1 \hypertarget{2Dpfold_8h}{\section{2\-Dpfold.h}
2 \label{2Dpfold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/2\-Dpfold.\-h}}
6 00001 \textcolor{comment}{/*}
7 00002 \textcolor{comment}{ minimum free energy}
8 00003 \textcolor{comment}{ RNA secondary structure with}
9 00004 \textcolor{comment}{ basepair distance d to reference structure prediction}
10 00005 \textcolor{comment}{}
11 00006 \textcolor{comment}{*/}
12 00007 \textcolor{preprocessor}{#ifndef \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
13 00008 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define \_\_VIENNA\_RNA\_PACKAGE\_TWO\_D\_PF\_FOLD\_H\_\_}
14 00009 \textcolor{preprocessor}{}
15 00010 \textcolor{preprocessor}{#include "\hyperlink{data__structures_8h}{data\_structures.h}"}
17 00012 \textcolor{preprocessor}{#ifdef \_\_GNUC\_\_}
18 00013 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func \_\_attribute\_\_ ((deprecated))}
19 00014 \textcolor{preprocessor}{}\textcolor{preprocessor}{#else}
20 00015 \textcolor{preprocessor}{}\textcolor{preprocessor}{#define DEPRECATED(func) func}
21 00016 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
22 00017 \textcolor{preprocessor}{}
23 00042 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\_TwoDpfold\_variables}( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,
24 00043 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure1,
25 00044 \textcolor{keywordtype}{char} *structure2,
26 00045 \textcolor{keywordtype}{int} circ);
28 00059 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *\hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\_TwoDpfold\_variables\_from\_MFE}(
29 \hyperlink{structTwoDfold__vars}{TwoDfold\_vars} *mfe\_vars);
31 00071 \textcolor{keywordtype}{void} \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\_TwoDpfold\_variables}(
32 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars);
34 00094 \hyperlink{structTwoDpfold__solution}{TwoDpfold\_solution} *\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList}(
35 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars,
36 00095 \textcolor{keywordtype}{int} maxDistance1,
37 00096 \textcolor{keywordtype}{int} maxDistance2);
38 00097 \textcolor{comment}{/* End of group kl\_neighborhood\_pf */}
40 00123 \textcolor{keywordtype}{char} *\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_pbacktrack}(\hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars,
41 00124 \textcolor{keywordtype}{int} d1,
42 00125 \textcolor{keywordtype}{int} d2);
44 00146 \textcolor{keywordtype}{char} *\hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold\_pbacktrack5}( \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *vars,
45 00147 \textcolor{keywordtype}{int} d1,
46 00148 \textcolor{keywordtype}{int} d2,
47 00149 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length);
48 00150 \textcolor{comment}{/* End of group kl\_neighborhood\_stochbt */}
50 00158 DEPRECATED(FLT\_OR\_DBL **TwoDpfold(\hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *our\_variables,
51 00159 \textcolor{keywordtype}{int} maxDistance1,
52 00160 \textcolor{keywordtype}{int} maxDistance2));
54 00167 DEPRECATED(FLT\_OR\_DBL **TwoDpfold\_circ(
55 00168 \hyperlink{structTwoDpfold__vars}{TwoDpfold\_vars} *our\_variables,
56 00169 \textcolor{keywordtype}{int} maxDistance1,
57 00170 \textcolor{keywordtype}{int} maxDistance2));
60 00173 \textcolor{preprocessor}{#endif}