binaries/src/ViennaRNA/doc/html/gquad_8h.html

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  70
  71 <p>Various functions related to G-quadruplex computations.
  72 <a href="#details">More...</a></p>
  73 <div class="textblock"><div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
  74   <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Include dependency graph for gquad.h:</div>
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  81 </div>
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  83 <p><a href="gquad_8h_source.html">Go to the source code of this file.</a></p>
  84 <table class="memberdecls">
  85 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  86 Functions</h2></td></tr>
  87 <tr class="memitem:a8b0784c14fa1208d0aebbebdc1318b7a"><td class="memItemLeft" align="right" valign="top">int *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a8b0784c14fa1208d0aebbebdc1318b7a">get_gquad_matrix</a> (short *S, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
  88 <tr class="memdesc:a8b0784c14fa1208d0aebbebdc1318b7a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes.  <a href="#a8b0784c14fa1208d0aebbebdc1318b7a"></a><br/></td></tr>
  89 <tr class="memitem:ae41763215b9c64d2a7b67f0df8a28078"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#ae41763215b9c64d2a7b67f0df8a28078">parse_gquad</a> (const char *struc, int *L, int l[3])</td></tr>
  90 <tr class="memitem:a54475a8eb898fa1e8af8ab5f5375f3be"><td class="memItemLeft" align="right" valign="top">PRIVATE int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a54475a8eb898fa1e8af8ab5f5375f3be">backtrack_GQuad_IntLoop</a> (int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
  91 <tr class="memitem:a118ec7289f1936bd810be7fe50b98212"><td class="memItemLeft" align="right" valign="top">PRIVATE int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gquad_8h.html#a118ec7289f1936bd810be7fe50b98212">backtrack_GQuad_IntLoop_L</a> (int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, <a class="el" href="structparamT.html">paramT</a> *P)</td></tr>
  92 </table>
  93 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
  94 <div class="textblock"><p>Various functions related to G-quadruplex computations. </p>
  95 </div><hr/><h2>Function Documentation</h2>
  96 <a class="anchor" id="a8b0784c14fa1208d0aebbebdc1318b7a"></a>
  97 <div class="memitem">
  98 <div class="memproto">
  99       <table class="memname">
 100         <tr>
 101           <td class="memname">int* get_gquad_matrix </td>
 102           <td>(</td>
 103           <td class="paramtype">short *&#160;</td>
 104           <td class="paramname"><em>S</em>, </td>
 105         </tr>
 106         <tr>
 107           <td class="paramkey"></td>
 108           <td></td>
 109           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&#160;</td>
 110           <td class="paramname"><em>P</em>&#160;</td>
 111         </tr>
 112         <tr>
 113           <td></td>
 114           <td>)</td>
 115           <td></td><td></td>
 116         </tr>
 117       </table>
 118 </div><div class="memdoc">
 119
 120 <p>Get a triangular matrix prefilled with minimum free energy contributions of G-quadruplexes. </p>
 121 <p>At each position ij in the matrix, the minimum free energy of any G-quadruplex delimited by i and j is stored. If no G-quadruplex formation is possible, the matrix element is set to INF. Access the elements in the matrix via matrix[indx[j]+i]. To get the integer array indx see get_jindx().</p>
 122 <dl class="section see"><dt>See also:</dt><dd>get_jindx(), encode_sequence()</dd></dl>
 123 <dl class="params"><dt>Parameters:</dt><dd>
 124   <table class="params">
 125     <tr><td class="paramname">S</td><td>The encoded sequence </td></tr>
 126     <tr><td class="paramname">P</td><td>A pointer to the data structure containing the precomputed energy contributions </td></tr>
 127   </table>
 128   </dd>
 129 </dl>
 130 <dl class="section return"><dt>Returns:</dt><dd>A pointer to the G-quadruplex contribution matrix </dd></dl>
 131
 132 </div>
 133 </div>
 134 <a class="anchor" id="ae41763215b9c64d2a7b67f0df8a28078"></a>
 135 <div class="memitem">
 136 <div class="memproto">
 137       <table class="memname">
 138         <tr>
 139           <td class="memname">int parse_gquad </td>
 140           <td>(</td>
 141           <td class="paramtype">const char *&#160;</td>
 142           <td class="paramname"><em>struc</em>, </td>
 143         </tr>
 144         <tr>
 145           <td class="paramkey"></td>
 146           <td></td>
 147           <td class="paramtype">int *&#160;</td>
 148           <td class="paramname"><em>L</em>, </td>
 149         </tr>
 150         <tr>
 151           <td class="paramkey"></td>
 152           <td></td>
 153           <td class="paramtype">int&#160;</td>
 154           <td class="paramname"><em>l</em>[3]&#160;</td>
 155         </tr>
 156         <tr>
 157           <td></td>
 158           <td>)</td>
 159           <td></td><td></td>
 160         </tr>
 161       </table>
 162 </div><div class="memdoc">
 163 <p>given a dot-bracket structure (possibly) containing gquads encoded by '+' signs, find first gquad, return end position or 0 if none found Upon return L and l[] contain the number of stacked layers, as well as the lengths of the linker regions. To parse a string with many gquads, call parse_gquad repeatedly e.g. end1 = parse_gquad(struc, &amp;L, l); ... ; end2 = parse_gquad(struc+end1, &amp;L, l); end2+=end1; ... ; end3 = parse_gquad(struc+end2, &amp;L, l); end3+=end2; ... ; </p>
 164
 165 </div>
 166 </div>
 167 <a class="anchor" id="a54475a8eb898fa1e8af8ab5f5375f3be"></a>
 168 <div class="memitem">
 169 <div class="memproto">
 170       <table class="memname">
 171         <tr>
 172           <td class="memname">PRIVATE int backtrack_GQuad_IntLoop </td>
 173           <td>(</td>
 174           <td class="paramtype">int&#160;</td>
 175           <td class="paramname"><em>c</em>, </td>
 176         </tr>
 177         <tr>
 178           <td class="paramkey"></td>
 179           <td></td>
 180           <td class="paramtype">int&#160;</td>
 181           <td class="paramname"><em>i</em>, </td>
 182         </tr>
 183         <tr>
 184           <td class="paramkey"></td>
 185           <td></td>
 186           <td class="paramtype">int&#160;</td>
 187           <td class="paramname"><em>j</em>, </td>
 188         </tr>
 189         <tr>
 190           <td class="paramkey"></td>
 191           <td></td>
 192           <td class="paramtype">int&#160;</td>
 193           <td class="paramname"><em>type</em>, </td>
 194         </tr>
 195         <tr>
 196           <td class="paramkey"></td>
 197           <td></td>
 198           <td class="paramtype">short *&#160;</td>
 199           <td class="paramname"><em>S</em>, </td>
 200         </tr>
 201         <tr>
 202           <td class="paramkey"></td>
 203           <td></td>
 204           <td class="paramtype">int *&#160;</td>
 205           <td class="paramname"><em>ggg</em>, </td>
 206         </tr>
 207         <tr>
 208           <td class="paramkey"></td>
 209           <td></td>
 210           <td class="paramtype">int *&#160;</td>
 211           <td class="paramname"><em>index</em>, </td>
 212         </tr>
 213         <tr>
 214           <td class="paramkey"></td>
 215           <td></td>
 216           <td class="paramtype">int *&#160;</td>
 217           <td class="paramname"><em>p</em>, </td>
 218         </tr>
 219         <tr>
 220           <td class="paramkey"></td>
 221           <td></td>
 222           <td class="paramtype">int *&#160;</td>
 223           <td class="paramname"><em>q</em>, </td>
 224         </tr>
 225         <tr>
 226           <td class="paramkey"></td>
 227           <td></td>
 228           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&#160;</td>
 229           <td class="paramname"><em>P</em>&#160;</td>
 230         </tr>
 231         <tr>
 232           <td></td>
 233           <td>)</td>
 234           <td></td><td></td>
 235         </tr>
 236       </table>
 237 </div><div class="memdoc">
 238 <p>backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j)</p>
 239 <dl class="params"><dt>Parameters:</dt><dd>
 240   <table class="params">
 241     <tr><td class="paramname">c</td><td>The total contribution the loop should resemble </td></tr>
 242     <tr><td class="paramname">i</td><td>position i of enclosing pair </td></tr>
 243     <tr><td class="paramname">j</td><td>position j of enclosing pair </td></tr>
 244     <tr><td class="paramname">type</td><td>base pair type of enclosing pair (must be reverse type) </td></tr>
 245     <tr><td class="paramname">S</td><td>integer encoded sequence </td></tr>
 246     <tr><td class="paramname">ggg</td><td>triangular matrix containing g-quadruplex contributions </td></tr>
 247     <tr><td class="paramname">index</td><td>the index for accessing the triangular matrix </td></tr>
 248     <tr><td class="paramname">p</td><td>here the 5' position of the gquad is stored </td></tr>
 249     <tr><td class="paramname">q</td><td>here the 3' position of the gquad is stored </td></tr>
 250     <tr><td class="paramname">P</td><td>the datastructure containing the precalculated contibutions</td></tr>
 251   </table>
 252   </dd>
 253 </dl>
 254 <dl class="section return"><dt>Returns:</dt><dd>1 on success, 0 if no gquad found </dd></dl>
 255
 256 </div>
 257 </div>
 258 <a class="anchor" id="a118ec7289f1936bd810be7fe50b98212"></a>
 259 <div class="memitem">
 260 <div class="memproto">
 261       <table class="memname">
 262         <tr>
 263           <td class="memname">PRIVATE int backtrack_GQuad_IntLoop_L </td>
 264           <td>(</td>
 265           <td class="paramtype">int&#160;</td>
 266           <td class="paramname"><em>c</em>, </td>
 267         </tr>
 268         <tr>
 269           <td class="paramkey"></td>
 270           <td></td>
 271           <td class="paramtype">int&#160;</td>
 272           <td class="paramname"><em>i</em>, </td>
 273         </tr>
 274         <tr>
 275           <td class="paramkey"></td>
 276           <td></td>
 277           <td class="paramtype">int&#160;</td>
 278           <td class="paramname"><em>j</em>, </td>
 279         </tr>
 280         <tr>
 281           <td class="paramkey"></td>
 282           <td></td>
 283           <td class="paramtype">int&#160;</td>
 284           <td class="paramname"><em>type</em>, </td>
 285         </tr>
 286         <tr>
 287           <td class="paramkey"></td>
 288           <td></td>
 289           <td class="paramtype">short *&#160;</td>
 290           <td class="paramname"><em>S</em>, </td>
 291         </tr>
 292         <tr>
 293           <td class="paramkey"></td>
 294           <td></td>
 295           <td class="paramtype">int **&#160;</td>
 296           <td class="paramname"><em>ggg</em>, </td>
 297         </tr>
 298         <tr>
 299           <td class="paramkey"></td>
 300           <td></td>
 301           <td class="paramtype">int&#160;</td>
 302           <td class="paramname"><em>maxdist</em>, </td>
 303         </tr>
 304         <tr>
 305           <td class="paramkey"></td>
 306           <td></td>
 307           <td class="paramtype">int *&#160;</td>
 308           <td class="paramname"><em>p</em>, </td>
 309         </tr>
 310         <tr>
 311           <td class="paramkey"></td>
 312           <td></td>
 313           <td class="paramtype">int *&#160;</td>
 314           <td class="paramname"><em>q</em>, </td>
 315         </tr>
 316         <tr>
 317           <td class="paramkey"></td>
 318           <td></td>
 319           <td class="paramtype"><a class="el" href="structparamT.html">paramT</a> *&#160;</td>
 320           <td class="paramname"><em>P</em>&#160;</td>
 321         </tr>
 322         <tr>
 323           <td></td>
 324           <td>)</td>
 325           <td></td><td></td>
 326         </tr>
 327       </table>
 328 </div><div class="memdoc">
 329 <p>backtrack an interior loop like enclosed g-quadruplex with closing pair (i,j) with underlying Lfold matrix</p>
 330 <dl class="params"><dt>Parameters:</dt><dd>
 331   <table class="params">
 332     <tr><td class="paramname">c</td><td>The total contribution the loop should resemble </td></tr>
 333     <tr><td class="paramname">i</td><td>position i of enclosing pair </td></tr>
 334     <tr><td class="paramname">j</td><td>position j of enclosing pair </td></tr>
 335     <tr><td class="paramname">type</td><td>base pair type of enclosing pair (must be reverse type) </td></tr>
 336     <tr><td class="paramname">S</td><td>integer encoded sequence </td></tr>
 337     <tr><td class="paramname">ggg</td><td>triangular matrix containing g-quadruplex contributions </td></tr>
 338     <tr><td class="paramname">p</td><td>here the 5' position of the gquad is stored </td></tr>
 339     <tr><td class="paramname">q</td><td>here the 3' position of the gquad is stored </td></tr>
 340     <tr><td class="paramname">P</td><td>the datastructure containing the precalculated contibutions</td></tr>
 341   </table>
 342   </dd>
 343 </dl>
 344 <dl class="section return"><dt>Returns:</dt><dd>1 on success, 0 if no gquad found </dd></dl>
 345
 346 </div>
 347 </div>
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