binaries/src/ViennaRNA/doc/latex/RNAstruct_8h.tex

   1 \hypertarget{RNAstruct_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.h File Reference}
   2 \label{RNAstruct_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\-R\-N\-Astruct.\-h}}
   3 }
   4
   5
   6 Parsing and Coarse Graining of Structures.
   7
   8
   9 \subsection*{Functions}
  10 \begin{DoxyCompactItemize}
  11 \item
  12 char $\ast$ \hyperlink{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}{b2\-H\-I\-T} (const char $\ast$structure)
  13 \begin{DoxyCompactList}\small\item\em Converts the full structure from bracket notation to the H\-I\-T notation including root. \end{DoxyCompactList}\item
  14 char $\ast$ \hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2\-C} (const char $\ast$structure)
  15 \begin{DoxyCompactList}\small\item\em Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. \end{DoxyCompactList}\item
  16 char $\ast$ \hyperlink{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}{b2\-Shapiro} (const char $\ast$structure)
  17 \begin{DoxyCompactList}\small\item\em Converts the full structure from bracket notation to the {\itshape weighted} coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers. \end{DoxyCompactList}\item
  18 char $\ast$ \hyperlink{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}{add\-\_\-root} (const char $\ast$structure)
  19 \begin{DoxyCompactList}\small\item\em Adds a root to an un-\/rooted tree in any except bracket notation. \end{DoxyCompactList}\item
  20 char $\ast$ \hyperlink{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}{expand\-\_\-\-Shapiro} (const char $\ast$coarse)
  21 \begin{DoxyCompactList}\small\item\em Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from \hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2\-C()}. \end{DoxyCompactList}\item
  22 char $\ast$ \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\-\_\-\-Full} (const char $\ast$structure)
  23 \begin{DoxyCompactList}\small\item\em Convert the full structure from bracket notation to the expanded notation including root. \end{DoxyCompactList}\item
  24 char $\ast$ \hyperlink{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}{unexpand\-\_\-\-Full} (const char $\ast$ffull)
  25 \begin{DoxyCompactList}\small\item\em Restores the bracket notation from an expanded full or H\-I\-T tree, that is any tree using only identifiers 'U' 'P' and 'R'. \end{DoxyCompactList}\item
  26 char $\ast$ \hyperlink{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}{unweight} (const char $\ast$wcoarse)
  27 \begin{DoxyCompactList}\small\item\em Strip weights from any weighted tree. \end{DoxyCompactList}\item
  28 void \hyperlink{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{unexpand\-\_\-aligned\-\_\-\-F} (char $\ast$align\mbox{[}2\mbox{]})
  29 \begin{DoxyCompactList}\small\item\em Converts two aligned structures in expanded notation. \end{DoxyCompactList}\item
  30 void \hyperlink{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}{parse\-\_\-structure} (const char $\ast$structure)
  31 \begin{DoxyCompactList}\small\item\em Collects a statistic of structure elements of the full structure in bracket notation. \end{DoxyCompactList}\end{DoxyCompactItemize}
  32 \subsection*{Variables}
  33 \begin{DoxyCompactItemize}
  34 \item
  35 \hypertarget{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{int \hyperlink{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{loop\-\_\-size} \mbox{[}S\-T\-R\-U\-C\mbox{]}}\label{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}
  36
  37 \begin{DoxyCompactList}\small\item\em contains a list of all loop sizes. loop\-\_\-size\mbox{[}0\mbox{]} contains the number of external bases. \end{DoxyCompactList}\item
  38 \hypertarget{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{int \hyperlink{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{helix\-\_\-size} \mbox{[}S\-T\-R\-U\-C\mbox{]}}\label{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}
  39
  40 \begin{DoxyCompactList}\small\item\em contains a list of all stack sizes. \end{DoxyCompactList}\item
  41 \hypertarget{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{int \hyperlink{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{loop\-\_\-degree} \mbox{[}S\-T\-R\-U\-C\mbox{]}}\label{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}
  42
  43 \begin{DoxyCompactList}\small\item\em contains the corresponding list of loop degrees. \end{DoxyCompactList}\item
  44 \hypertarget{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{int \hyperlink{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{loops}}\label{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}
  45
  46 \begin{DoxyCompactList}\small\item\em contains the number of loops ( and therefore of stacks ). \end{DoxyCompactList}\item
  47 \hypertarget{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{int \hyperlink{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{unpaired}}\label{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}
  48
  49 \begin{DoxyCompactList}\small\item\em contains the number of unpaired bases. \end{DoxyCompactList}\item
  50 \hypertarget{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{int \hyperlink{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{pairs}}\label{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}
  51
  52 \begin{DoxyCompactList}\small\item\em contains the number of base pairs in the last parsed structure. \end{DoxyCompactList}\end{DoxyCompactItemize}
  53
  54
  55 \subsection{Detailed Description}
  56 Parsing and Coarse Graining of Structures. \begin{DoxyVerb}Example:
  57 \end{DoxyVerb}
  58  \begin{DoxyVerb}*   .((..(((...)))..((..)))).   is the bracket or full tree
  59 *   becomes expanded:   - expand_Full() -
  60 *   ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)
  61 *   HIT:                - b2HIT() -
  62 *   ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)
  63 *   Coarse:             - b2C() -
  64 *   ((H)((H)M)R)
  65 *   becomes expanded:   - expand_Shapiro() -
  66 *   (((((H)S)((H)S)M)S)R)
  67 *   weighted Shapiro:   - b2Shapiro() -
  68 *   ((((((H3)S3)((H2)S2)M4)S2)E2)R)
  69 *  \end{DoxyVerb}
  70
  71
  72 \subsection{Function Documentation}
  73 \hypertarget{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!b2\-H\-I\-T@{b2\-H\-I\-T}}
  74 \index{b2\-H\-I\-T@{b2\-H\-I\-T}!RNAstruct.h@{R\-N\-Astruct.\-h}}
  75 \subsubsection[{b2\-H\-I\-T}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ b2\-H\-I\-T (
  76 \begin{DoxyParamCaption}
  77 \item[{const char $\ast$}]{structure}
  78 \end{DoxyParamCaption}
  79 )}}\label{RNAstruct_8h_a07b7e90e712559a1992fba3ac6d21bbd}
  80
  81
  82 Converts the full structure from bracket notation to the H\-I\-T notation including root.
  83
  84
  85 \begin{DoxyParams}{Parameters}
  86 {\em structure} & \\
  87 \hline
  88 \end{DoxyParams}
  89 \begin{DoxyReturn}{Returns}
  90
  91 \end{DoxyReturn}
  92 \hypertarget{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!b2\-C@{b2\-C}}
  93 \index{b2\-C@{b2\-C}!RNAstruct.h@{R\-N\-Astruct.\-h}}
  94 \subsubsection[{b2\-C}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ b2\-C (
  95 \begin{DoxyParamCaption}
  96 \item[{const char $\ast$}]{structure}
  97 \end{DoxyParamCaption}
  98 )}}\label{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}
  99
 100
 101 Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.
 102
 103
 104 \begin{DoxyParams}{Parameters}
 105 {\em structure} & \\
 106 \hline
 107 \end{DoxyParams}
 108 \begin{DoxyReturn}{Returns}
 109
 110 \end{DoxyReturn}
 111 \hypertarget{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!b2\-Shapiro@{b2\-Shapiro}}
 112 \index{b2\-Shapiro@{b2\-Shapiro}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 113 \subsubsection[{b2\-Shapiro}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ b2\-Shapiro (
 114 \begin{DoxyParamCaption}
 115 \item[{const char $\ast$}]{structure}
 116 \end{DoxyParamCaption}
 117 )}}\label{RNAstruct_8h_a5cd2feb367feeacad0c03cb7ddba5f10}
 118
 119
 120 Converts the full structure from bracket notation to the {\itshape weighted} coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers.
 121
 122
 123 \begin{DoxyParams}{Parameters}
 124 {\em structure} & \\
 125 \hline
 126 \end{DoxyParams}
 127 \begin{DoxyReturn}{Returns}
 128
 129 \end{DoxyReturn}
 130 \hypertarget{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!add\-\_\-root@{add\-\_\-root}}
 131 \index{add\-\_\-root@{add\-\_\-root}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 132 \subsubsection[{add\-\_\-root}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ add\-\_\-root (
 133 \begin{DoxyParamCaption}
 134 \item[{const char $\ast$}]{structure}
 135 \end{DoxyParamCaption}
 136 )}}\label{RNAstruct_8h_a880d33066dd95441e5fbb73c57ed1c3e}
 137
 138
 139 Adds a root to an un-\/rooted tree in any except bracket notation.
 140
 141
 142 \begin{DoxyParams}{Parameters}
 143 {\em structure} & \\
 144 \hline
 145 \end{DoxyParams}
 146 \begin{DoxyReturn}{Returns}
 147
 148 \end{DoxyReturn}
 149 \hypertarget{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!expand\-\_\-\-Shapiro@{expand\-\_\-\-Shapiro}}
 150 \index{expand\-\_\-\-Shapiro@{expand\-\_\-\-Shapiro}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 151 \subsubsection[{expand\-\_\-\-Shapiro}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ expand\-\_\-\-Shapiro (
 152 \begin{DoxyParamCaption}
 153 \item[{const char $\ast$}]{coarse}
 154 \end{DoxyParamCaption}
 155 )}}\label{RNAstruct_8h_abe3d815b420dc4553bfb23511198b4c6}
 156
 157
 158 Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from \hyperlink{RNAstruct_8h_a9c80d92391f2833549a8b6dac92233f0}{b2\-C()}.
 159
 160
 161 \begin{DoxyParams}{Parameters}
 162 {\em coarse} & \\
 163 \hline
 164 \end{DoxyParams}
 165 \begin{DoxyReturn}{Returns}
 166
 167 \end{DoxyReturn}
 168 \hypertarget{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!expand\-\_\-\-Full@{expand\-\_\-\-Full}}
 169 \index{expand\-\_\-\-Full@{expand\-\_\-\-Full}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 170 \subsubsection[{expand\-\_\-\-Full}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ expand\-\_\-\-Full (
 171 \begin{DoxyParamCaption}
 172 \item[{const char $\ast$}]{structure}
 173 \end{DoxyParamCaption}
 174 )}}\label{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}
 175
 176
 177 Convert the full structure from bracket notation to the expanded notation including root.
 178
 179
 180 \begin{DoxyParams}{Parameters}
 181 {\em structure} & \\
 182 \hline
 183 \end{DoxyParams}
 184 \begin{DoxyReturn}{Returns}
 185
 186 \end{DoxyReturn}
 187 \hypertarget{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!unexpand\-\_\-\-Full@{unexpand\-\_\-\-Full}}
 188 \index{unexpand\-\_\-\-Full@{unexpand\-\_\-\-Full}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 189 \subsubsection[{unexpand\-\_\-\-Full}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ unexpand\-\_\-\-Full (
 190 \begin{DoxyParamCaption}
 191 \item[{const char $\ast$}]{ffull}
 192 \end{DoxyParamCaption}
 193 )}}\label{RNAstruct_8h_a260c4b622093b76a883bf96628280de1}
 194
 195
 196 Restores the bracket notation from an expanded full or H\-I\-T tree, that is any tree using only identifiers 'U' 'P' and 'R'.
 197
 198
 199 \begin{DoxyParams}{Parameters}
 200 {\em ffull} & \\
 201 \hline
 202 \end{DoxyParams}
 203 \begin{DoxyReturn}{Returns}
 204
 205 \end{DoxyReturn}
 206 \hypertarget{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!unweight@{unweight}}
 207 \index{unweight@{unweight}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 208 \subsubsection[{unweight}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ unweight (
 209 \begin{DoxyParamCaption}
 210 \item[{const char $\ast$}]{wcoarse}
 211 \end{DoxyParamCaption}
 212 )}}\label{RNAstruct_8h_a09a80253ac7b6bae606871ba7c6e5136}
 213
 214
 215 Strip weights from any weighted tree.
 216
 217
 218 \begin{DoxyParams}{Parameters}
 219 {\em wcoarse} & \\
 220 \hline
 221 \end{DoxyParams}
 222 \begin{DoxyReturn}{Returns}
 223
 224 \end{DoxyReturn}
 225 \hypertarget{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!unexpand\-\_\-aligned\-\_\-\-F@{unexpand\-\_\-aligned\-\_\-\-F}}
 226 \index{unexpand\-\_\-aligned\-\_\-\-F@{unexpand\-\_\-aligned\-\_\-\-F}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 227 \subsubsection[{unexpand\-\_\-aligned\-\_\-\-F}]{\setlength{\rightskip}{0pt plus 5cm}void unexpand\-\_\-aligned\-\_\-\-F (
 228 \begin{DoxyParamCaption}
 229 \item[{char $\ast$}]{align\mbox{[}2\mbox{]}}
 230 \end{DoxyParamCaption}
 231 )}}\label{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}
 232
 233
 234 Converts two aligned structures in expanded notation.
 235
 236 Takes two aligned structures as produced by \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\-\_\-edit\-\_\-distance()} function back to bracket notation with '\-\_\-' as the gap character. The result overwrites the input.
 237
 238
 239 \begin{DoxyParams}{Parameters}
 240 {\em align} & \\
 241 \hline
 242 \end{DoxyParams}
 243 \hypertarget{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}{\index{R\-N\-Astruct.\-h@{R\-N\-Astruct.\-h}!parse\-\_\-structure@{parse\-\_\-structure}}
 244 \index{parse\-\_\-structure@{parse\-\_\-structure}!RNAstruct.h@{R\-N\-Astruct.\-h}}
 245 \subsubsection[{parse\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}void parse\-\_\-structure (
 246 \begin{DoxyParamCaption}
 247 \item[{const char $\ast$}]{structure}
 248 \end{DoxyParamCaption}
 249 )}}\label{RNAstruct_8h_a3c79042e6bf6f01706bf30ec9e69e8ac}
 250
 251
 252 Collects a statistic of structure elements of the full structure in bracket notation.
 253
 254 The function writes to the following global variables\-: \hyperlink{RNAstruct_8h_a3f31e0e48125601bfa57b52f8b038e8e}{loop\-\_\-size}, \hyperlink{RNAstruct_8h_aef14e2f8ab3f61e8e659ba6b9003b08a}{loop\-\_\-degree}, \hyperlink{RNAstruct_8h_a8218c0d581a3fba2a1a56a196abe19a5}{helix\-\_\-size}, \hyperlink{RNAstruct_8h_a439fcb9f8d4f9f4d2227fde5fbfecb30}{loops}, \hyperlink{RNAstruct_8h_a6341cbb704924824e0236c1dce791032}{pairs}, \hyperlink{RNAstruct_8h_add2f952597e02d66e1116a9d11d252d6}{unpaired}
 255
 256
 257 \begin{DoxyParams}{Parameters}
 258 {\em structure} & \\
 259 \hline
 260 \end{DoxyParams}
 261 \begin{DoxyReturn}{Returns}
 262
 263 \end{DoxyReturn}