1\hypertarget{fold__compound_8h_source}{}\doxysection{fold\+\_\+compound.\+h}
2\label{fold__compound_8h_source}\index{ViennaRNA/fold\_compound.h@{ViennaRNA/fold\_compound.h}}
3
4\begin{DoxyCode}{0}
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6\DoxyCodeLine{00002 \textcolor{preprocessor}{\#define VIENNA\_RNA\_PACKAGE\_FOLD\_COMPOUND\_H}}
7\DoxyCodeLine{00003 }
8\DoxyCodeLine{00026 \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fc\_s}} \mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}};}
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13\DoxyCodeLine{00068                                               \textcolor{keywordtype}{void}          *data);}
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17\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00084}\mbox{\hyperlink{group__fold__compound_ga47c900ca76e56e59e2e83a06e0bde641}{00084}} \textcolor{preprocessor}{\#define VRNA\_STATUS\_MFE\_POST    (unsigned char)2}}
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23\DoxyCodeLine{00100 }
24\DoxyCodeLine{00101 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{model_8h}{ViennaRNA/model.h}}>}}
25\DoxyCodeLine{00102 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{params_2basic_8h}{ViennaRNA/params/basic.h}}>}}
26\DoxyCodeLine{00103 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{sequence_8h}{ViennaRNA/sequence.h}}>}}
27\DoxyCodeLine{00104 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{dp__matrices_8h}{ViennaRNA/dp\_matrices.h}}>}}
28\DoxyCodeLine{00105 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{hard_8h}{ViennaRNA/constraints/hard.h}}>}}
29\DoxyCodeLine{00106 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{soft_8h}{ViennaRNA/constraints/soft.h}}>}}
30\DoxyCodeLine{00107 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{grammar_8h}{ViennaRNA/grammar.h}}>}}
31\DoxyCodeLine{00108 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{structured__domains_8h}{ViennaRNA/structured\_domains.h}}>}}
32\DoxyCodeLine{00109 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{unstructured__domains_8h}{ViennaRNA/unstructured\_domains.h}}>}}
33\DoxyCodeLine{00110 }
34\DoxyCodeLine{00111 \textcolor{preprocessor}{\#ifdef VRNA\_WITH\_SVM}}
35\DoxyCodeLine{00112 \textcolor{preprocessor}{\#include <ViennaRNA/zscore.h>}}
36\DoxyCodeLine{00113 \textcolor{preprocessor}{\#endif}}
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53\DoxyCodeLine{00159   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}      strands;}
54\DoxyCodeLine{00160   \mbox{\hyperlink{group__alphabet__utils_structvrna__sequence__s}{vrna\_seq\_t}}        *nucleotides;}
55\DoxyCodeLine{00161   \mbox{\hyperlink{group__alphabet__utils_structvrna__alignment__s}{vrna\_msa\_t}}        *alignment;}
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67\DoxyCodeLine{00200   \textcolor{comment}{/* data structure to adjust additional structural domains, such as G-\/quadruplexes */}}
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120\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00326}\mbox{\hyperlink{group__fold__compound_a54c0b979274b285a7e093ed54aa3252e}{00326}}   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}  *\mbox{\hyperlink{group__fold__compound_a54c0b979274b285a7e093ed54aa3252e}{mm2}};             }
121\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00338}\mbox{\hyperlink{group__fold__compound_adacbf7cdfb47d3072683ab509de735f6}{00338}}   \textcolor{keywordtype}{int}   \mbox{\hyperlink{group__fold__compound_adacbf7cdfb47d3072683ab509de735f6}{window\_size}};              }
122\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00339}\mbox{\hyperlink{group__fold__compound_a2ecb8ff5e21190936a8a146be7a251ff}{00339}}   \textcolor{keywordtype}{char}  **\mbox{\hyperlink{group__fold__compound_a2ecb8ff5e21190936a8a146be7a251ff}{ptype\_local}};            }
123\DoxyCodeLine{00340 \textcolor{preprocessor}{\#ifdef VRNA\_WITH\_SVM}}
124\DoxyCodeLine{00341   vrna\_zsc\_dat\_t  zscore\_data;}
125\DoxyCodeLine{00342 \textcolor{preprocessor}{\#endif}}
126\DoxyCodeLine{00343 }
127\DoxyCodeLine{00347 \};}
128\DoxyCodeLine{00348 }
129\DoxyCodeLine{00349 }
130\DoxyCodeLine{00350 \textcolor{comment}{/* the definitions below should be used for functions that return/receive/destroy fold compound data structures */}}
131\DoxyCodeLine{00351 }
132\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00355}\mbox{\hyperlink{group__fold__compound_gacea5b7ee6181c485f36e2afa0e9089e4}{00355}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_DEFAULT         0U}}
133\DoxyCodeLine{00356 }
134\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00363}\mbox{\hyperlink{group__fold__compound_gae63be9127fe7dcc1f9bb14f5bb1064ee}{00363}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_MFE             1U}}
135\DoxyCodeLine{00364 }
136\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00371}\mbox{\hyperlink{group__fold__compound_gabfbadcddda3e74ce7f49035ef8f058f7}{00371}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_PF              2U}}
137\DoxyCodeLine{00372 }
138\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00376}\mbox{\hyperlink{group__fold__compound_ga8f681fa12b8d4b348bf58415fd1fc82f}{00376}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_HYBRID          4U}}
139\DoxyCodeLine{00377 }
140\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00387}\mbox{\hyperlink{group__fold__compound_ga61469c423131552c8483229f8b6c7e0e}{00387}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_EVAL\_ONLY       8U}}
141\DoxyCodeLine{00388 }
142\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00392}\mbox{\hyperlink{group__fold__compound_ga2b2a8009ccdccc3eb1571556261aee8e}{00392}} \textcolor{preprocessor}{\#define VRNA\_OPTION\_WINDOW          16U}}
143\DoxyCodeLine{00393 }
144\DoxyCodeLine{00431 \mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *}
145\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00432}\mbox{\hyperlink{group__fold__compound_ga283cf113a37614a75c1388c4ec6d7b2f}{00432}} \mbox{\hyperlink{group__fold__compound_ga283cf113a37614a75c1388c4ec6d7b2f}{vrna\_fold\_compound}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char}       *sequence,}
146\DoxyCodeLine{00433                    \textcolor{keyword}{const} \mbox{\hyperlink{group__model__details_structvrna__md__s}{vrna\_md\_t}}  *md\_p,}
147\DoxyCodeLine{00434                    \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}     options);}
148\DoxyCodeLine{00435 }
149\DoxyCodeLine{00436 }
150\DoxyCodeLine{00474 \mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *}
151\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00475}\mbox{\hyperlink{group__fold__compound_gad6bacc816af274922b13d947f708aa0c}{00475}} \mbox{\hyperlink{group__fold__compound_gad6bacc816af274922b13d947f708aa0c}{vrna\_fold\_compound\_comparative}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char}   **sequences,}
152\DoxyCodeLine{00476                                \mbox{\hyperlink{group__model__details_structvrna__md__s}{vrna\_md\_t}}    *md\_p,}
153\DoxyCodeLine{00477                                \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options);}
154\DoxyCodeLine{00478 }
155\DoxyCodeLine{00479 }
156\DoxyCodeLine{00480 \mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *}
157\DoxyCodeLine{00481 vrna\_fold\_compound\_comparative2(\textcolor{keyword}{const} \textcolor{keywordtype}{char}                **sequences,}
158\DoxyCodeLine{00482                                 \textcolor{keyword}{const} \textcolor{keywordtype}{char}                **names,}
159\DoxyCodeLine{00483                                 \textcolor{keyword}{const} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{char}       *orientation,}
160\DoxyCodeLine{00484                                 \textcolor{keyword}{const} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} \textcolor{keywordtype}{long}  *start,}
161\DoxyCodeLine{00485                                 \textcolor{keyword}{const} \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{long} \textcolor{keywordtype}{long}  *genome\_size,}
162\DoxyCodeLine{00486                                 \mbox{\hyperlink{group__model__details_structvrna__md__s}{vrna\_md\_t}}                 *md\_p,}
163\DoxyCodeLine{00487                                 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}              options);}
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166\DoxyCodeLine{00490 \mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *}
167\DoxyCodeLine{00491 vrna\_fold\_compound\_TwoD(\textcolor{keyword}{const} \textcolor{keywordtype}{char}    *sequence,}
168\DoxyCodeLine{00492                         \textcolor{keyword}{const} \textcolor{keywordtype}{char}    *s1,}
169\DoxyCodeLine{00493                         \textcolor{keyword}{const} \textcolor{keywordtype}{char}    *s2,}
170\DoxyCodeLine{00494                         \mbox{\hyperlink{group__model__details_structvrna__md__s}{vrna\_md\_t}}     *md\_p,}
171\DoxyCodeLine{00495                         \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}  options);}
172\DoxyCodeLine{00496 }
173\DoxyCodeLine{00497 }
174\DoxyCodeLine{00498 \textcolor{keywordtype}{int}}
175\DoxyCodeLine{00499 vrna\_fold\_compound\_prepare(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *fc,}
176\DoxyCodeLine{00500                            \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int}         options);}
177\DoxyCodeLine{00501 }
178\DoxyCodeLine{00502 }
179\DoxyCodeLine{00510 \textcolor{keywordtype}{void}}
180\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00511}\mbox{\hyperlink{group__fold__compound_ga576a077b418a9c3650e06f8e5d296fc2}{00511}} \mbox{\hyperlink{group__fold__compound_ga576a077b418a9c3650e06f8e5d296fc2}{vrna\_fold\_compound\_free}}(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *fc);}
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183\DoxyCodeLine{00531 \textcolor{keywordtype}{void}}
184\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00532}\mbox{\hyperlink{group__fold__compound_gafc44c76a1aacf61bfccb8cd698772b98}{00532}} \mbox{\hyperlink{group__fold__compound_gafc44c76a1aacf61bfccb8cd698772b98}{vrna\_fold\_compound\_add\_auxdata}}(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}}       *fc,}
185\DoxyCodeLine{00533                                \textcolor{keywordtype}{void}                       *data,}
186\DoxyCodeLine{00534                                \mbox{\hyperlink{group__fold__compound_ga7806651f51b195013839a218b3bbd5a3}{vrna\_callback\_free\_auxdata}} *f);}
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189\DoxyCodeLine{00552 \textcolor{keywordtype}{void}}
190\DoxyCodeLine{\Hypertarget{fold__compound_8h_source_l00553}\mbox{\hyperlink{group__fold__compound_ga680ddfe1e67d1459689b1e92c80b9c4c}{00553}} \mbox{\hyperlink{group__fold__compound_ga680ddfe1e67d1459689b1e92c80b9c4c}{vrna\_fold\_compound\_add\_callback}}(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}}            *fc,}
191\DoxyCodeLine{00554                                 \mbox{\hyperlink{group__fold__compound_gac86036fa8cad1108832335063243cdc8}{vrna\_callback\_recursion\_status}}  *f);}
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194\DoxyCodeLine{00561 \textcolor{preprocessor}{\#endif}}
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197