binaries/src/ViennaRNA/doc/latex/fold_8h.tex

   1 \hypertarget{fold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.h File Reference}
   2 \label{fold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h}}
   3 }
   4
   5
   6 M\-F\-E calculations and energy evaluations for single R\-N\-A sequences.
   7
   8
   9 Include dependency graph for fold.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{fold_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 float \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par} (const char $\ast$sequence, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int is\-\_\-constrained, int is\-\_\-circular)
  21 \begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item
  22 float \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold} (const char $\ast$sequence, char $\ast$structure)
  23 \begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item
  24 float \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold} (const char $\ast$sequence, char $\ast$structure)
  25 \begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of a circular R\-N\-A sequence. \end{DoxyCompactList}\item
  26 float \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
  27 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A using global model detail settings. \end{DoxyCompactList}\item
  28 float \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
  29 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
  30 float \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
  31 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item
  32 float \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
  33 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item
  34 int \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, int verbosity\-\_\-level)
  35 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
  36 int \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
  37 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
  38 \hypertarget{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{void \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\-\_\-arrays} (void)}\label{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}
  39
  40 \begin{DoxyCompactList}\small\item\em Free arrays for mfe folding. \end{DoxyCompactList}\item
  41 void \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\-\_\-structure} (char $\ast$structure, \hyperlink{structbondT}{bond\-T} $\ast$bp, int length)
  42 \begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack. \end{DoxyCompactList}\item
  43 void \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\-\_\-zuker} (char $\ast$structure, \hyperlink{structbondT}{bond\-T} $\ast$bp, int length)
  44 \begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c. \end{DoxyCompactList}\item
  45 \hypertarget{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{void \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\-\_\-fold\-\_\-params} (void)}\label{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}
  46
  47 \begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
  48 float \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move} (const char $\ast$string, const char $\ast$structure, int m1, int m2)
  49 \begin{DoxyCompactList}\small\item\em Calculate energy of a move (closing or opening of a base pair) \end{DoxyCompactList}\item
  50 int \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy\-\_\-of\-\_\-move\-\_\-pt} (short $\ast$pt, short $\ast$s, short $\ast$s1, int m1, int m2)
  51 \begin{DoxyCompactList}\small\item\em Calculate energy of a move (closing or opening of a base pair) \end{DoxyCompactList}\item
  52 int \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop\-\_\-energy} (short $\ast$ptable, short $\ast$s, short $\ast$s1, int i)
  53 \begin{DoxyCompactList}\small\item\em Calculate energy of a loop. \end{DoxyCompactList}\item
  54 void \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\-\_\-plist\-\_\-from\-\_\-db} (\hyperlink{structplist}{plist} $\ast$$\ast$pl, const char $\ast$struc, float \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
  55 \begin{DoxyCompactList}\small\item\em Create a plist from a dot-\/bracket string. \end{DoxyCompactList}\item
  56 int \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{Loop\-Energy} (int n1, int n2, int type, int type\-\_\-2, int si1, int sj1, int sp1, int sq1)
  57 \item
  58 int \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{Hairpin\-E} (int size, int type, int si1, int sj1, const char $\ast$string)
  59 \item
  60 void \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\-\_\-fold} (int length)
  61 \item
  62 float \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct} (const char $\ast$string, const char $\ast$structure)
  63 \item
  64 int \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1)
  65 \item
  66 float \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct} (const char $\ast$string, const char $\ast$structure)
  67 \end{DoxyCompactItemize}
  68 \subsection*{Variables}
  69 \begin{DoxyCompactItemize}
  70 \item
  71 \hypertarget{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{int \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L}}\label{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}
  72
  73 \begin{DoxyCompactList}\small\item\em if nonzero use logarithmic M\-L energy in energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\item
  74 \hypertarget{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{int \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\-\_\-\-M\-L}}\label{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}
  75
  76 \begin{DoxyCompactList}\small\item\em do M\-L decomposition uniquely (for subopt) \end{DoxyCompactList}\item
  77 \hypertarget{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{int \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point}}\label{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}
  78
  79 \begin{DoxyCompactList}\small\item\em set to first pos of second seq for cofolding \end{DoxyCompactList}\item
  80 \hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5}
  81
  82 \begin{DoxyCompactList}\small\item\em verbose info from energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\end{DoxyCompactItemize}
  83
  84
  85 \subsection{Detailed Description}
  86 M\-F\-E calculations and energy evaluations for single R\-N\-A sequences. This file includes (almost) all function declarations within the R\-N\-Alib that are related to M\-F\-E folding...
  87
  88 \subsection{Function Documentation}
  89 \hypertarget{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{\index{fold.\-h@{fold.\-h}!parenthesis\-\_\-structure@{parenthesis\-\_\-structure}}
  90 \index{parenthesis\-\_\-structure@{parenthesis\-\_\-structure}!fold.h@{fold.\-h}}
  91 \subsubsection[{parenthesis\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}void parenthesis\-\_\-structure (
  92 \begin{DoxyParamCaption}
  93 \item[{char $\ast$}]{structure, }
  94 \item[{{\bf bond\-T} $\ast$}]{bp, }
  95 \item[{int}]{length}
  96 \end{DoxyParamCaption}
  97 )}}\label{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}
  98
  99
 100 Create a dot-\/backet/parenthesis structure from backtracking stack.
 101
 102 \begin{DoxyNote}{Note}
 103 This function is threadsafe
 104 \end{DoxyNote}
 105 \hypertarget{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{\index{fold.\-h@{fold.\-h}!parenthesis\-\_\-zuker@{parenthesis\-\_\-zuker}}
 106 \index{parenthesis\-\_\-zuker@{parenthesis\-\_\-zuker}!fold.h@{fold.\-h}}
 107 \subsubsection[{parenthesis\-\_\-zuker}]{\setlength{\rightskip}{0pt plus 5cm}void parenthesis\-\_\-zuker (
 108 \begin{DoxyParamCaption}
 109 \item[{char $\ast$}]{structure, }
 110 \item[{{\bf bond\-T} $\ast$}]{bp, }
 111 \item[{int}]{length}
 112 \end{DoxyParamCaption}
 113 )}}\label{fold_8h_a325f3835c68f34fe833b2b7a5828857f}
 114
 115
 116 Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c.
 117
 118 \begin{DoxyNote}{Note}
 119 This function is threadsafe
 120 \end{DoxyNote}
 121 \hypertarget{fold_8h_a539ecaed89730f7644c202f304d7529b}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-move@{energy\-\_\-of\-\_\-move}}
 122 \index{energy\-\_\-of\-\_\-move@{energy\-\_\-of\-\_\-move}!fold.h@{fold.\-h}}
 123 \subsubsection[{energy\-\_\-of\-\_\-move}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-move (
 124 \begin{DoxyParamCaption}
 125 \item[{const char $\ast$}]{string, }
 126 \item[{const char $\ast$}]{structure, }
 127 \item[{int}]{m1, }
 128 \item[{int}]{m2}
 129 \end{DoxyParamCaption}
 130 )}}\label{fold_8h_a539ecaed89730f7644c202f304d7529b}
 131
 132
 133 Calculate energy of a move (closing or opening of a base pair)
 134
 135 If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
 136
 137 \begin{DoxySeeAlso}{See Also}
 138 \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move()}
 139 \end{DoxySeeAlso}
 140
 141 \begin{DoxyParams}{Parameters}
 142 {\em string} & R\-N\-A sequence \\
 143 \hline
 144 {\em structure} & secondary structure in dot-\/bracket notation \\
 145 \hline
 146 {\em m1} & first coordinate of base pair \\
 147 \hline
 148 {\em m2} & second coordinate of base pair \\
 149 \hline
 150 \end{DoxyParams}
 151 \begin{DoxyReturn}{Returns}
 152 energy change of the move in kcal/mol
 153 \end{DoxyReturn}
 154 \hypertarget{fold_8h_a49e0ee561be69faf0568213546f6a53f}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-move\-\_\-pt@{energy\-\_\-of\-\_\-move\-\_\-pt}}
 155 \index{energy\-\_\-of\-\_\-move\-\_\-pt@{energy\-\_\-of\-\_\-move\-\_\-pt}!fold.h@{fold.\-h}}
 156 \subsubsection[{energy\-\_\-of\-\_\-move\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-move\-\_\-pt (
 157 \begin{DoxyParamCaption}
 158 \item[{short $\ast$}]{pt, }
 159 \item[{short $\ast$}]{s, }
 160 \item[{short $\ast$}]{s1, }
 161 \item[{int}]{m1, }
 162 \item[{int}]{m2}
 163 \end{DoxyParamCaption}
 164 )}}\label{fold_8h_a49e0ee561be69faf0568213546f6a53f}
 165
 166
 167 Calculate energy of a move (closing or opening of a base pair)
 168
 169 If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
 170
 171 \begin{DoxySeeAlso}{See Also}
 172 \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move()}
 173 \end{DoxySeeAlso}
 174
 175 \begin{DoxyParams}{Parameters}
 176 {\em pt} & the pair table of the secondary structure \\
 177 \hline
 178 {\em s} & encoded R\-N\-A sequence \\
 179 \hline
 180 {\em s1} & encoded R\-N\-A sequence \\
 181 \hline
 182 {\em m1} & first coordinate of base pair \\
 183 \hline
 184 {\em m2} & second coordinate of base pair \\
 185 \hline
 186 \end{DoxyParams}
 187 \begin{DoxyReturn}{Returns}
 188 energy change of the move in 10cal/mol
 189 \end{DoxyReturn}
 190 \hypertarget{fold_8h_a507d4fd93f4b398d793ba2402731388d}{\index{fold.\-h@{fold.\-h}!loop\-\_\-energy@{loop\-\_\-energy}}
 191 \index{loop\-\_\-energy@{loop\-\_\-energy}!fold.h@{fold.\-h}}
 192 \subsubsection[{loop\-\_\-energy}]{\setlength{\rightskip}{0pt plus 5cm}int loop\-\_\-energy (
 193 \begin{DoxyParamCaption}
 194 \item[{short $\ast$}]{ptable, }
 195 \item[{short $\ast$}]{s, }
 196 \item[{short $\ast$}]{s1, }
 197 \item[{int}]{i}
 198 \end{DoxyParamCaption}
 199 )}}\label{fold_8h_a507d4fd93f4b398d793ba2402731388d}
 200
 201
 202 Calculate energy of a loop.
 203
 204
 205 \begin{DoxyParams}{Parameters}
 206 {\em ptable} & the pair table of the secondary structure \\
 207 \hline
 208 {\em s} & encoded R\-N\-A sequence \\
 209 \hline
 210 {\em s1} & encoded R\-N\-A sequence \\
 211 \hline
 212 {\em i} & position of covering base pair \\
 213 \hline
 214 \end{DoxyParams}
 215 \begin{DoxyReturn}{Returns}
 216 free energy of the loop in 10cal/mol
 217 \end{DoxyReturn}
 218 \hypertarget{fold_8h_adaa59b81664e2e36cb9932e891558fae}{\index{fold.\-h@{fold.\-h}!assign\-\_\-plist\-\_\-from\-\_\-db@{assign\-\_\-plist\-\_\-from\-\_\-db}}
 219 \index{assign\-\_\-plist\-\_\-from\-\_\-db@{assign\-\_\-plist\-\_\-from\-\_\-db}!fold.h@{fold.\-h}}
 220 \subsubsection[{assign\-\_\-plist\-\_\-from\-\_\-db}]{\setlength{\rightskip}{0pt plus 5cm}void assign\-\_\-plist\-\_\-from\-\_\-db (
 221 \begin{DoxyParamCaption}
 222 \item[{{\bf plist} $\ast$$\ast$}]{pl, }
 223 \item[{const char $\ast$}]{struc, }
 224 \item[{float}]{pr}
 225 \end{DoxyParamCaption}
 226 )}}\label{fold_8h_adaa59b81664e2e36cb9932e891558fae}
 227
 228
 229 Create a plist from a dot-\/bracket string.
 230
 231 The dot-\/bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.
 232
 233 The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries
 234
 235 This function is threadsafe
 236
 237
 238 \begin{DoxyParams}{Parameters}
 239 {\em pl} & A pointer to the plist that is to be created \\
 240 \hline
 241 {\em struc} & The secondary structure in dot-\/bracket notation \\
 242 \hline
 243 {\em pr} & The probability for each base pair \\
 244 \hline
 245 \end{DoxyParams}
 246 \hypertarget{fold_8h_a2163034a25c6115d894b199e97e03f6c}{\index{fold.\-h@{fold.\-h}!Loop\-Energy@{Loop\-Energy}}
 247 \index{Loop\-Energy@{Loop\-Energy}!fold.h@{fold.\-h}}
 248 \subsubsection[{Loop\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}int Loop\-Energy (
 249 \begin{DoxyParamCaption}
 250 \item[{int}]{n1, }
 251 \item[{int}]{n2, }
 252 \item[{int}]{type, }
 253 \item[{int}]{type\-\_\-2, }
 254 \item[{int}]{si1, }
 255 \item[{int}]{sj1, }
 256 \item[{int}]{sp1, }
 257 \item[{int}]{sq1}
 258 \end{DoxyParamCaption}
 259 )}}\label{fold_8h_a2163034a25c6115d894b199e97e03f6c}
 260 \begin{DoxyRefDesc}{Deprecated}
 261 \item[\hyperlink{deprecated__deprecated000002}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\-\_\-\-Int\-Loop()} instead!\} \end{DoxyRefDesc}
 262 \hypertarget{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{\index{fold.\-h@{fold.\-h}!Hairpin\-E@{Hairpin\-E}}
 263 \index{Hairpin\-E@{Hairpin\-E}!fold.h@{fold.\-h}}
 264 \subsubsection[{Hairpin\-E}]{\setlength{\rightskip}{0pt plus 5cm}int Hairpin\-E (
 265 \begin{DoxyParamCaption}
 266 \item[{int}]{size, }
 267 \item[{int}]{type, }
 268 \item[{int}]{si1, }
 269 \item[{int}]{sj1, }
 270 \item[{const char $\ast$}]{string}
 271 \end{DoxyParamCaption}
 272 )}}\label{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}
 273 \begin{DoxyRefDesc}{Deprecated}
 274 \item[\hyperlink{deprecated__deprecated000003}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\-\_\-\-Hairpin()} instead!\} \end{DoxyRefDesc}
 275 \hypertarget{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{\index{fold.\-h@{fold.\-h}!initialize\-\_\-fold@{initialize\-\_\-fold}}
 276 \index{initialize\-\_\-fold@{initialize\-\_\-fold}!fold.h@{fold.\-h}}
 277 \subsubsection[{initialize\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void initialize\-\_\-fold (
 278 \begin{DoxyParamCaption}
 279 \item[{int}]{length}
 280 \end{DoxyParamCaption}
 281 )}}\label{fold_8h_ac3f0a28d9cb609d388b155445073fd20}
 282 Allocate arrays for folding\par
 283  \begin{DoxyRefDesc}{Deprecated}
 284 \item[\hyperlink{deprecated__deprecated000004}{Deprecated}]\{This function is deprecated and will be removed soon!\}\end{DoxyRefDesc}
 285 \hypertarget{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-struct@{energy\-\_\-of\-\_\-struct}}
 286 \index{energy\-\_\-of\-\_\-struct@{energy\-\_\-of\-\_\-struct}!fold.h@{fold.\-h}}
 287 \subsubsection[{energy\-\_\-of\-\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct (
 288 \begin{DoxyParamCaption}
 289 \item[{const char $\ast$}]{string, }
 290 \item[{const char $\ast$}]{structure}
 291 \end{DoxyParamCaption}
 292 )}}\label{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}
 293 Calculate the free energy of an already folded R\-N\-A
 294
 295 \begin{DoxyNote}{Note}
 296 This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par
 297
 298 \end{DoxyNote}
 299 \begin{DoxyRefDesc}{Deprecated}
 300 \item[\hyperlink{deprecated__deprecated000005}{Deprecated}]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()} instead!\end{DoxyRefDesc}
 301
 302
 303 \begin{DoxySeeAlso}{See Also}
 304 \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure}, \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct()}, \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt()}
 305 \end{DoxySeeAlso}
 306
 307 \begin{DoxyParams}{Parameters}
 308 {\em string} & R\-N\-A sequence \\
 309 \hline
 310 {\em structure} & secondary structure in dot-\/bracket notation \\
 311 \hline
 312 \end{DoxyParams}
 313 \begin{DoxyReturn}{Returns}
 314 the free energy of the input structure given the input sequence in kcal/mol
 315 \end{DoxyReturn}
 316 \hypertarget{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-struct\-\_\-pt@{energy\-\_\-of\-\_\-struct\-\_\-pt}}
 317 \index{energy\-\_\-of\-\_\-struct\-\_\-pt@{energy\-\_\-of\-\_\-struct\-\_\-pt}!fold.h@{fold.\-h}}
 318 \subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt (
 319 \begin{DoxyParamCaption}
 320 \item[{const char $\ast$}]{string, }
 321 \item[{short $\ast$}]{ptable, }
 322 \item[{short $\ast$}]{s, }
 323 \item[{short $\ast$}]{s1}
 324 \end{DoxyParamCaption}
 325 )}}\label{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}
 326 Calculate the free energy of an already folded R\-N\-A
 327
 328 \begin{DoxyNote}{Note}
 329 This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par
 330
 331 \end{DoxyNote}
 332 \begin{DoxyRefDesc}{Deprecated}
 333 \item[\hyperlink{deprecated__deprecated000006}{Deprecated}]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()} instead!\end{DoxyRefDesc}
 334
 335
 336 \begin{DoxySeeAlso}{See Also}
 337 \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()}
 338 \end{DoxySeeAlso}
 339
 340 \begin{DoxyParams}{Parameters}
 341 {\em string} & R\-N\-A sequence \\
 342 \hline
 343 {\em ptable} & the pair table of the secondary structure \\
 344 \hline
 345 {\em s} & encoded R\-N\-A sequence \\
 346 \hline
 347 {\em s1} & encoded R\-N\-A sequence \\
 348 \hline
 349 \end{DoxyParams}
 350 \begin{DoxyReturn}{Returns}
 351 the free energy of the input structure given the input sequence in 10kcal/mol
 352 \end{DoxyReturn}
 353 \hypertarget{fold_8h_a657222e2758c46bf13b416ef3032e417}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-circ\-\_\-struct@{energy\-\_\-of\-\_\-circ\-\_\-struct}}
 354 \index{energy\-\_\-of\-\_\-circ\-\_\-struct@{energy\-\_\-of\-\_\-circ\-\_\-struct}!fold.h@{fold.\-h}}
 355 \subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct (
 356 \begin{DoxyParamCaption}
 357 \item[{const char $\ast$}]{string, }
 358 \item[{const char $\ast$}]{structure}
 359 \end{DoxyParamCaption}
 360 )}}\label{fold_8h_a657222e2758c46bf13b416ef3032e417}
 361 Calculate the free energy of an already folded circular R\-N\-A
 362
 363 \begin{DoxyNote}{Note}
 364 This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par
 365
 366 \end{DoxyNote}
 367 \begin{DoxyRefDesc}{Deprecated}
 368 \item[\hyperlink{deprecated__deprecated000007}{Deprecated}]This function is deprecated and should not be used in future programs Use \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()} instead!\end{DoxyRefDesc}
 369
 370
 371 \begin{DoxySeeAlso}{See Also}
 372 \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct()}, \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt()}
 373 \end{DoxySeeAlso}
 374
 375 \begin{DoxyParams}{Parameters}
 376 {\em string} & R\-N\-A sequence \\
 377 \hline
 378 {\em structure} & secondary structure in dot-\/bracket notation \\
 379 \hline
 380 \end{DoxyParams}
 381 \begin{DoxyReturn}{Returns}
 382 the free energy of the input structure given the input sequence in kcal/mol
 383 \end{DoxyReturn}