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}}
6 Here all all declarations of the global variables used throughout R\-N\-Alib.
9 Include dependency graph for fold\-\_\-vars.\-h\-:
14 \includegraphics[width=250pt]{fold__vars_8h__incl}
17 This graph shows which files directly or indirectly include this file\-:
22 \includegraphics[width=350pt]{fold__vars_8h__dep__incl}
25 \subsection*{Functions}
26 \begin{DoxyCompactItemize}
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}
33 \hypertarget{fold__vars_8h_a0afc287c2464866d94858c39175154af}{int \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}}\label{fold__vars_8h_a0afc287c2464866d94858c39175154af}
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}
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}
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}
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}
55 \begin{DoxyCompactList}\small\item\em generate comma seperated output \end{DoxyCompactList}\item
56 int \hyperlink{fold__vars_8h_ac408868ba00671cbc7d1d535105af045}{old\-Ali\-En}
58 int \hyperlink{fold__vars_8h_a0656afca1d2853f9ee6591172f5638de}{ribo}
60 char $\ast$ \hyperlink{fold__vars_8h_a5dbaa0cca2c8c82048a0f0e38e164944}{Ribosum\-File}
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}
68 int \hyperlink{fold__vars_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L}
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}
86 \begin{DoxyCompactList}\small\item\em Allow G-\/quadruplex formation. \end{DoxyCompactList}\end{DoxyCompactItemize}
89 \subsection{Detailed Description}
90 Here all all declarations of the global variables used throughout R\-N\-Alib.
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}
102 Set default model details.
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
106 \begin{DoxySeeAlso}{See Also}
110 \begin{DoxyParams}{Parameters}
111 {\em md} & A pointer to the data structure that shall be initialized \\
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}
122 Global switch to avoid/allow helices of length 1.
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}
129 Switch the energy model for dangling end contributions (0, 1, 2, 3)
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.
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}
139 Include special stabilizing energies for some tri-\/, tetra-\/ and hexa-\/loops;.
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}
146 0 = B\-P; 1=any mit G\-C; 2=any mit A\-U-\/parameter
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}
162 contains allowed non standard base pairs
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}
169 Rescale energy parameters to a temperature in deg\-C.
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}
182 Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence.
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}
189 Contains a list of base pairs after a call to \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}.
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}
198 A pointer to the base pair probability matrix.
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}
207 index array to move through pr.
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}
216 A scaling factor used by \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} to avoid overflows.
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}
224 do backtracking, i.\-e. compute secondary structures or base pair probabilities
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}
231 A backtrack array marker for \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()}
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.