binaries/src/ViennaRNA/doc/latex/fold__vars_8h.tex

   1 \hypertarget{fold__vars_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.h File Reference}
   2 \label{fold__vars_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold\-\_\-vars.\-h}}
   3 }
   4
   5
   6 Here all all declarations of the global variables used throughout R\-N\-Alib.
   7
   8
   9 Include dependency graph for fold\-\_\-vars.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{fold__vars_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 This graph shows which files directly or indirectly include this file\-:
  18 \nopagebreak
  19 \begin{figure}[H]
  20 \begin{center}
  21 \leavevmode
  22 \includegraphics[width=350pt]{fold__vars_8h__dep__incl}
  23 \end{center}
  24 \end{figure}
  25 \subsection*{Functions}
  26 \begin{DoxyCompactItemize}
  27 \item
  28 void \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\-\_\-model\-\_\-details} (\hyperlink{structmodel__detailsT}{model\-\_\-details\-T} $\ast$md)
  29 \begin{DoxyCompactList}\small\item\em Set default model details. \end{DoxyCompactList}\end{DoxyCompactItemize}
  30 \subsection*{Variables}
  31 \begin{DoxyCompactItemize}
  32 \item
  33 \hypertarget{fold__vars_8h_a0afc287c2464866d94858c39175154af}{int \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}}\label{fold__vars_8h_a0afc287c2464866d94858c39175154af}
  34
  35 \begin{DoxyCompactList}\small\item\em Global switch to activate/deactivate folding with structure constraints. \end{DoxyCompactList}\item
  36 int \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs}
  37 \begin{DoxyCompactList}\small\item\em Global switch to avoid/allow helices of length 1. \end{DoxyCompactList}\item
  38 int \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}
  39 \begin{DoxyCompactList}\small\item\em Switch the energy model for dangling end contributions (0, 1, 2, 3) \end{DoxyCompactList}\item
  40 \hypertarget{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{int \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}}\label{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}
  41
  42 \begin{DoxyCompactList}\small\item\em Global switch to forbid/allow G\-U base pairs at all. \end{DoxyCompactList}\item
  43 \hypertarget{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{int \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}}\label{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}
  44
  45 \begin{DoxyCompactList}\small\item\em G\-U allowed only inside stacks if set to 1. \end{DoxyCompactList}\item
  46 int \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop}
  47 \begin{DoxyCompactList}\small\item\em Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;. \end{DoxyCompactList}\item
  48 int \hyperlink{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{energy\-\_\-set}
  49 \begin{DoxyCompactList}\small\item\em 0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter \end{DoxyCompactList}\item
  50 \hypertarget{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ}}\label{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}
  51
  52 \begin{DoxyCompactList}\small\item\em backward compatibility variable.. this does not effect anything \end{DoxyCompactList}\item
  53 \hypertarget{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{int \hyperlink{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}{csv}}\label{fold__vars_8h_af2763d55a74663a5e60652b8880baa5b}
  54
  55 \begin{DoxyCompactList}\small\item\em generate comma seperated output \end{DoxyCompactList}\item
  56 int \hyperlink{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{old\-Ali\-En}
  57 \item
  58 int \hyperlink{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{ribo}
  59 \item
  60 char $\ast$ \hyperlink{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{Ribosum\-File}
  61 \item
  62 char $\ast$ \hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards}
  63 \begin{DoxyCompactList}\small\item\em contains allowed non standard base pairs \end{DoxyCompactList}\item
  64 double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}
  65 \begin{DoxyCompactList}\small\item\em Rescale energy parameters to a temperature in deg\-C. \end{DoxyCompactList}\item
  66 int \hyperlink{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{james\-\_\-rule}
  67 \item
  68 int \hyperlink{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L}
  69 \item
  70 int \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point}
  71 \begin{DoxyCompactList}\small\item\em Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence. \end{DoxyCompactList}\item
  72 \hyperlink{structbondT}{bond\-T} $\ast$ \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair}
  73 \begin{DoxyCompactList}\small\item\em Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}. \end{DoxyCompactList}\item
  74 double $\ast$ \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr}
  75 \begin{DoxyCompactList}\small\item\em A pointer to the base pair probability matrix. \end{DoxyCompactList}\item
  76 int $\ast$ \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx}
  77 \begin{DoxyCompactList}\small\item\em index array to move through pr. \end{DoxyCompactList}\item
  78 double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale}
  79 \begin{DoxyCompactList}\small\item\em A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows. \end{DoxyCompactList}\item
  80 int \hyperlink{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{do\-\_\-backtrack}
  81 \begin{DoxyCompactList}\small\item\em do backtracking, i.\-e. compute secondary structures or base pair probabilities \end{DoxyCompactList}\item
  82 char \hyperlink{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{backtrack\-\_\-type}
  83 \begin{DoxyCompactList}\small\item\em A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()} \end{DoxyCompactList}\item
  84 \hypertarget{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{int \hyperlink{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}{gquad}}\label{fold__vars_8h_a25f2bdcdf56e813d288845484a13d704}
  85
  86 \begin{DoxyCompactList}\small\item\em Allow G-\/quadruplex formation. \end{DoxyCompactList}\end{DoxyCompactItemize}
  87
  88
  89 \subsection{Detailed Description}
  90 Here all all declarations of the global variables used throughout R\-N\-Alib.
  91
  92 \subsection{Function Documentation}
  93 \hypertarget{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!set\-\_\-model\-\_\-details@{set\-\_\-model\-\_\-details}}
  94 \index{set\-\_\-model\-\_\-details@{set\-\_\-model\-\_\-details}!fold_vars.h@{fold\-\_\-vars.\-h}}
  95 \subsubsection[{set\-\_\-model\-\_\-details}]{\setlength{\rightskip}{0pt plus 5cm}void set\-\_\-model\-\_\-details (
  96 \begin{DoxyParamCaption}
  97 \item[{{\bf model\-\_\-details\-T} $\ast$}]{md}
  98 \end{DoxyParamCaption}
  99 )}}\label{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}
 100
 101
 102 Set default model details.
 103
 104 Use this function if you wish to initialize a \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} data structure with its default values, i.\-e. the global model settings
 105
 106 \begin{DoxySeeAlso}{See Also}
 107
 108 \end{DoxySeeAlso}
 109
 110 \begin{DoxyParams}{Parameters}
 111 {\em md} & A pointer to the data structure that shall be initialized \\
 112 \hline
 113 \end{DoxyParams}
 114
 115
 116 \subsection{Variable Documentation}
 117 \hypertarget{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!no\-Lonely\-Pairs@{no\-Lonely\-Pairs}}
 118 \index{no\-Lonely\-Pairs@{no\-Lonely\-Pairs}!fold_vars.h@{fold\-\_\-vars.\-h}}
 119 \subsubsection[{no\-Lonely\-Pairs}]{\setlength{\rightskip}{0pt plus 5cm}int no\-Lonely\-Pairs}}\label{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}
 120
 121
 122 Global switch to avoid/allow helices of length 1.
 123
 124 Disallow all pairs which can only occur as lonely pairs (i.\-e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases. \hypertarget{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!dangles@{dangles}}
 125 \index{dangles@{dangles}!fold_vars.h@{fold\-\_\-vars.\-h}}
 126 \subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int dangles}}\label{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}
 127
 128
 129 Switch the energy model for dangling end contributions (0, 1, 2, 3)
 130
 131 If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} these checks are neglected. If \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles} is set to 2, all folding routines will follow this convention. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-\/axial stacking.\par
 132  If dangles = 3 co-\/axial stacking is explicitly included for adjacent helices in mutli-\/loops. The option affects only mfe folding and energy evaluation (\hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} and \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()}), as well as suboptimal folding (\hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()}) via re-\/evaluation of energies. Co-\/axial stacking with one intervening mismatch is not considered so far.
 133
 134 Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2 \hypertarget{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!tetra\-\_\-loop@{tetra\-\_\-loop}}
 135 \index{tetra\-\_\-loop@{tetra\-\_\-loop}!fold_vars.h@{fold\-\_\-vars.\-h}}
 136 \subsubsection[{tetra\-\_\-loop}]{\setlength{\rightskip}{0pt plus 5cm}int tetra\-\_\-loop}}\label{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}
 137
 138
 139 Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;.
 140
 141 default is 1. \hypertarget{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!energy\-\_\-set@{energy\-\_\-set}}
 142 \index{energy\-\_\-set@{energy\-\_\-set}!fold_vars.h@{fold\-\_\-vars.\-h}}
 143 \subsubsection[{energy\-\_\-set}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-set}}\label{fold__vars_8h_afb1ef1166da85092ae8a325e02dcae71}
 144
 145
 146 0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter
 147
 148 If set to 1 or 2\-: fold sequences from an artificial alphabet A\-B\-C\-D..., where A pairs B, C pairs D, etc. using either G\-C (1) or A\-U parameters (2); default is 0, you probably don't want to change it. \hypertarget{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!old\-Ali\-En@{old\-Ali\-En}}
 149 \index{old\-Ali\-En@{old\-Ali\-En}!fold_vars.h@{fold\-\_\-vars.\-h}}
 150 \subsubsection[{old\-Ali\-En}]{\setlength{\rightskip}{0pt plus 5cm}int old\-Ali\-En}}\label{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}
 151 use old alifold energies (with gaps) \hypertarget{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!ribo@{ribo}}
 152 \index{ribo@{ribo}!fold_vars.h@{fold\-\_\-vars.\-h}}
 153 \subsubsection[{ribo}]{\setlength{\rightskip}{0pt plus 5cm}int ribo}}\label{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}
 154 use ribosum matrices \hypertarget{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!Ribosum\-File@{Ribosum\-File}}
 155 \index{Ribosum\-File@{Ribosum\-File}!fold_vars.h@{fold\-\_\-vars.\-h}}
 156 \subsubsection[{Ribosum\-File}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Ribosum\-File}}\label{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}
 157 warning this variable will vanish in the future ribosums will be compiled in instead \hypertarget{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!nonstandards@{nonstandards}}
 158 \index{nonstandards@{nonstandards}!fold_vars.h@{fold\-\_\-vars.\-h}}
 159 \subsubsection[{nonstandards}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ nonstandards}}\label{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}
 160
 161
 162 contains allowed non standard base pairs
 163
 164 Lists additional base pairs that will be allowed to form in addition to G\-C, C\-G, A\-U, U\-A, G\-U and U\-G. Nonstandard base pairs are given a stacking energy of 0. \hypertarget{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!temperature@{temperature}}
 165 \index{temperature@{temperature}!fold_vars.h@{fold\-\_\-vars.\-h}}
 166 \subsubsection[{temperature}]{\setlength{\rightskip}{0pt plus 5cm}double temperature}}\label{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}
 167
 168
 169 Rescale energy parameters to a temperature in deg\-C.
 170
 171 Default is 37\-C. You have to call the update\-\_\-...\-\_\-params() functions after changing this parameter. \hypertarget{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!james\-\_\-rule@{james\-\_\-rule}}
 172 \index{james\-\_\-rule@{james\-\_\-rule}!fold_vars.h@{fold\-\_\-vars.\-h}}
 173 \subsubsection[{james\-\_\-rule}]{\setlength{\rightskip}{0pt plus 5cm}int james\-\_\-rule}}\label{fold__vars_8h_af349001ad3b4d008d0051d935b1b6261}
 174 interior loops of size 2 get energy 0.\-8\-Kcal and no mismatches, default 1 \hypertarget{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!log\-M\-L@{log\-M\-L}}
 175 \index{log\-M\-L@{log\-M\-L}!fold_vars.h@{fold\-\_\-vars.\-h}}
 176 \subsubsection[{log\-M\-L}]{\setlength{\rightskip}{0pt plus 5cm}int log\-M\-L}}\label{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}
 177 use logarithmic multiloop energy function \hypertarget{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!cut\-\_\-point@{cut\-\_\-point}}
 178 \index{cut\-\_\-point@{cut\-\_\-point}!fold_vars.h@{fold\-\_\-vars.\-h}}
 179 \subsubsection[{cut\-\_\-point}]{\setlength{\rightskip}{0pt plus 5cm}int cut\-\_\-point}}\label{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}
 180
 181
 182 Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence.
 183
 184 To evaluate the energy of a duplex structure (a structure formed by two strands), concatenate the to sequences and set it to the first base of the second strand in the concatenated sequence. The default value of -\/1 stands for single molecule folding. The cut\-\_\-point variable is also used by \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{P\-S\-\_\-rna\-\_\-plot()} and \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot()} to mark the chain break in postscript plots. \hypertarget{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!base\-\_\-pair@{base\-\_\-pair}}
 185 \index{base\-\_\-pair@{base\-\_\-pair}!fold_vars.h@{fold\-\_\-vars.\-h}}
 186 \subsubsection[{base\-\_\-pair}]{\setlength{\rightskip}{0pt plus 5cm}{\bf bond\-T}$\ast$ base\-\_\-pair}}\label{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}
 187
 188
 189 Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}.
 190
 191 base\-\_\-pair\mbox{[}0\mbox{]}.i contains the total number of pairs. \begin{DoxyRefDesc}{Deprecated}
 192 \item[\hyperlink{deprecated__deprecated000008}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc}
 193 \hypertarget{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!pr@{pr}}
 194 \index{pr@{pr}!fold_vars.h@{fold\-\_\-vars.\-h}}
 195 \subsubsection[{pr}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ pr}}\label{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}
 196
 197
 198 A pointer to the base pair probability matrix.
 199
 200 \begin{DoxyRefDesc}{Deprecated}
 201 \item[\hyperlink{deprecated__deprecated000009}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc}
 202 \hypertarget{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!iindx@{iindx}}
 203 \index{iindx@{iindx}!fold_vars.h@{fold\-\_\-vars.\-h}}
 204 \subsubsection[{iindx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ iindx}}\label{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}
 205
 206
 207 index array to move through pr.
 208
 209 The probability for base i and j to form a pair is in pr\mbox{[}iindx\mbox{[}i\mbox{]}-\/j\mbox{]}. \begin{DoxyRefDesc}{Deprecated}
 210 \item[\hyperlink{deprecated__deprecated000010}{Deprecated}]Do not use this variable anymore! \end{DoxyRefDesc}
 211 \hypertarget{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!pf\-\_\-scale@{pf\-\_\-scale}}
 212 \index{pf\-\_\-scale@{pf\-\_\-scale}!fold_vars.h@{fold\-\_\-vars.\-h}}
 213 \subsubsection[{pf\-\_\-scale}]{\setlength{\rightskip}{0pt plus 5cm}double pf\-\_\-scale}}\label{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}
 214
 215
 216 A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows.
 217
 218 Should be set to approximately $exp{((-F/kT)/length)}$, where $F$ is an estimate for the ensemble free energy, for example the minimum free energy. You must call \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\-\_\-pf\-\_\-params()} after changing this parameter.\par
 219  If pf\-\_\-scale is -\/1 (the default) , an estimate will be provided automatically when computing partition functions, e.\-g. \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} The automatic estimate is usually insufficient for sequences more than a few hundred bases long. \hypertarget{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!do\-\_\-backtrack@{do\-\_\-backtrack}}
 220 \index{do\-\_\-backtrack@{do\-\_\-backtrack}!fold_vars.h@{fold\-\_\-vars.\-h}}
 221 \subsubsection[{do\-\_\-backtrack}]{\setlength{\rightskip}{0pt plus 5cm}int do\-\_\-backtrack}}\label{fold__vars_8h_ad512b5dd4dbec60faccfe137bb474489}
 222
 223
 224 do backtracking, i.\-e. compute secondary structures or base pair probabilities
 225
 226 If 0, do not calculate pair probabilities in \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}; this is about twice as fast. Default is 1. \hypertarget{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}{\index{fold\-\_\-vars.\-h@{fold\-\_\-vars.\-h}!backtrack\-\_\-type@{backtrack\-\_\-type}}
 227 \index{backtrack\-\_\-type@{backtrack\-\_\-type}!fold_vars.h@{fold\-\_\-vars.\-h}}
 228 \subsubsection[{backtrack\-\_\-type}]{\setlength{\rightskip}{0pt plus 5cm}char backtrack\-\_\-type}}\label{fold__vars_8h_a83bdb43472a259c71e69fa9f70f420c3}
 229
 230
 231 A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()}
 232
 233 If set to 'C'\-: force (1,N) to be paired, 'M' fold as if the sequence were inside a multi-\/loop. Otherwise ('F') the usual mfe structure is computed.