>
1582   <compound kind="file">
1583     <name>plot_layouts.h</name>
1584     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1585     <filename>plot__layouts_8h</filename>
1586     <member kind="define">
1587       <type>#define</type>
1588       <name>VRNA_PLOT_TYPE_SIMPLE</name>
1589       <anchorfile>plot__layouts_8h.html</anchorfile>
1590       <anchor>ae6d17b9f0a53cf5205a9181e0f8422e9</anchor>
1591       <arglist></arglist>
1592     </member>
1593     <member kind="define">
1594       <type>#define</type>
1595       <name>VRNA_PLOT_TYPE_NAVIEW</name>
1596       <anchorfile>plot__layouts_8h.html</anchorfile>
1597       <anchor>a94d4c863ecac2f220f76658afb92f964</anchor>
1598       <arglist></arglist>
1599     </member>
1600     <member kind="define">
1601       <type>#define</type>
1602       <name>VRNA_PLOT_TYPE_CIRCULAR</name>
1603       <anchorfile>plot__layouts_8h.html</anchorfile>
1604       <anchor>a8c9eac631348da92136c8363ecdd9fb9</anchor>
1605       <arglist></arglist>
1606     </member>
1607     <member kind="function">
1608       <type>int</type>
1609       <name>simple_xy_coordinates</name>
1610       <anchorfile>plot__layouts_8h.html</anchorfile>
1611       <anchor>af4b9173e7d3fd361c3c85e6def194123</anchor>
1612       <arglist>(short *pair_table, float *X, float *Y)</arglist>
1613     </member>
1614     <member kind="function">
1615       <type>int</type>
1616       <name>simple_circplot_coordinates</name>
1617       <anchorfile>plot__layouts_8h.html</anchorfile>
1618       <anchor>ac4ea13d35308f09940178d2b05a248c2</anchor>
1619       <arglist>(short *pair_table, float *x, float *y)</arglist>
1620     </member>
1621     <member kind="variable">
1622       <type>int</type>
1623       <name>rna_plot_type</name>
1624       <anchorfile>plot__layouts_8h.html</anchorfile>
1625       <anchor>a5964c4581431b098b80027d6e14dcdd4</anchor>
1626       <arglist></arglist>
1627     </member>
1628   </compound>
1629   <compound kind="file">
1630     <name>profiledist.h</name>
1631     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1632     <filename>profiledist_8h</filename>
1633     <member kind="function">
1634       <type>float</type>
1635       <name>profile_edit_distance</name>
1636       <anchorfile>profiledist_8h.html</anchorfile>
1637       <anchor>abe75e90e00a1e5dd8862944ed53dad5d</anchor>
1638       <arglist>(const float *T1, const float *T2)</arglist>
1639     </member>
1640     <member kind="function">
1641       <type>float *</type>
1642       <name>Make_bp_profile_bppm</name>
1643       <anchorfile>profiledist_8h.html</anchorfile>
1644       <anchor>a8822fd5268be115c6e6cdc92009436cc</anchor>
1645       <arglist>(double *bppm, int length)</arglist>
1646     </member>
1647     <member kind="function">
1648       <type>void</type>
1649       <name>print_bppm</name>
1650       <anchorfile>profiledist_8h.html</anchorfile>
1651       <anchor>a8e0b4fe3698b3502945116ecc0ba6160</anchor>
1652       <arglist>(const float *T)</arglist>
1653     </member>
1654     <member kind="function">
1655       <type>void</type>
1656       <name>free_profile</name>
1657       <anchorfile>profiledist_8h.html</anchorfile>
1658       <anchor>a9b0b84a5a45761bf42d7c835dcdb3b85</anchor>
1659       <arglist>(float *T)</arglist>
1660     </member>
1661     <member kind="function">
1662       <type>float *</type>
1663       <name>Make_bp_profile</name>
1664       <anchorfile>profiledist_8h.html</anchorfile>
1665       <anchor>a904c7eaf4a2413567c00ac4891749d18</anchor>
1666       <arglist>(int length)</arglist>
1667     </member>
1668   </compound>
1669   <compound kind="file">
1670     <name>PS_dot.h</name>
1671     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1672     <filename>PS__dot_8h</filename>
1673     <member kind="function">
1674       <type>int</type>
1675       <name>PS_rna_plot</name>
1676       <anchorfile>PS__dot_8h.html</anchorfile>
1677       <anchor>a0873c7cc4cd7a11c9a2cea19dde7e9c9</anchor>
1678       <arglist>(char *string, char *structure, char *file)</arglist>
1679     </member>
1680     <member kind="function">
1681       <type>int</type>
1682       <name>PS_rna_plot_a</name>
1683       <anchorfile>PS__dot_8h.html</anchorfile>
1684       <anchor>a47856b2504b566588785597b6ebb8271</anchor>
1685       <arglist>(char *string, char *structure, char *file, char *pre, char *post)</arglist>
1686     </member>
1687     <member kind="function">
1688       <type>int</type>
1689       <name>gmlRNA</name>
1690       <anchorfile>PS__dot_8h.html</anchorfile>
1691       <anchor>a70834bc8c0aad4fe6824ff76ccb8f329</anchor>
1692       <arglist>(char *string, char *structure, char *ssfile, char option)</arglist>
1693     </member>
1694     <member kind="function">
1695       <type>int</type>
1696       <name>ssv_rna_plot</name>
1697       <anchorfile>PS__dot_8h.html</anchorfile>
1698       <anchor>add368528755f9a830727b680243541df</anchor>
1699       <arglist>(char *string, char *structure, char *ssfile)</arglist>
1700     </member>
1701     <member kind="function">
1702       <type>int</type>
1703       <name>svg_rna_plot</name>
1704       <anchorfile>PS__dot_8h.html</anchorfile>
1705       <anchor>ae7853539b5df98f294b4af434e979304</anchor>
1706       <arglist>(char *string, char *structure, char *ssfile)</arglist>
1707     </member>
1708     <member kind="function">
1709       <type>int</type>
1710       <name>xrna_plot</name>
1711       <anchorfile>PS__dot_8h.html</anchorfile>
1712       <anchor>a2f6d5953e6a323df898896b8d6614483</anchor>
1713       <arglist>(char *string, char *structure, char *ssfile)</arglist>
1714     </member>
1715     <member kind="function">
1716       <type>int</type>
1717       <name>PS_dot_plot_list</name>
1718       <anchorfile>PS__dot_8h.html</anchorfile>
1719       <anchor>a00ea223b5cf02eb2faae5ff29f0d5e12</anchor>
1720       <arglist>(char *seq, char *filename, plist *pl, plist *mf, char *comment)</arglist>
1721     </member>
1722     <member kind="function">
1723       <type>int</type>
1724       <name>aliPS_color_aln</name>
1725       <anchorfile>PS__dot_8h.html</anchorfile>
1726       <anchor>aab48d4dac655d688abe921389ac2847c</anchor>
1727       <arglist>(const char *structure, const char *filename, const char *seqs[], const char *names[])</arglist>
1728     </member>
1729     <member kind="function">
1730       <type>int</type>
1731       <name>PS_dot_plot</name>
1732       <anchorfile>PS__dot_8h.html</anchorfile>
1733       <anchor>a689a97a7e3b8a2df14728b8204d9d57b</anchor>
1734       <arglist>(char *string, char *file)</arglist>
1735     </member>
1736   </compound>
1737   <compound kind="file">
1738     <name>read_epars.h</name>
1739     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1740     <filename>read__epars_8h</filename>
1741     <member kind="function">
1742       <type>void</type>
1743       <name>read_parameter_file</name>
1744       <anchorfile>group__energy__parameters__rw.html</anchorfile>
1745       <anchor>ga165a142a3c68fb6655c69ef4ab7cd749</anchor>
1746       <arglist>(const char fname[])</arglist>
1747     </member>
1748     <member kind="function">
1749       <type>void</type>
1750       <name>write_parameter_file</name>
1751       <anchorfile>group__energy__parameters__rw.html</anchorfile>
1752       <anchor>ga8a43459be386a7489feeab68dc2c6c76</anchor>
1753       <arglist>(const char fname[])</arglist>
1754     </member>
1755   </compound>
1756   <compound kind="file">
1757     <name>RNAstruct.h</name>
1758     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1759     <filename>RNAstruct_8h</filename>
1760     <member kind="function">
1761       <type>char *</type>
1762       <name>b2HIT</name>
1763       <anchorfile>RNAstruct_8h.html</anchorfile>
1764       <anchor>a07b7e90e712559a1992fba3ac6d21bbd</anchor>
1765       <arglist>(const char *structure)</arglist>
1766     </member>
1767     <member kind="function">
1768       <type>char *</type>
1769       <name>b2C</name>
1770       <anchorfile>RNAstruct_8h.html</anchorfile>
1771       <anchor>a9c80d92391f2833549a8b6dac92233f0</anchor>
1772       <arglist>(const char *structure)</arglist>
1773     </member>
1774     <member kind="function">
1775       <type>char *</type>
1776       <name>b2Shapiro</name>
1777       <anchorfile>RNAstruct_8h.html</anchorfile>
1778       <anchor>a5cd2feb367feeacad0c03cb7ddba5f10</anchor>
1779       <arglist>(const char *structure)</arglist>
1780     </member>
1781     <member kind="function">
1782       <type>char *</type>
1783       <name>add_root</name>
1784       <anchorfile>RNAstruct_8h.html</anchorfile>
1785       <anchor>a880d33066dd95441e5fbb73c57ed1c3e</anchor>
1786       <arglist>(const char *structure)</arglist>
1787     </member>
1788     <member kind="function">
1789       <type>char *</type>
1790       <name>expand_Shapiro</name>
1791       <anchorfile>RNAstruct_8h.html</anchorfile>
1792       <anchor>abe3d815b420dc4553bfb23511198b4c6</anchor>
1793       <arglist>(const char *coarse)</arglist>
1794     </member>
1795     <member kind="function">
1796       <type>char *</type>
1797       <name>expand_Full</name>
1798       <anchorfile>RNAstruct_8h.html</anchorfile>
1799       <anchor>a78d73cd54a068ef2812812771cdddc6f</anchor>
1800       <arglist>(const char *structure)</arglist>
1801     </member>
1802     <member kind="function">
1803       <type>char *</type>
1804       <name>unexpand_Full</name>
1805       <anchorfile>RNAstruct_8h.html</anchorfile>
1806       <anchor>a260c4b622093b76a883bf96628280de1</anchor>
1807       <arglist>(const char *ffull)</arglist>
1808     </member>
1809     <member kind="function">
1810       <type>char *</type>
1811       <name>unweight</name>
1812       <anchorfile>RNAstruct_8h.html</anchorfile>
1813       <anchor>a09a80253ac7b6bae606871ba7c6e5136</anchor>
1814       <arglist>(const char *wcoarse)</arglist>
1815     </member>
1816     <member kind="function">
1817       <type>void</type>
1818       <name>unexpand_aligned_F</name>
1819       <anchorfile>RNAstruct_8h.html</anchorfile>
1820       <anchor>a1054c4477d53b31d79d4cb132100e87a</anchor>
1821       <arglist>(char *align[2])</arglist>
1822     </member>
1823     <member kind="function">
1824       <type>void</type>
1825       <name>parse_structure</name>
1826       <anchorfile>RNAstruct_8h.html</anchorfile>
1827       <anchor>a3c79042e6bf6f01706bf30ec9e69e8ac</anchor>
1828       <arglist>(const char *structure)</arglist>
1829     </member>
1830     <member kind="variable">
1831       <type>int</type>
1832       <name>loop_size</name>
1833       <anchorfile>RNAstruct_8h.html</anchorfile>
1834       <anchor>a3f31e0e48125601bfa57b52f8b038e8e</anchor>
1835       <arglist>[STRUC]</arglist>
1836     </member>
1837     <member kind="variable">
1838       <type>int</type>
1839       <name>helix_size</name>
1840       <anchorfile>RNAstruct_8h.html</anchorfile>
1841       <anchor>a8218c0d581a3fba2a1a56a196abe19a5</anchor>
1842       <arglist>[STRUC]</arglist>
1843     </member>
1844     <member kind="variable">
1845       <type>int</type>
1846       <name>loop_degree</name>
1847       <anchorfile>RNAstruct_8h.html</anchorfile>
1848       <anchor>aef14e2f8ab3f61e8e659ba6b9003b08a</anchor>
1849       <arglist>[STRUC]</arglist>
1850     </member>
1851     <member kind="variable">
1852       <type>int</type>
1853       <name>loops</name>
1854       <anchorfile>RNAstruct_8h.html</anchorfile>
1855       <anchor>a439fcb9f8d4f9f4d2227fde5fbfecb30</anchor>
1856       <arglist></arglist>
1857     </member>
1858     <member kind="variable">
1859       <type>int</type>
1860       <name>unpaired</name>
1861       <anchorfile>RNAstruct_8h.html</anchorfile>
1862       <anchor>add2f952597e02d66e1116a9d11d252d6</anchor>
1863       <arglist></arglist>
1864     </member>
1865     <member kind="variable">
1866       <type>int</type>
1867       <name>pairs</name>
1868       <anchorfile>RNAstruct_8h.html</anchorfile>
1869       <anchor>a6341cbb704924824e0236c1dce791032</anchor>
1870       <arglist></arglist>
1871     </member>
1872   </compound>
1873   <compound kind="file">
1874     <name>stringdist.h</name>
1875     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1876     <filename>stringdist_8h</filename>
1877     <member kind="function">
1878       <type>swString *</type>
1879       <name>Make_swString</name>
1880       <anchorfile>stringdist_8h.html</anchorfile>
1881       <anchor>a3125991b3a403b3f89230474deb3f22e</anchor>
1882       <arglist>(char *string)</arglist>
1883     </member>
1884     <member kind="function">
1885       <type>float</type>
1886       <name>string_edit_distance</name>
1887       <anchorfile>stringdist_8h.html</anchorfile>
1888       <anchor>a89e3c335ef17780576d7c0e713830db9</anchor>
1889       <arglist>(swString *T1, swString *T2)</arglist>
1890     </member>
1891   </compound>
1892   <compound kind="file">
1893     <name>subopt.h</name>
1894     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1895     <filename>subopt_8h</filename>
1896     <member kind="function">
1897       <type>SOLUTION *</type>
1898       <name>subopt</name>
1899       <anchorfile>group__subopt__wuchty.html</anchorfile>
1900       <anchor>ga700f662506a233e42dd7fda74fafd40e</anchor>
1901       <arglist>(char *seq, char *structure, int delta, FILE *fp)</arglist>
1902     </member>
1903     <member kind="function">
1904       <type>SOLUTION *</type>
1905       <name>subopt_par</name>
1906       <anchorfile>group__subopt__wuchty.html</anchorfile>
1907       <anchor>ga554dedfcdb249fdf151caade58666e4d</anchor>
1908       <arglist>(char *seq, char *structure, paramT *parameters, int delta, int is_constrained, int is_circular, FILE *fp)</arglist>
1909     </member>
1910     <member kind="function">
1911       <type>SOLUTION *</type>
1912       <name>subopt_circ</name>
1913       <anchorfile>group__subopt__wuchty.html</anchorfile>
1914       <anchor>ga8634516e4740e0b6c9a46d2bae940340</anchor>
1915       <arglist>(char *seq, char *sequence, int delta, FILE *fp)</arglist>
1916     </member>
1917     <member kind="variable">
1918       <type>int</type>
1919       <name>subopt_sorted</name>
1920       <anchorfile>group__subopt__wuchty.html</anchorfile>
1921       <anchor>ga873cf8ed69e0437f8efa8b1fec854a0e</anchor>
1922       <arglist></arglist>
1923     </member>
1924     <member kind="variable">
1925       <type>double</type>
1926       <name>print_energy</name>
1927       <anchorfile>group__subopt__wuchty.html</anchorfile>
1928       <anchor>ga5e57d914bcb5feeecdf520e25313fcfe</anchor>
1929       <arglist></arglist>
1930     </member>
1931     <member kind="variable">
1932       <type>int</type>
1933       <name>density_of_states</name>
1934       <anchorfile>group__dos.html</anchorfile>
1935       <anchor>ga937634a76b46a22530a74906f1957a9e</anchor>
1936       <arglist>[MAXDOS+1]</arglist>
1937     </member>
1938   </compound>
1939   <compound kind="file">
1940     <name>treedist.h</name>
1941     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1942     <filename>treedist_8h</filename>
1943     <member kind="function">
1944       <type>Tree *</type>
1945       <name>make_tree</name>
1946       <anchorfile>treedist_8h.html</anchorfile>
1947       <anchor>a08fe4d5afd385dce593b86eaf010c6e3</anchor>
1948       <arglist>(char *struc)</arglist>
1949     </member>
1950     <member kind="function">
1951       <type>float</type>
1952       <name>tree_edit_distance</name>
1953       <anchorfile>treedist_8h.html</anchorfile>
1954       <anchor>a3b21f1925f7071f46d93431a835217bb</anchor>
1955       <arglist>(Tree *T1, Tree *T2)</arglist>
1956     </member>
1957     <member kind="function">
1958       <type>void</type>
1959       <name>print_tree</name>
1960       <anchorfile>treedist_8h.html</anchorfile>
1961       <anchor>a21ad4de3ba4055aeef08b28c9ad48894</anchor>
1962       <arglist>(Tree *t)</arglist>
1963     </member>
1964     <member kind="function">
1965       <type>void</type>
1966       <name>free_tree</name>
1967       <anchorfile>treedist_8h.html</anchorfile>
1968       <anchor>acbc1cb9bce582ea945e4a467c76a57aa</anchor>
1969       <arglist>(Tree *t)</arglist>
1970     </member>
1971   </compound>
1972   <compound kind="file">
1973     <name>utils.h</name>
1974     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
1975     <filename>utils_8h</filename>
1976     <member kind="define">
1977       <type>#define</type>
1978       <name>VRNA_INPUT_ERROR</name>
1979       <anchorfile>utils_8h.html</anchorfile>
1980       <anchor>ad403c9ea58f1836689404c2931419c8c</anchor>
1981       <arglist></arglist>
1982     </member>
1983     <member kind="define">
1984       <type>#define</type>
1985       <name>VRNA_INPUT_QUIT</name>
1986       <anchorfile>utils_8h.html</anchorfile>
1987       <anchor>a72f3c6ca5c83d2b9baed2922d19c403d</anchor>
1988       <arglist></arglist>
1989     </member>
1990     <member kind="define">
1991       <type>#define</type>
1992       <name>VRNA_INPUT_MISC</name>
1993       <anchorfile>utils_8h.html</anchorfile>
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2412     <name>1.8.4_epars.h</name>
2413     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/</path>
2414     <filename>1_88_84__epars_8h</filename>
2415   </compound>
2416   <compound kind="file">
2417     <name>1.8.4_intloops.h</name>
2418     <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/</path>
2419     <filename>1_88_84__intloops_8h</filename>
2420   </compound>
2421   <compound kind="page">
2422     <name>mp_parse</name>
2423     <title>Parsing and Comparing - Functions to Manipulate Structures</title>
2424     <filename>mp_parse</filename>
2425   </compound>
2426   <compound kind="page">
2427     <name>mp_utils</name>
2428     <title>Utilities - Odds and Ends</title>
2429     <filename>mp_utils</filename>
2430     <docanchor file="mp_utils">utils_struc</docanchor>
2431     <docanchor file="mp_utils">utils_dot</docanchor>
2432     <docanchor file="mp_utils">toc</docanchor>
2433     <docanchor file="mp_utils">utils_misc</docanchor>
2434     <docanchor file="mp_utils">utils_ss</docanchor>
2435     <docanchor file="mp_utils">utils_seq</docanchor>
2436     <docanchor file="mp_utils">utils_aln</docanchor>
2437   </compound>
2438   <compound kind="page">
2439     <name>mp_example</name>
2440     <title>Example - A Small Example Program</title>
2441     <filename>mp_example</filename>
2442   </compound>
2443   <compound kind="group">
2444     <name>folding_routines</name>
2445     <title>RNA Secondary Structure Folding</title>
2446     <filename>group__folding__routines.html</filename>
2447     <subgroup>mfe_fold</subgroup>
2448     <subgroup>pf_fold</subgroup>
2449     <subgroup>subopt_fold</subgroup>
2450     <subgroup>cofold</subgroup>
2451     <subgroup>consensus_fold</subgroup>
2452     <subgroup>local_fold</subgroup>
2453     <subgroup>energy_parameters</subgroup>
2454     <subgroup>eval</subgroup>
2455     <subgroup>inverse_fold</subgroup>
2456     <subgroup>class_fold</subgroup>
2457   </compound>
2458   <compound kind="group">
2459     <name>mfe_fold</name>
2460     <title>Calculating Minimum Free Energy (MFE) Structures</title>
2461     <filename>group__mfe__fold.html</filename>
2462     <subgroup>mfe_cofold</subgroup>
2463     <subgroup>consensus_mfe_fold</subgroup>
2464     <subgroup>local_mfe_fold</subgroup>
2465     <subgroup>kl_neighborhood_mfe</subgroup>
2466     <member kind="function">
2467       <type>float</type>
2468       <name>fold_par</name>
2469       <anchorfile>group__mfe__fold.html</anchorfile>
2470       <anchor>gadb973133c241d57c04b253df35e4d34e</anchor>
2471       <arglist>(const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular)</arglist>
2472     </member>
2473     <member kind="function">
2474       <type>float</type>
2475       <name>fold</name>
2476       <anchorfile>group__mfe__fold.html</anchorfile>
2477       <anchor>gaadafcb0f140795ae62e5ca027e335a9b</anchor>
2478       <arglist>(const char *sequence, char *structure)</arglist>
2479     </member>
2480     <member kind="function">
2481       <type>float</type>
2482       <name>circfold</name>
2483       <anchorfile>group__mfe__fold.html</anchorfile>
2484       <anchor>ga4ac63ab3e8d9a80ced28b8052d94e423</anchor>
2485       <arglist>(const char *sequence, char *structure)</arglist>
2486     </member>
2487     <member kind="function">
2488       <type>void</type>
2489       <name>free_arrays</name>
2490       <anchorfile>group__mfe__fold.html</anchorfile>
2491       <anchor>ga107fdfe5fd641868156bfd849f6866c7</anchor>
2492       <arglist>(void)</arglist>
2493     </member>
2494     <member kind="function">
2495       <type>void</type>
2496       <name>update_fold_params</name>
2497       <anchorfile>group__mfe__fold.html</anchorfile>
2498       <anchor>ga41bf8f6fa15b94471f7095cad9f0ccf3</anchor>
2499       <arglist>(void)</arglist>
2500     </member>
2501   </compound>
2502   <compound kind="group">
2503     <name>pf_fold</name>
2504     <title>Calculating Partition Functions and Pair Probabilities</title>
2505     <filename>group__pf__fold.html</filename>
2506     <subgroup>mea_fold</subgroup>
2507     <subgroup>centroid_fold</subgroup>
2508     <subgroup>pf_cofold</subgroup>
2509     <subgroup>up_cofold</subgroup>
2510     <subgroup>consensus_pf_fold</subgroup>
2511     <subgroup>local_pf_fold</subgroup>
2512     <subgroup>kl_neighborhood_pf</subgroup>
2513     <member kind="function">
2514       <type>float</type>
2515       <name>pf_fold_par</name>
2516       <anchorfile>group__pf__fold.html</anchorfile>
2517       <anchor>ga1839c61275760944b3a007c41d5c0823</anchor>
2518       <arglist>(const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
2519     </member>
2520     <member kind="function">
2521       <type>float</type>
2522       <name>pf_fold</name>
2523       <anchorfile>group__pf__fold.html</anchorfile>
2524       <anchor>gadc3db3d98742427e7001a7fd36ef28c2</anchor>
2525       <arglist>(const char *sequence, char *structure)</arglist>
2526     </member>
2527     <member kind="function">
2528       <type>float</type>
2529       <name>pf_circ_fold</name>
2530       <anchorfile>group__pf__fold.html</anchorfile>
2531       <anchor>ga819ce5fca8984004ac81c4a3b04cb735</anchor>
2532       <arglist>(const char *sequence, char *structure)</arglist>
2533     </member>
2534     <member kind="function">
2535       <type>void</type>
2536       <name>free_pf_arrays</name>
2537       <anchorfile>group__pf__fold.html</anchorfile>
2538       <anchor>gae73db3f49a94f0f72e067ecd12681dbd</anchor>
2539       <arglist>(void)</arglist>
2540     </member>
2541     <member kind="function">
2542       <type>void</type>
2543       <name>update_pf_params</name>
2544       <anchorfile>group__pf__fold.html</anchorfile>
2545       <anchor>ga384e927890f9c034ff09fa66da102d28</anchor>
2546       <arglist>(int length)</arglist>
2547     </member>
2548     <member kind="function">
2549       <type>void</type>
2550       <name>update_pf_params_par</name>
2551       <anchorfile>group__pf__fold.html</anchorfile>
2552       <anchor>ga0733527a94de3b79eee3c3c03c99c1bc</anchor>
2553       <arglist>(int length, pf_paramT *parameters)</arglist>
2554     </member>
2555     <member kind="function">
2556       <type>double *</type>
2557       <name>export_bppm</name>
2558       <anchorfile>group__pf__fold.html</anchorfile>
2559       <anchor>ga6d463707d5f64bdc4d21515b7dd9b115</anchor>
2560       <arglist>(void)</arglist>
2561     </member>
2562     <member kind="function">
2563       <type>void</type>
2564       <name>assign_plist_from_pr</name>
2565       <anchorfile>group__pf__fold.html</anchorfile>
2566       <anchor>ga03e15e831a31b1154855ab47edbdb019</anchor>
2567       <arglist>(plist **pl, double *probs, int length, double cutoff)</arglist>
2568     </member>
2569     <member kind="function">
2570       <type>int</type>
2571       <name>get_pf_arrays</name>
2572       <anchorfile>group__pf__fold.html</anchorfile>
2573       <anchor>ga18607e79e106cad827f482eedd2f632e</anchor>
2574       <arglist>(short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)</arglist>
2575     </member>
2576     <member kind="function">
2577       <type>double</type>
2578       <name>mean_bp_distance</name>
2579       <anchorfile>group__pf__fold.html</anchorfile>
2580       <anchor>ga79cbc375af65f11609feb6b055269e7d</anchor>
2581       <arglist>(int length)</arglist>
2582     </member>
2583     <member kind="function">
2584       <type>double</type>
2585       <name>mean_bp_distance_pr</name>
2586       <anchorfile>group__pf__fold.html</anchorfile>
2587       <anchor>ga72d84525f0afd3a9d60d830a2f501fa5</anchor>
2588       <arglist>(int length, double *pr)</arglist>
2589     </member>
2590   </compound>
2591   <compound kind="group">
2592     <name>mea_fold</name>
2593     <title>Compute the structure with maximum expected accuracy (MEA)</title>
2594     <filename>group__mea__fold.html</filename>
2595   </compound>
2596   <compound kind="group">
2597     <name>centroid_fold</name>
2598     <title>Compute the centroid structure</title>
2599     <filename>group__centroid__fold.html</filename>
2600     <member kind="function">
2601       <type>char *</type>
2602       <name>get_centroid_struct_pl</name>
2603       <anchorfile>group__centroid__fold.html</anchorfile>
2604       <anchor>ga9aba0ba1433a6d259331e0fe9fc4a9a6</anchor>
2605       <arglist>(int length, double *dist, plist *pl)</arglist>
2606     </member>
2607     <member kind="function">
2608       <type>char *</type>
2609       <name>get_centroid_struct_pr</name>
2610       <anchorfile>group__centroid__fold.html</anchorfile>
2611       <anchor>gacdabece4aa1e20c9eaa97acb4c4dcc38</anchor>
2612       <arglist>(int length, double *dist, double *pr)</arglist>
2613     </member>
2614   </compound>
2615   <compound kind="group">
2616     <name>subopt_fold</name>
2617     <title>Enumerating Suboptimal Structures</title>
2618     <filename>group__subopt__fold.html</filename>
2619     <subgroup>subopt_zuker</subgroup>
2620     <subgroup>subopt_wuchty</subgroup>
2621     <subgroup>subopt_stochbt</subgroup>
2622   </compound>
2623   <compound kind="group">
2624     <name>subopt_zuker</name>
2625     <title>Suboptimal structures according to Zuker et al. 1989</title>
2626     <filename>group__subopt__zuker.html</filename>
2627     <member kind="function">
2628       <type>SOLUTION *</type>
2629       <name>zukersubopt</name>
2630       <anchorfile>group__subopt__zuker.html</anchorfile>
2631       <anchor>ga0d5104e3ecf119d8eabd40aa5fe47f90</anchor>
2632       <arglist>(const char *string)</arglist>
2633     </member>
2634     <member kind="function">
2635       <type>SOLUTION *</type>
2636       <name>zukersubopt_par</name>
2637       <anchorfile>group__subopt__zuker.html</anchorfile>
2638       <anchor>ga6d98a9450d1affadf144ac79f543da8c</anchor>
2639       <arglist>(const char *string, paramT *parameters)</arglist>
2640     </member>
2641   </compound>
2642   <compound kind="group">
2643     <name>subopt_wuchty</name>
2644     <title>Suboptimal structures within an energy band arround the MFE</title>
2645     <filename>group__subopt__wuchty.html</filename>
2646     <member kind="function">
2647       <type>SOLUTION *</type>
2648       <name>subopt</name>
2649       <anchorfile>group__subopt__wuchty.html</anchorfile>
2650       <anchor>ga700f662506a233e42dd7fda74fafd40e</anchor>
2651       <arglist>(char *seq, char *structure, int delta, FILE *fp)</arglist>
2652     </member>
2653     <member kind="function">
2654       <type>SOLUTION *</type>
2655       <name>subopt_par</name>
2656       <anchorfile>group__subopt__wuchty.html</anchorfile>
2657       <anchor>ga554dedfcdb249fdf151caade58666e4d</anchor>
2658       <arglist>(char *seq, char *structure, paramT *parameters, int delta, int is_constrained, int is_circular, FILE *fp)</arglist>
2659     </member>
2660     <member kind="function">
2661       <type>SOLUTION *</type>
2662       <name>subopt_circ</name>
2663       <anchorfile>group__subopt__wuchty.html</anchorfile>
2664       <anchor>ga8634516e4740e0b6c9a46d2bae940340</anchor>
2665       <arglist>(char *seq, char *sequence, int delta, FILE *fp)</arglist>
2666     </member>
2667     <member kind="variable">
2668       <type>int</type>
2669       <name>subopt_sorted</name>
2670       <anchorfile>group__subopt__wuchty.html</anchorfile>
2671       <anchor>ga873cf8ed69e0437f8efa8b1fec854a0e</anchor>
2672       <arglist></arglist>
2673     </member>
2674     <member kind="variable">
2675       <type>double</type>
2676       <name>print_energy</name>
2677       <anchorfile>group__subopt__wuchty.html</anchorfile>
2678       <anchor>ga5e57d914bcb5feeecdf520e25313fcfe</anchor>
2679       <arglist></arglist>
2680     </member>
2681   </compound>
2682   <compound kind="group">
2683     <name>subopt_stochbt</name>
2684     <title>Stochastic backtracking in the Ensemble</title>
2685     <filename>group__subopt__stochbt.html</filename>
2686     <subgroup>consensus_stochbt</subgroup>
2687     <subgroup>kl_neighborhood_stochbt</subgroup>
2688     <member kind="function">
2689       <type>char *</type>
2690       <name>pbacktrack</name>
2691       <anchorfile>group__subopt__stochbt.html</anchorfile>
2692       <anchor>gac03ca6db186bb3bf0a2a326d7fb3ba03</anchor>
2693       <arglist>(char *sequence)</arglist>
2694     </member>
2695     <member kind="function">
2696       <type>char *</type>
2697       <name>pbacktrack_circ</name>
2698       <anchorfile>group__subopt__stochbt.html</anchorfile>
2699       <anchor>ga00474051204ac9ad576b3e45174d03ff</anchor>
2700       <arglist>(char *sequence)</arglist>
2701     </member>
2702     <member kind="variable">
2703       <type>int</type>
2704       <name>st_back</name>
2705       <anchorfile>group__subopt__stochbt.html</anchorfile>
2706       <anchor>gacd79b1a570e6ad9be24cb11fe8cae30a</anchor>
2707       <arglist></arglist>
2708     </member>
2709   </compound>
2710   <compound kind="group">
2711     <name>cofold</name>
2712     <title>Calculate Secondary Structures of two RNAs upon Dimerization</title>
2713     <filename>group__cofold.html</filename>
2714     <subgroup>mfe_cofold</subgroup>
2715     <subgroup>pf_cofold</subgroup>
2716     <subgroup>up_cofold</subgroup>
2717   </compound>
2718   <compound kind="group">
2719     <name>mfe_cofold</name>
2720     <title>MFE Structures of two hybridized Sequences</title>
2721     <filename>group__mfe__cofold.html</filename>
2722     <file>cofold.h</file>
2723     <member kind="function">
2724       <type>float</type>
2725       <name>cofold</name>
2726       <anchorfile>group__mfe__cofold.html</anchorfile>
2727       <anchor>gabc8517f22cfe70595ee81fc837910d52</anchor>
2728       <arglist>(const char *sequence, char *structure)</arglist>
2729     </member>
2730     <member kind="function">
2731       <type>float</type>
2732       <name>cofold_par</name>
2733       <anchorfile>group__mfe__cofold.html</anchorfile>
2734       <anchor>gafe430060533f14b11fc611f60b3f1f6f</anchor>
2735       <arglist>(const char *string, char *structure, paramT *parameters, int is_constrained)</arglist>
2736     </member>
2737     <member kind="function">
2738       <type>void</type>
2739       <name>free_co_arrays</name>
2740       <anchorfile>group__mfe__cofold.html</anchorfile>
2741       <anchor>gaafb33d7473eb9af9d1b168ca8761c41a</anchor>
2742       <arglist>(void)</arglist>
2743     </member>
2744     <member kind="function">
2745       <type>void</type>
2746       <name>update_cofold_params</name>
2747       <anchorfile>group__mfe__cofold.html</anchorfile>
2748       <anchor>ga4fcbf34e77b99bfbb2333d2ab0c41a57</anchor>
2749       <arglist>(void)</arglist>
2750     </member>
2751     <member kind="function">
2752       <type>void</type>
2753       <name>export_cofold_arrays_gq</name>
2754       <anchorfile>group__mfe__cofold.html</anchorfile>
2755       <anchor>ga5f5bf4df35d0554f6ace9579f8744c48</anchor>
2756       <arglist>(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)</arglist>
2757     </member>
2758     <member kind="function">
2759       <type>void</type>
2760       <name>export_cofold_arrays</name>
2761       <anchorfile>group__mfe__cofold.html</anchorfile>
2762       <anchor>ga5cb6b59983f1f74ccc00b9b9c4e84482</anchor>
2763       <arglist>(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)</arglist>
2764     </member>
2765   </compound>
2766   <compound kind="group">
2767     <name>pf_cofold</name>
2768     <title>Partition Function for two hybridized Sequences</title>
2769     <filename>group__pf__cofold.html</filename>
2770     <file>part_func_co.h</file>
2771     <member kind="function">
2772       <type>cofoldF</type>
2773       <name>co_pf_fold</name>
2774       <anchorfile>group__pf__cofold.html</anchorfile>
2775       <anchor>gaa86a5f998789ed71813d23d7307a791b</anchor>
2776       <arglist>(char *sequence, char *structure)</arglist>
2777     </member>
2778     <member kind="function">
2779       <type>cofoldF</type>
2780       <name>co_pf_fold_par</name>
2781       <anchorfile>group__pf__cofold.html</anchorfile>
2782       <anchor>gabd873b450832ab5f21101fc5ab354d21</anchor>
2783       <arglist>(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)</arglist>
2784     </member>
2785     <member kind="function">
2786       <type>double *</type>
2787       <name>export_co_bppm</name>
2788       <anchorfile>group__pf__cofold.html</anchorfile>
2789       <anchor>ga11f0252c1d2c4697253ff4b5bd392d3c</anchor>
2790       <arglist>(void)</arglist>
2791     </member>
2792     <member kind="function">
2793       <type>void</type>
2794       <name>free_co_pf_arrays</name>
2795       <anchorfile>group__pf__cofold.html</anchorfile>
2796       <anchor>gade3ce34ae8214811374b1d28a40dc247</anchor>
2797       <arglist>(void)</arglist>
2798     </member>
2799     <member kind="function">
2800       <type>void</type>
2801       <name>update_co_pf_params</name>
2802       <anchorfile>group__pf__cofold.html</anchorfile>
2803       <anchor>ga6e0f36c1f9b7d9dd4bfbad914c1119e5</anchor>
2804       <arglist>(int length)</arglist>
2805     </member>
2806     <member kind="function">
2807       <type>void</type>
2808       <name>update_co_pf_params_par</name>
2809       <anchorfile>group__pf__cofold.html</anchorfile>
2810       <anchor>ga117d880df45bef444d5e2785ffa40a53</anchor>
2811       <arglist>(int length, pf_paramT *parameters)</arglist>
2812     </member>
2813     <member kind="function">
2814       <type>void</type>
2815       <name>compute_probabilities</name>
2816       <anchorfile>group__pf__cofold.html</anchorfile>
2817       <anchor>ga15ae04ac5ab84e876dcf0093120cb617</anchor>
2818       <arglist>(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)</arglist>
2819     </member>
2820     <member kind="function">
2821       <type>ConcEnt *</type>
2822       <name>get_concentrations</name>
2823       <anchorfile>group__pf__cofold.html</anchorfile>
2824       <anchor>ga5545cb936ac4ff93c7d699d46e72e8c7</anchor>
2825       <arglist>(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)</arglist>
2826     </member>
2827     <member kind="variable">
2828       <type>int</type>
2829       <name>mirnatog</name>
2830       <anchorfile>group__pf__cofold.html</anchorfile>
2831       <anchor>gaff27888c4088cc1f60fd59cbd589474c</anchor>
2832       <arglist></arglist>
2833     </member>
2834     <member kind="variable">
2835       <type>double</type>
2836       <name>F_monomer</name>
2837       <anchorfile>group__pf__cofold.html</anchorfile>
2838       <anchor>gac2d1851a710a8561390861155ca988fe</anchor>
2839       <arglist>[2]</arglist>
2840     </member>
2841   </compound>
2842   <compound kind="group">
2843     <name>up_cofold</name>
2844     <title>Partition Function for two hybridized Sequences as a stepwise Process</title>
2845     <filename>group__up__cofold.html</filename>
2846     <file>part_func_up.h</file>
2847     <member kind="function">
2848       <type>pu_contrib *</type>
2849       <name>pf_unstru</name>
2850       <anchorfile>group__up__cofold.html</anchorfile>
2851       <anchor>ga5b4ee40e190d2f633cd01cf0d2fe93cf</anchor>
2852       <arglist>(char *sequence, int max_w)</arglist>
2853     </member>
2854     <member kind="function">
2855       <type>interact *</type>
2856       <name>pf_interact</name>
2857       <anchorfile>group__up__cofold.html</anchorfile>
2858       <anchor>ga1aa0aa02bc3a724f87360c03097afd00</anchor>
2859       <arglist>(const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5)</arglist>
2860     </member>
2861     <member kind="function">
2862       <type>void</type>
2863       <name>free_interact</name>
2864       <anchorfile>group__up__cofold.html</anchorfile>
2865       <anchor>gadde308fd5f696dc271b1532aa96fd12f</anchor>
2866       <arglist>(interact *pin)</arglist>
2867     </member>
2868     <member kind="function">
2869       <type>void</type>
2870       <name>free_pu_contrib_struct</name>
2871       <anchorfile>group__up__cofold.html</anchorfile>
2872       <anchor>gac20bd61824981d45ce0dc9934aa56df8</anchor>
2873       <arglist>(pu_contrib *pu)</arglist>
2874     </member>
2875   </compound>
2876   <compound kind="group">
2877     <name>consensus_fold</name>
2878     <title>Predicting Consensus Structures from Alignment(s)</title>
2879     <filename>group__consensus__fold.html</filename>
2880     <subgroup>consensus_mfe_fold</subgroup>
2881     <subgroup>consensus_pf_fold</subgroup>
2882     <subgroup>consensus_stochbt</subgroup>
2883     <subgroup>local_consensus_fold</subgroup>
2884     <member kind="function">
2885       <type>int</type>
2886       <name>get_mpi</name>
2887       <anchorfile>group__consensus__fold.html</anchorfile>
2888       <anchor>gaa2d600be90844094ec145ea14a314d2f</anchor>
2889       <arglist>(char *Alseq[], int n_seq, int length, int *mini)</arglist>
2890     </member>
2891     <member kind="function">
2892       <type>float **</type>
2893       <name>readribosum</name>
2894       <anchorfile>group__consensus__fold.html</anchorfile>
2895       <anchor>ga5e125c9586fcd4e2e1559fe76f7289cc</anchor>
2896       <arglist>(char *name)</arglist>
2897     </member>
2898     <member kind="function">
2899       <type>float</type>
2900       <name>energy_of_alistruct</name>
2901       <anchorfile>group__consensus__fold.html</anchorfile>
2902       <anchor>ga1c48869c03b49a342bf4cbdd61900081</anchor>
2903       <arglist>(const char **sequences, const char *structure, int n_seq, float *energy)</arglist>
2904     </member>
2905     <member kind="function">
2906       <type>void</type>
2907       <name>encode_ali_sequence</name>
2908       <anchorfile>group__consensus__fold.html</anchorfile>
2909       <anchor>gaa3e40277c837d6f7603afe319884c786</anchor>
2910       <arglist>(const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)</arglist>
2911     </member>
2912     <member kind="function">
2913       <type>void</type>
2914       <name>alloc_sequence_arrays</name>
2915       <anchorfile>group__consensus__fold.html</anchorfile>
2916       <anchor>ga8a560930f7f2582cc3967723a86cfdfa</anchor>
2917       <arglist>(const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)</arglist>
2918     </member>
2919     <member kind="function">
2920       <type>void</type>
2921       <name>free_sequence_arrays</name>
2922       <anchorfile>group__consensus__fold.html</anchorfile>
2923       <anchor>ga298a420a8c879202e2617b3f724fde38</anchor>
2924       <arglist>(unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)</arglist>
2925     </member>
2926     <member kind="function">
2927       <type>int</type>
2928       <name>get_alipf_arrays</name>
2929       <anchorfile>group__consensus__fold.html</anchorfile>
2930       <anchor>ga5349960075b1847720a2e9df021e2675</anchor>
2931       <arglist>(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)</arglist>
2932     </member>
2933     <member kind="variable">
2934       <type>double</type>
2935       <name>cv_fact</name>
2936       <anchorfile>group__consensus__fold.html</anchorfile>
2937       <anchor>gaf3cbac6ff5d706d6e414677841ddf94c</anchor>
2938       <arglist></arglist>
2939     </member>
2940     <member kind="variable">
2941       <type>double</type>
2942       <name>nc_fact</name>
2943       <anchorfile>group__consensus__fold.html</anchorfile>
2944       <anchor>ga502948a122a2af5b914355b1f3ea2f61</anchor>
2945       <arglist></arglist>
2946     </member>
2947   </compound>
2948   <compound kind="group">
2949     <name>consensus_mfe_fold</name>
2950     <title>MFE Consensus Structures for Sequence Alignment(s)</title>
2951     <filename>group__consensus__mfe__fold.html</filename>
2952     <member kind="function">
2953       <type>float</type>
2954       <name>alifold</name>
2955       <anchorfile>group__consensus__mfe__fold.html</anchorfile>
2956       <anchor>ga4cf00f0659e5f0480335d69e797f05b1</anchor>
2957       <arglist>(const char **strings, char *structure)</arglist>
2958     </member>
2959     <member kind="function">
2960       <type>float</type>
2961       <name>circalifold</name>
2962       <anchorfile>group__consensus__mfe__fold.html</anchorfile>
2963       <anchor>gadbd3b0b1c144cbfb4efe704b2b260f96</anchor>
2964       <arglist>(const char **strings, char *structure)</arglist>
2965     </member>
2966     <member kind="function">
2967       <type>void</type>
2968       <name>free_alifold_arrays</name>
2969       <anchorfile>group__consensus__mfe__fold.html</anchorfile>
2970       <anchor>ga72095e4554b5d577250ea14c42acc49e</anchor>
2971       <arglist>(void)</arglist>
2972     </member>
2973   </compound>
2974   <compound kind="group">
2975     <name>consensus_pf_fold</name>
2976     <title>Partition Function and Base Pair Probabilities for Sequence Alignment(s)</title>
2977     <filename>group__consensus__pf__fold.html</filename>
2978     <member kind="function">
2979       <type>float</type>
2980       <name>alipf_fold_par</name>
2981       <anchorfile>group__consensus__pf__fold.html</anchorfile>
2982       <anchor>ga4d2ff54d8210fc7cceeeff389d4dbd1d</anchor>
2983       <arglist>(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)</arglist>
2984     </member>
2985     <member kind="function">
2986       <type>float</type>
2987       <name>alipf_fold</name>
2988       <anchorfile>group__consensus__pf__fold.html</anchorfile>
2989       <anchor>gad32ded7d753ccaf211ab35782d1f42a9</anchor>
2990       <arglist>(const char **sequences, char *structure, plist **pl)</arglist>
2991     </member>
2992     <member kind="function">
2993       <type>float</type>
2994       <name>alipf_circ_fold</name>
2995       <anchorfile>group__consensus__pf__fold.html</anchorfile>
2996       <anchor>ga6b4dde1d43b79ab3753508c46cf50363</anchor>
2997       <arglist>(const char **sequences, char *structure, plist **pl)</arglist>
2998     </member>
2999     <member kind="function">
3000       <type>FLT_OR_DBL *</type>
3001       <name>export_ali_bppm</name>
3002       <anchorfile>group__consensus__pf__fold.html</anchorfile>
3003       <anchor>ga11b6ab8bd9be1821fea352b190a01cab</anchor>
3004       <arglist>(void)</arglist>
3005     </member>
3006   </compound>
3007   <compound kind="group">
3008     <name>consensus_stochbt</name>
3009     <title>Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)</title>
3010     <filename>group__consensus__stochbt.html</filename>
3011     <member kind="function">
3012       <type>char *</type>
3013       <name>alipbacktrack</name>
3014       <anchorfile>group__consensus__stochbt.html</anchorfile>
3015       <anchor>ga0df40248788f0fb17ebdc59d74116d1c</anchor>
3016       <arglist>(double *prob)</arglist>
3017     </member>
3018   </compound>
3019   <compound kind="group">
3020     <name>local_fold</name>
3021     <title>Predicting Locally stable structures of large sequences</title>
3022     <filename>group__local__fold.html</filename>
3023     <subgroup>local_mfe_fold</subgroup>
3024     <subgroup>local_pf_fold</subgroup>
3025     <subgroup>local_consensus_fold</subgroup>
3026   </compound>
3027   <compound kind="group">
3028     <name>local_mfe_fold</name>
3029     <title>Local MFE structure Prediction and Z-scores</title>
3030     <filename>group__local__mfe__fold.html</filename>
3031     <member kind="function">
3032       <type>float</type>
3033       <name>Lfold</name>
3034       <anchorfile>group__local__mfe__fold.html</anchorfile>
3035       <anchor>ga16e5a70e60835bb969eaecbe6482f1be</anchor>
3036       <arglist>(const char *string, char *structure, int maxdist)</arglist>
3037     </member>
3038     <member kind="function">
3039       <type>float</type>
3040       <name>Lfoldz</name>
3041       <anchorfile>group__local__mfe__fold.html</anchorfile>
3042       <anchor>gab6d79eecc180f586679f7b85cce5cbe9</anchor>
3043       <arglist>(const char *string, char *structure, int maxdist, int zsc, double min_z)</arglist>
3044     </member>
3045   </compound>
3046   <compound kind="group">
3047     <name>local_pf_fold</name>
3048     <title>Partition functions for locally stable secondary structures</title>
3049     <filename>group__local__pf__fold.html</filename>
3050     <member kind="function">
3051       <type>void</type>
3052       <name>update_pf_paramsLP</name>
3053       <anchorfile>group__local__pf__fold.html</anchorfile>
3054       <anchor>ga5a019014d37fe6105131dfc2fc447880</anchor>
3055       <arglist>(int length)</arglist>
3056     </member>
3057     <member kind="function">
3058       <type>plist *</type>
3059       <name>pfl_fold</name>
3060       <anchorfile>group__local__pf__fold.html</anchorfile>
3061       <anchor>gaa1ecd401617ebc748a0220026543c777</anchor>
3062       <arglist>(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup)</arglist>
3063     </member>
3064     <member kind="function">
3065       <type>plist *</type>
3066       <name>pfl_fold_par</name>
3067       <anchorfile>group__local__pf__fold.html</anchorfile>
3068       <anchor>gab354507e8028f3e1c52ef96bb1eb9df8</anchor>
3069       <arglist>(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters)</arglist>
3070     </member>
3071     <member kind="function">
3072       <type>void</type>
3073       <name>putoutpU_prob</name>
3074       <anchorfile>group__local__pf__fold.html</anchorfile>
3075       <anchor>ga0bcb751860bbf34e3dfee8c2fbdb3ef3</anchor>
3076       <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
3077     </member>
3078     <member kind="function">
3079       <type>void</type>
3080       <name>putoutpU_prob_bin</name>
3081       <anchorfile>group__local__pf__fold.html</anchorfile>
3082       <anchor>ga9acb00ee10e96b1ca4ea394cd8bcec75</anchor>
3083       <arglist>(double **pU, int length, int ulength, FILE *fp, int energies)</arglist>
3084     </member>
3085   </compound>
3086   <compound kind="group">
3087     <name>local_consensus_fold</name>
3088     <title>Local MFE consensus structures for Sequence Alignments</title>
3089     <filename>group__local__consensus__fold.html</filename>
3090     <member kind="function">
3091       <type>float</type>
3092       <name>aliLfold</name>
3093       <anchorfile>group__local__consensus__fold.html</anchorfile>
3094       <anchor>ga20a173a3cdb83f5d1778e36c1a6b1f2b</anchor>
3095       <arglist>(const char **strings, char *structure, int maxdist)</arglist>
3096     </member>
3097   </compound>
3098   <compound kind="group">
3099     <name>energy_parameters</name>
3100     <title>Change and Precalculate Energy Parameter Sets and Boltzmann Factors</title>
3101     <filename>group__energy__parameters.html</filename>
3102     <subgroup>energy_parameters_rw</subgroup>
3103     <file>params.h</file>
3104     <member kind="function">
3105       <type>paramT *</type>
3106       <name>scale_parameters</name>
3107       <anchorfile>group__energy__parameters.html</anchorfile>
3108       <anchor>ga527ef619cd8210b84d5d53be1e0e29b6</anchor>
3109       <arglist>(void)</arglist>
3110     </member>
3111     <member kind="function">
3112       <type>paramT *</type>
3113       <name>get_scaled_parameters</name>
3114       <anchorfile>group__energy__parameters.html</anchorfile>
3115       <anchor>gac2f3ca440b7eaf4d999fb27da949fe72</anchor>
3116       <arglist>(double temperature, model_detailsT md)</arglist>
3117     </member>
3118     <member kind="function">
3119       <type>pf_paramT *</type>
3120       <name>get_scaled_pf_parameters</name>
3121       <anchorfile>group__energy__parameters.html</anchorfile>
3122       <anchor>gab85f6b6da051f380371deb0d8921bdba</anchor>
3123       <arglist>(void)</arglist>
3124     </member>
3125     <member kind="function">
3126       <type>pf_paramT *</type>
3127       <name>get_boltzmann_factors</name>
3128       <anchorfile>group__energy__parameters.html</anchorfile>
3129       <anchor>ga6fc2f3eef5a3024d44963ac59a42e39d</anchor>
3130       <arglist>(double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
3131     </member>
3132     <member kind="function">
3133       <type>pf_paramT *</type>
3134       <name>get_boltzmann_factor_copy</name>
3135       <anchorfile>group__energy__parameters.html</anchorfile>
3136       <anchor>gacba212326a051734797e65987260fdd0</anchor>
3137       <arglist>(pf_paramT *parameters)</arglist>
3138     </member>
3139     <member kind="function">
3140       <type>pf_paramT *</type>
3141       <name>get_scaled_alipf_parameters</name>
3142       <anchorfile>group__energy__parameters.html</anchorfile>
3143       <anchor>gaa6a4297a2b91d6f7ae47dd61ca1862a0</anchor>
3144       <arglist>(unsigned int n_seq)</arglist>
3145     </member>
3146     <member kind="function">
3147       <type>pf_paramT *</type>
3148       <name>get_boltzmann_factors_ali</name>
3149       <anchorfile>group__energy__parameters.html</anchorfile>
3150       <anchor>gaf0c74574b40f2778556535bf9d382828</anchor>
3151       <arglist>(unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale)</arglist>
3152     </member>
3153   </compound>
3154   <compound kind="group">
3155     <name>energy_parameters_rw</name>
3156     <title>Reading/Writing energy parameter sets from/to File</title>
3157     <filename>group__energy__parameters__rw.html</filename>
3158     <subgroup>energy_parameters_convert</subgroup>
3159     <file>read_epars.h</file>
3160     <member kind="function">
3161       <type>void</type>
3162       <name>read_parameter_file</name>
3163       <anchorfile>group__energy__parameters__rw.html</anchorfile>
3164       <anchor>ga165a142a3c68fb6655c69ef4ab7cd749</anchor>
3165       <arglist>(const char fname[])</arglist>
3166     </member>
3167     <member kind="function">
3168       <type>void</type>
3169       <name>write_parameter_file</name>
3170       <anchorfile>group__energy__parameters__rw.html</anchorfile>
3171       <anchor>ga8a43459be386a7489feeab68dc2c6c76</anchor>
3172       <arglist>(const char fname[])</arglist>
3173     </member>
3174   </compound>
3175   <compound kind="group">
3176     <name>energy_parameters_convert</name>
3177     <title>Converting energy parameter files</title>
3178     <filename>group__energy__parameters__convert.html</filename>
3179     <file>convert_epars.h</file>
3180     <member kind="define">
3181       <type>#define</type>
3182       <name>VRNA_CONVERT_OUTPUT_ALL</name>
3183       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3184       <anchor>ga8dc6aee5a806c49b71557152f9616bc4</anchor>
3185       <arglist></arglist>
3186     </member>
3187     <member kind="define">
3188       <type>#define</type>
3189       <name>VRNA_CONVERT_OUTPUT_HP</name>
3190       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3191       <anchor>gaf66fe2cb11dfcfd32d791049c254a8a4</anchor>
3192       <arglist></arglist>
3193     </member>
3194     <member kind="define">
3195       <type>#define</type>
3196       <name>VRNA_CONVERT_OUTPUT_STACK</name>
3197       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3198       <anchor>gad23522d63f8d4c50d5a5deee9bee3ef2</anchor>
3199       <arglist></arglist>
3200     </member>
3201     <member kind="define">
3202       <type>#define</type>
3203       <name>VRNA_CONVERT_OUTPUT_MM_HP</name>
3204       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3205       <anchor>gaa892c7b4957459090f3e08da298cc347</anchor>
3206       <arglist></arglist>
3207     </member>
3208     <member kind="define">
3209       <type>#define</type>
3210       <name>VRNA_CONVERT_OUTPUT_MM_INT</name>
3211       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3212       <anchor>ga4ff223fb1f9c62cd92d9ab811ad03d55</anchor>
3213       <arglist></arglist>
3214     </member>
3215     <member kind="define">
3216       <type>#define</type>
3217       <name>VRNA_CONVERT_OUTPUT_MM_INT_1N</name>
3218       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3219       <anchor>gaf5d3743219f83c6348155cd81e755bbb</anchor>
3220       <arglist></arglist>
3221     </member>
3222     <member kind="define">
3223       <type>#define</type>
3224       <name>VRNA_CONVERT_OUTPUT_MM_INT_23</name>
3225       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3226       <anchor>ga78382ec622ba99e0ac2262317bdd7316</anchor>
3227       <arglist></arglist>
3228     </member>
3229     <member kind="define">
3230       <type>#define</type>
3231       <name>VRNA_CONVERT_OUTPUT_MM_MULTI</name>
3232       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3233       <anchor>gae67af9f1cdf7baf2865481282a5d1034</anchor>
3234       <arglist></arglist>
3235     </member>
3236     <member kind="define">
3237       <type>#define</type>
3238       <name>VRNA_CONVERT_OUTPUT_MM_EXT</name>
3239       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3240       <anchor>gaf14ead7ef1fdbe725ade653750fc51e3</anchor>
3241       <arglist></arglist>
3242     </member>
3243     <member kind="define">
3244       <type>#define</type>
3245       <name>VRNA_CONVERT_OUTPUT_DANGLE5</name>
3246       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3247       <anchor>ga036ffd996d8c8a9acf631760dd1da24b</anchor>
3248       <arglist></arglist>
3249     </member>
3250     <member kind="define">
3251       <type>#define</type>
3252       <name>VRNA_CONVERT_OUTPUT_DANGLE3</name>
3253       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3254       <anchor>ga34a8a5479ef885834ef32f3fb43d79bc</anchor>
3255       <arglist></arglist>
3256     </member>
3257     <member kind="define">
3258       <type>#define</type>
3259       <name>VRNA_CONVERT_OUTPUT_INT_11</name>
3260       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3261       <anchor>ga079aafefd5f8ab57ee5120099a34bd25</anchor>
3262       <arglist></arglist>
3263     </member>
3264     <member kind="define">
3265       <type>#define</type>
3266       <name>VRNA_CONVERT_OUTPUT_INT_21</name>
3267       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3268       <anchor>gacf770881d9034431ebe741642342a1f9</anchor>
3269       <arglist></arglist>
3270     </member>
3271     <member kind="define">
3272       <type>#define</type>
3273       <name>VRNA_CONVERT_OUTPUT_INT_22</name>
3274       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3275       <anchor>gaa307671e2631cdacad9cbe4c6583b05f</anchor>
3276       <arglist></arglist>
3277     </member>
3278     <member kind="define">
3279       <type>#define</type>
3280       <name>VRNA_CONVERT_OUTPUT_BULGE</name>
3281       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3282       <anchor>ga7092fe0be4de6f02cc0bf08e81af726a</anchor>
3283       <arglist></arglist>
3284     </member>
3285     <member kind="define">
3286       <type>#define</type>
3287       <name>VRNA_CONVERT_OUTPUT_INT</name>
3288       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3289       <anchor>gac5c2289fdf8ff1b980976d1613ff943a</anchor>
3290       <arglist></arglist>
3291     </member>
3292     <member kind="define">
3293       <type>#define</type>
3294       <name>VRNA_CONVERT_OUTPUT_ML</name>
3295       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3296       <anchor>gaf2c8755d64eff3852aa45df9ac80a4fe</anchor>
3297       <arglist></arglist>
3298     </member>
3299     <member kind="define">
3300       <type>#define</type>
3301       <name>VRNA_CONVERT_OUTPUT_MISC</name>
3302       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3303       <anchor>ga46d5b1535ae86060b6317565b7c6b40b</anchor>
3304       <arglist></arglist>
3305     </member>
3306     <member kind="define">
3307       <type>#define</type>
3308       <name>VRNA_CONVERT_OUTPUT_SPECIAL_HP</name>
3309       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3310       <anchor>gaa1ff48a79642d69579d1766561ec6db6</anchor>
3311       <arglist></arglist>
3312     </member>
3313     <member kind="define">
3314       <type>#define</type>
3315       <name>VRNA_CONVERT_OUTPUT_VANILLA</name>
3316       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3317       <anchor>ga0d4e8a836bb4864ab5129c085dbf592d</anchor>
3318       <arglist></arglist>
3319     </member>
3320     <member kind="define">
3321       <type>#define</type>
3322       <name>VRNA_CONVERT_OUTPUT_NINIO</name>
3323       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3324       <anchor>ga2eb0462f16939ddacdaf751a88d675ce</anchor>
3325       <arglist></arglist>
3326     </member>
3327     <member kind="define">
3328       <type>#define</type>
3329       <name>VRNA_CONVERT_OUTPUT_DUMP</name>
3330       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3331       <anchor>gac86976e9c2a55b3a6481ea60044f6098</anchor>
3332       <arglist></arglist>
3333     </member>
3334     <member kind="function">
3335       <type>void</type>
3336       <name>convert_parameter_file</name>
3337       <anchorfile>group__energy__parameters__convert.html</anchorfile>
3338       <anchor>gafbe538bc4eb2cf2a33326e1010005f8a</anchor>
3339       <arglist>(const char *iname, const char *oname, unsigned int options)</arglist>
3340     </member>
3341   </compound>
3342   <compound kind="group">
3343     <name>eval</name>
3344     <title>Energy evaluation</title>
3345     <filename>group__eval.html</filename>
3346     <member kind="function">
3347       <type>float</type>
3348       <name>energy_of_structure</name>
3349       <anchorfile>group__eval.html</anchorfile>
3350       <anchor>gaf93986cb3cb29770ec9cca69c9fab8cf</anchor>
3351       <arglist>(const char *string, const char *structure, int verbosity_level)</arglist>
3352     </member>
3353     <member kind="function">
3354       <type>float</type>
3355       <name>energy_of_struct_par</name>
3356       <anchorfile>group__eval.html</anchorfile>
3357       <anchor>gab5169ea4f72f250e43811463a33f4e40</anchor>
3358       <arglist>(const char *string, const char *structure, paramT *parameters, int verbosity_level)</arglist>
3359     </member>
3360     <member kind="function">
3361       <type>float</type>
3362       <name>energy_of_circ_structure</name>
3363       <anchorfile>group__eval.html</anchorfile>
3364       <anchor>gaeb14f3664aec67fc03268ac75253f0f8</anchor>
3365       <arglist>(const char *string, const char *structure, int verbosity_level)</arglist>
3366     </member>
3367     <member kind="function">
3368       <type>float</type>
3369       <name>energy_of_circ_struct_par</name>
3370       <anchorfile>group__eval.html</anchorfile>
3371       <anchor>ga75dc765ee4a1177832bc817c94cf88e5</anchor>
3372       <arglist>(const char *string, const char *structure, paramT *parameters, int verbosity_level)</arglist>
3373     </member>
3374     <member kind="function">
3375       <type>int</type>
3376       <name>energy_of_structure_pt</name>
3377       <anchorfile>group__eval.html</anchorfile>
3378       <anchor>ga8831445966b761417e713360791299d8</anchor>
3379       <arglist>(const char *string, short *ptable, short *s, short *s1, int verbosity_level)</arglist>
3380     </member>
3381     <member kind="function">
3382       <type>int</type>
3383       <name>energy_of_struct_pt_par</name>
3384       <anchorfile>group__eval.html</anchorfile>
3385       <anchor>gada4701dd7519b29da75ceac147601f4e</anchor>
3386       <arglist>(const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level)</arglist>
3387     </member>
3388     <member kind="variable">
3389       <type>int</type>
3390       <name>eos_debug</name>
3391       <anchorfile>group__eval.html</anchorfile>
3392       <anchor>ga567530678f6260a1a649a5beca5da4c5</anchor>
3393       <arglist></arglist>
3394     </member>
3395   </compound>
3396   <compound kind="group">
3397     <name>inverse_fold</name>
3398     <title>Searching Sequences for Predefined Structures</title>
3399     <filename>group__inverse__fold.html</filename>
3400     <file>inverse.h</file>
3401     <member kind="function">
3402       <type>float</type>
3403       <name>inverse_fold</name>
3404       <anchorfile>group__inverse__fold.html</anchorfile>
3405       <anchor>ga7af026de55d4babad879f2c92559cbbc</anchor>
3406       <arglist>(char *start, const char *target)</arglist>
3407     </member>
3408     <member kind="function">
3409       <type>float</type>
3410       <name>inverse_pf_fold</name>
3411       <anchorfile>group__inverse__fold.html</anchorfile>
3412       <anchor>gaeef52ecbf2a2450ad585a344f9826806</anchor>
3413       <arglist>(char *start, const char *target)</arglist>
3414     </member>
3415     <member kind="variable">
3416       <type>char *</type>
3417       <name>symbolset</name>
3418       <anchorfile>group__inverse__fold.html</anchorfile>
3419       <anchor>ga8f791e7740a5a28b9f6fafb4e60301d9</anchor>
3420       <arglist></arglist>
3421     </member>
3422     <member kind="variable">
3423       <type>float</type>
3424       <name>final_cost</name>
3425       <anchorfile>group__inverse__fold.html</anchorfile>
3426       <anchor>ga7f17d3b169af048d32bb185039a9c09c</anchor>
3427       <arglist></arglist>
3428     </member>
3429     <member kind="variable">
3430       <type>int</type>
3431       <name>give_up</name>
3432       <anchorfile>group__inverse__fold.html</anchorfile>
3433       <anchor>ga7ec4ba51f86e1717a1e174264e4a75ce</anchor>
3434       <arglist></arglist>
3435     </member>
3436     <member kind="variable">
3437       <type>int</type>
3438       <name>inv_verbose</name>
3439       <anchorfile>group__inverse__fold.html</anchorfile>
3440       <anchor>gafcfc65fba01b9cca5946726ed9057a63</anchor>
3441       <arglist></arglist>
3442     </member>
3443   </compound>
3444   <compound kind="group">
3445     <name>class_fold</name>
3446     <title>Classified Dynamic Programming</title>
3447     <filename>group__class__fold.html</filename>
3448     <subgroup>kl_neighborhood</subgroup>
3449     <subgroup>dos</subgroup>
3450   </compound>
3451   <compound kind="group">
3452     <name>kl_neighborhood</name>
3453     <title>Distance based partitioning of the Secondary Structure Space</title>
3454     <filename>group__kl__neighborhood.html</filename>
3455     <subgroup>kl_neighborhood_mfe</subgroup>
3456     <subgroup>kl_neighborhood_pf</subgroup>
3457     <subgroup>kl_neighborhood_stochbt</subgroup>
3458   </compound>
3459   <compound kind="group">
3460     <name>kl_neighborhood_mfe</name>
3461     <title>Calculating MFE representatives of a Distance Based Partitioning</title>
3462     <filename>group__kl__neighborhood__mfe.html</filename>
3463     <file>2Dfold.h</file>
3464     <member kind="function">
3465       <type>TwoDfold_vars *</type>
3466       <name>get_TwoDfold_variables</name>
3467       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
3468       <anchor>gac9284f132cf0eaa0a2f43590eda05488</anchor>
3469       <arglist>(const char *seq, const char *structure1, const char *structure2, int circ)</arglist>
3470     </member>
3471     <member kind="function">
3472       <type>void</type>
3473       <name>destroy_TwoDfold_variables</name>
3474       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
3475       <anchor>ga05bf4f31d216b1b160fd2d3d68e9b487</anchor>
3476       <arglist>(TwoDfold_vars *our_variables)</arglist>
3477     </member>
3478     <member kind="function">
3479       <type>TwoDfold_solution *</type>
3480       <name>TwoDfoldList</name>
3481       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
3482       <anchor>ga47da790166020558d27323aef489703e</anchor>
3483       <arglist>(TwoDfold_vars *vars, int distance1, int distance2)</arglist>
3484     </member>
3485     <member kind="function">
3486       <type>char *</type>
3487       <name>TwoDfold_backtrack_f5</name>
3488       <anchorfile>group__kl__neighborhood__mfe.html</anchorfile>
3489       <anchor>gaf4dc05bf8fc1ea53acd7aeb798ba80c2</anchor>
3490       <arglist>(unsigned int j, int k, int l, TwoDfold_vars *vars)</arglist>
3491     </member>
3492   </compound>
3493   <compound kind="group">
3494     <name>kl_neighborhood_pf</name>
3495     <title>Calculate Partition Functions of a Distance Based Partitioning</title>
3496     <filename>group__kl__neighborhood__pf.html</filename>
3497     <file>2Dpfold.h</file>
3498     <member kind="function">
3499       <type>TwoDpfold_vars *</type>
3500       <name>get_TwoDpfold_variables</name>
3501       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
3502       <anchor>ga1aca740e2a75ab2b2951538266e53d64</anchor>
3503       <arglist>(const char *seq, const char *structure1, char *structure2, int circ)</arglist>
3504     </member>
3505     <member kind="function">
3506       <type>TwoDpfold_vars *</type>
3507       <name>get_TwoDpfold_variables_from_MFE</name>
3508       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
3509       <anchor>gacc2f66da7ee62096cab629fce7112216</anchor>
3510       <arglist>(TwoDfold_vars *mfe_vars)</arglist>
3511     </member>
3512     <member kind="function">
3513       <type>void</type>
3514       <name>destroy_TwoDpfold_variables</name>
3515       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
3516       <anchor>gafe994291458ee2ac34d3eb825ef62a15</anchor>
3517       <arglist>(TwoDpfold_vars *vars)</arglist>
3518     </member>
3519     <member kind="function">
3520       <type>TwoDpfold_solution *</type>
3521       <name>TwoDpfoldList</name>
3522       <anchorfile>group__kl__neighborhood__pf.html</anchorfile>
3523       <anchor>ga3e1cd3b24eb635c65181182cbb4ae3eb</anchor>
3524       <arglist>(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)</arglist>
3525     </member>
3526   </compound>
3527   <compound kind="group">
3528     <name>kl_neighborhood_stochbt</name>
3529     <title>Stochastic Backtracking of Structures from Distance Based Partitioning</title>
3530     <filename>group__kl__neighborhood__stochbt.html</filename>
3531     <member kind="function">
3532       <type>char *</type>
3533       <name>TwoDpfold_pbacktrack</name>
3534       <anchorfile>group__kl__neighborhood__stochbt.html</anchorfile>
3535       <anchor>gae251288f50dd4ae7d315af0085775f71</anchor>
3536       <arglist>(TwoDpfold_vars *vars, int d1, int d2)</arglist>
3537     </member>
3538     <member kind="function">
3539       <type>char *</type>
3540       <name>TwoDpfold_pbacktrack5</name>
3541       <anchorfile>group__kl__neighborhood__stochbt.html</anchorfile>
3542       <anchor>ga13430ac6a7f90df426774f131647d2c7</anchor>
3543       <arglist>(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)</arglist>
3544     </member>
3545   </compound>
3546   <compound kind="group">
3547     <name>dos</name>
3548     <title>Compute the Density of States</title>
3549     <filename>group__dos.html</filename>
3550     <member kind="variable">
3551       <type>int</type>
3552       <name>density_of_states</name>
3553       <anchorfile>group__dos.html</anchorfile>
3554       <anchor>ga937634a76b46a22530a74906f1957a9e</anchor>
3555       <arglist>[MAXDOS+1]</arglist>
3556     </member>
3557   </compound>
3558   <compound kind="group">
3559     <name>parse</name>
3560     <title>Parsing and Comparing - Functions to Manipulate Structures</title>
3561     <filename>group__parse.html</filename>
3562   </compound>
3563   <compound kind="struct">
3564     <name>bondT</name>
3565     <filename>structbondT.html</filename>
3566   </compound>
3567   <compound kind="struct">
3568     <name>bondTEn</name>
3569     <filename>structbondTEn.html</filename>
3570   </compound>
3571   <compound kind="struct">
3572     <name>cofoldF</name>
3573     <filename>structcofoldF.html</filename>
3574     <member kind="variable">
3575       <type>double</type>
3576       <name>F0AB</name>
3577       <anchorfile>structcofoldF.html</anchorfile>
3578       <anchor>af6c496438321eb8bb907a21de1915c23</anchor>
3579       <arglist></arglist>
3580     </member>
3581     <member kind="variable">
3582       <type>double</type>
3583       <name>FAB</name>
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