1\hypertarget{perturbation__fold_8h_source}{}\doxysection{perturbation\+\_\+fold.\+h} 2\label{perturbation__fold_8h_source}\index{ViennaRNA/perturbation\_fold.h@{ViennaRNA/perturbation\_fold.h}} 3 4\begin{DoxyCode}{0} 5\DoxyCodeLine{00001 \textcolor{preprocessor}{\#ifndef VIENNA\_RNA\_PACKAGE\_PERTURBATION\_FOLD\_H}} 6\DoxyCodeLine{00002 \textcolor{preprocessor}{\#define VIENNA\_RNA\_PACKAGE\_PERTURBATION\_FOLD\_H}} 7\DoxyCodeLine{00003 } 8\DoxyCodeLine{00004 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{fold__compound_8h}{ViennaRNA/fold\_compound.h}}>}} 9\DoxyCodeLine{00005 } 10\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00024}\mbox{\hyperlink{group__perturbation_ga81e10993d1ae728e4e02022b33155a12}{00024}} \textcolor{preprocessor}{\#define VRNA\_OBJECTIVE\_FUNCTION\_QUADRATIC 0}} 11\DoxyCodeLine{00025 } 12\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00033}\mbox{\hyperlink{group__perturbation_gac070dfb9cafaeb14d5652bd9adf0f6b1}{00033}} \textcolor{preprocessor}{\#define VRNA\_OBJECTIVE\_FUNCTION\_ABSOLUTE 1}} 13\DoxyCodeLine{00034 } 14\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00040}\mbox{\hyperlink{group__perturbation_gae5126200d80dbb282f46083fffc606bf}{00040}} \textcolor{preprocessor}{\#define VRNA\_MINIMIZER\_DEFAULT 0}} 15\DoxyCodeLine{00041 } 16\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00049}\mbox{\hyperlink{group__perturbation_gab1d89db58e8c497795a5005f5dbc8c4a}{00049}} \textcolor{preprocessor}{\#define VRNA\_MINIMIZER\_CONJUGATE\_FR 1}} 17\DoxyCodeLine{00050 } 18\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00058}\mbox{\hyperlink{group__perturbation_ga5aaeafe1b0aa77a5cda18943ff94b02f}{00058}} \textcolor{preprocessor}{\#define VRNA\_MINIMIZER\_CONJUGATE\_PR 2}} 19\DoxyCodeLine{00059 } 20\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00067}\mbox{\hyperlink{group__perturbation_ga9be8a702cddf58235571ace11cc41b22}{00067}} \textcolor{preprocessor}{\#define VRNA\_MINIMIZER\_VECTOR\_BFGS 3}} 21\DoxyCodeLine{00068 } 22\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00076}\mbox{\hyperlink{group__perturbation_ga7b0a65c6c92fa1d8012383ba9d3dcb4f}{00076}} \textcolor{preprocessor}{\#define VRNA\_MINIMIZER\_VECTOR\_BFGS2 4}} 23\DoxyCodeLine{00077 } 24\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00085}\mbox{\hyperlink{group__perturbation_ga9ecd2144c2ebed7533233da3986521b0}{00085}} \textcolor{preprocessor}{\#define VRNA\_MINIMIZER\_STEEPEST\_DESCENT 5}} 25\DoxyCodeLine{00086 } 26\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00096}\mbox{\hyperlink{group__perturbation_gaa715397c7afd2d2955c315512a3d571a}{00096}} \textcolor{keyword}{typedef} void (*\mbox{\hyperlink{group__perturbation_gaa715397c7afd2d2955c315512a3d571a}{progress\_callback}})(\textcolor{keywordtype}{int} iteration,} 27\DoxyCodeLine{00097 \textcolor{keywordtype}{double} score,} 28\DoxyCodeLine{00098 \textcolor{keywordtype}{double} *epsilon);} 29\DoxyCodeLine{00099 } 30\DoxyCodeLine{\Hypertarget{perturbation__fold_8h_source_l00139}\mbox{\hyperlink{group__perturbation_gaa124bdc20d88001c38ade590c4bcc3c4}{00139}} \textcolor{keywordtype}{void} \mbox{\hyperlink{group__perturbation_gaa124bdc20d88001c38ade590c4bcc3c4}{vrna\_sc\_minimize\_pertubation}}(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *vc,} 31\DoxyCodeLine{00140 \textcolor{keyword}{const} \textcolor{keywordtype}{double} *q\_prob\_unpaired,} 32\DoxyCodeLine{00141 \textcolor{keywordtype}{int} objective\_function,} 33\DoxyCodeLine{00142 \textcolor{keywordtype}{double} sigma\_squared,} 34\DoxyCodeLine{00143 \textcolor{keywordtype}{double} tau\_squared,} 35\DoxyCodeLine{00144 \textcolor{keywordtype}{int} algorithm,} 36\DoxyCodeLine{00145 \textcolor{keywordtype}{int} sample\_size,} 37\DoxyCodeLine{00146 \textcolor{keywordtype}{double} *epsilon,} 38\DoxyCodeLine{00147 \textcolor{keywordtype}{double} initialStepSize,} 39\DoxyCodeLine{00148 \textcolor{keywordtype}{double} minStepSize,} 40\DoxyCodeLine{00149 \textcolor{keywordtype}{double} minImprovement,} 41\DoxyCodeLine{00150 \textcolor{keywordtype}{double} minimizerTolerance,} 42\DoxyCodeLine{00151 \mbox{\hyperlink{group__perturbation_gaa715397c7afd2d2955c315512a3d571a}{progress\_callback}} callback);} 43\DoxyCodeLine{00152 } 44\DoxyCodeLine{00153 } 45\DoxyCodeLine{00154 \textcolor{preprocessor}{\#endif}} 46 47\end{DoxyCode} 48