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

   1 \hypertarget{group__eval}{\section{Energy evaluation}
   2 \label{group__eval}\index{Energy evaluation@{Energy evaluation}}
   3 }
   4
   5
   6 This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
   7
   8
   9 Collaboration diagram for Energy evaluation\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=336pt]{group__eval}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 float \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
  21 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A using global model detail settings. \end{DoxyCompactList}\item
  22 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)
  23 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
  24 float \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
  25 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item
  26 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)
  27 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item
  28 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)
  29 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
  30 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)
  31 \begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\end{DoxyCompactItemize}
  32 \subsection*{Variables}
  33 \begin{DoxyCompactItemize}
  34 \item
  35 \hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5}
  36
  37 \begin{DoxyCompactList}\small\item\em verbose info from energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\end{DoxyCompactItemize}
  38
  39
  40 \subsection{Detailed Description}
  41 This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
  42
  43 \subsection{Function Documentation}
  44 \hypertarget{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}}
  45 \index{energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}!Energy evaluation@{Energy evaluation}}
  46 \subsubsection[{energy\-\_\-of\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-structure (
  47 \begin{DoxyParamCaption}
  48 \item[{const char $\ast$}]{string, }
  49 \item[{const char $\ast$}]{structure, }
  50 \item[{int}]{verbosity\-\_\-level}
  51 \end{DoxyParamCaption}
  52 )}}\label{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}
  53
  54
  55 Calculate the free energy of an already folded R\-N\-A using global model detail settings.
  56
  57 If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
  58
  59 \begin{DoxyNote}{Note}
  60 Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()} for a completely threadsafe implementation.
  61 \end{DoxyNote}
  62 \begin{DoxySeeAlso}{See Also}
  63 \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}
  64 \end{DoxySeeAlso}
  65
  66 \begin{DoxyParams}{Parameters}
  67 {\em string} & R\-N\-A sequence \\
  68 \hline
  69 {\em structure} & secondary structure in dot-\/bracket notation \\
  70 \hline
  71 {\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\
  72 \hline
  73 \end{DoxyParams}
  74 \begin{DoxyReturn}{Returns}
  75 the free energy of the input structure given the input sequence in kcal/mol
  76 \end{DoxyReturn}
  77 \hypertarget{group__eval_gab5169ea4f72f250e43811463a33f4e40}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}}
  78 \index{energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}}
  79 \subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct\-\_\-par (
  80 \begin{DoxyParamCaption}
  81 \item[{const char $\ast$}]{string, }
  82 \item[{const char $\ast$}]{structure, }
  83 \item[{{\bf param\-T} $\ast$}]{parameters, }
  84 \item[{int}]{verbosity\-\_\-level}
  85 \end{DoxyParamCaption}
  86 )}}\label{group__eval_gab5169ea4f72f250e43811463a33f4e40}
  87
  88
  89 Calculate the free energy of an already folded R\-N\-A.
  90
  91 If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
  92
  93 \begin{DoxySeeAlso}{See Also}
  94 \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
  95 \end{DoxySeeAlso}
  96
  97 \begin{DoxyParams}{Parameters}
  98 {\em string} & R\-N\-A sequence in uppercase letters \\
  99 \hline
 100 {\em structure} & Secondary structure in dot-\/bracket notation \\
 101 \hline
 102 {\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
 103 \hline
 104 {\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
 105 \hline
 106 \end{DoxyParams}
 107 \begin{DoxyReturn}{Returns}
 108 The free energy of the input structure given the input sequence in kcal/mol
 109 \end{DoxyReturn}
 110 \hypertarget{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}}
 111 \index{energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}!Energy evaluation@{Energy evaluation}}
 112 \subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-structure (
 113 \begin{DoxyParamCaption}
 114 \item[{const char $\ast$}]{string, }
 115 \item[{const char $\ast$}]{structure, }
 116 \item[{int}]{verbosity\-\_\-level}
 117 \end{DoxyParamCaption}
 118 )}}\label{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}
 119
 120
 121 Calculate the free energy of an already folded circular R\-N\-A.
 122
 123 \begin{DoxyNote}{Note}
 124 Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()} for a completely threadsafe implementation.
 125 \end{DoxyNote}
 126 If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
 127
 128 \begin{DoxySeeAlso}{See Also}
 129 \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}
 130 \end{DoxySeeAlso}
 131
 132 \begin{DoxyParams}{Parameters}
 133 {\em string} & R\-N\-A sequence \\
 134 \hline
 135 {\em structure} & Secondary structure in dot-\/bracket notation \\
 136 \hline
 137 {\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
 138 \hline
 139 \end{DoxyParams}
 140 \begin{DoxyReturn}{Returns}
 141 The free energy of the input structure given the input sequence in kcal/mol
 142 \end{DoxyReturn}
 143 \hypertarget{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}}
 144 \index{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}}
 145 \subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par (
 146 \begin{DoxyParamCaption}
 147 \item[{const char $\ast$}]{string, }
 148 \item[{const char $\ast$}]{structure, }
 149 \item[{{\bf param\-T} $\ast$}]{parameters, }
 150 \item[{int}]{verbosity\-\_\-level}
 151 \end{DoxyParamCaption}
 152 )}}\label{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}
 153
 154
 155 Calculate the free energy of an already folded circular R\-N\-A.
 156
 157 If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
 158
 159 \begin{DoxySeeAlso}{See Also}
 160 \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
 161 \end{DoxySeeAlso}
 162
 163 \begin{DoxyParams}{Parameters}
 164 {\em string} & R\-N\-A sequence \\
 165 \hline
 166 {\em structure} & Secondary structure in dot-\/bracket notation \\
 167 \hline
 168 {\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
 169 \hline
 170 {\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
 171 \hline
 172 \end{DoxyParams}
 173 \begin{DoxyReturn}{Returns}
 174 The free energy of the input structure given the input sequence in kcal/mol
 175 \end{DoxyReturn}
 176 \hypertarget{group__eval_ga8831445966b761417e713360791299d8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}}
 177 \index{energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}!Energy evaluation@{Energy evaluation}}
 178 \subsubsection[{energy\-\_\-of\-\_\-structure\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-structure\-\_\-pt (
 179 \begin{DoxyParamCaption}
 180 \item[{const char $\ast$}]{string, }
 181 \item[{short $\ast$}]{ptable, }
 182 \item[{short $\ast$}]{s, }
 183 \item[{short $\ast$}]{s1, }
 184 \item[{int}]{verbosity\-\_\-level}
 185 \end{DoxyParamCaption}
 186 )}}\label{group__eval_ga8831445966b761417e713360791299d8}
 187
 188
 189 Calculate the free energy of an already folded R\-N\-A.
 190
 191 If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
 192
 193 \begin{DoxyNote}{Note}
 194 Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()} for a completely threadsafe implementation.
 195 \end{DoxyNote}
 196 \begin{DoxySeeAlso}{See Also}
 197 \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()}
 198 \end{DoxySeeAlso}
 199
 200 \begin{DoxyParams}{Parameters}
 201 {\em string} & R\-N\-A sequence \\
 202 \hline
 203 {\em ptable} & the pair table of the secondary structure \\
 204 \hline
 205 {\em s} & encoded R\-N\-A sequence \\
 206 \hline
 207 {\em s1} & encoded R\-N\-A sequence \\
 208 \hline
 209 {\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\
 210 \hline
 211 \end{DoxyParams}
 212 \begin{DoxyReturn}{Returns}
 213 the free energy of the input structure given the input sequence in 10kcal/mol
 214 \end{DoxyReturn}
 215 \hypertarget{group__eval_gada4701dd7519b29da75ceac147601f4e}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}}
 216 \index{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}!Energy evaluation@{Energy evaluation}}
 217 \subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par (
 218 \begin{DoxyParamCaption}
 219 \item[{const char $\ast$}]{string, }
 220 \item[{short $\ast$}]{ptable, }
 221 \item[{short $\ast$}]{s, }
 222 \item[{short $\ast$}]{s1, }
 223 \item[{{\bf param\-T} $\ast$}]{parameters, }
 224 \item[{int}]{verbosity\-\_\-level}
 225 \end{DoxyParamCaption}
 226 )}}\label{group__eval_gada4701dd7519b29da75ceac147601f4e}
 227
 228
 229 Calculate the free energy of an already folded R\-N\-A.
 230
 231 If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
 232
 233 \begin{DoxySeeAlso}{See Also}
 234 \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
 235 \end{DoxySeeAlso}
 236
 237 \begin{DoxyParams}{Parameters}
 238 {\em string} & R\-N\-A sequence in uppercase letters \\
 239 \hline
 240 {\em ptable} & The pair table of the secondary structure \\
 241 \hline
 242 {\em s} & Encoded R\-N\-A sequence \\
 243 \hline
 244 {\em s1} & Encoded R\-N\-A sequence \\
 245 \hline
 246 {\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
 247 \hline
 248 {\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
 249 \hline
 250 \end{DoxyParams}
 251 \begin{DoxyReturn}{Returns}
 252 The free energy of the input structure given the input sequence in 10kcal/mol
 253 \end{DoxyReturn}