binaries/src/ViennaRNA/doc/html/RNAstruct_8h.html

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  65 <a href="#func-members">Functions</a> &#124;
  66 <a href="#var-members">Variables</a>  </div>
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  68 <div class="title">RNAstruct.h File Reference</div>  </div>
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  70 <div class="contents">
  71
  72 <p>Parsing and Coarse Graining of Structures.
  73 <a href="#details">More...</a></p>
  74
  75 <p><a href="RNAstruct_8h_source.html">Go to the source code of this file.</a></p>
  76 <table class="memberdecls">
  77 <tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
  78 Functions</h2></td></tr>
  79 <tr class="memitem:a07b7e90e712559a1992fba3ac6d21bbd"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a07b7e90e712559a1992fba3ac6d21bbd">b2HIT</a> (const char *structure)</td></tr>
  80 <tr class="memdesc:a07b7e90e712559a1992fba3ac6d21bbd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Converts the full structure from bracket notation to the HIT notation including root.  <a href="#a07b7e90e712559a1992fba3ac6d21bbd"></a><br/></td></tr>
  81 <tr class="memitem:a9c80d92391f2833549a8b6dac92233f0"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0">b2C</a> (const char *structure)</td></tr>
  82 <tr class="memdesc:a9c80d92391f2833549a8b6dac92233f0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.  <a href="#a9c80d92391f2833549a8b6dac92233f0"></a><br/></td></tr>
  83 <tr class="memitem:a5cd2feb367feeacad0c03cb7ddba5f10"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a5cd2feb367feeacad0c03cb7ddba5f10">b2Shapiro</a> (const char *structure)</td></tr>
  84 <tr class="memdesc:a5cd2feb367feeacad0c03cb7ddba5f10"><td class="mdescLeft">&#160;</td><td class="mdescRight">Converts the full structure from bracket notation to the <em>weighted</em> coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers.  <a href="#a5cd2feb367feeacad0c03cb7ddba5f10"></a><br/></td></tr>
  85 <tr class="memitem:a880d33066dd95441e5fbb73c57ed1c3e"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a880d33066dd95441e5fbb73c57ed1c3e">add_root</a> (const char *structure)</td></tr>
  86 <tr class="memdesc:a880d33066dd95441e5fbb73c57ed1c3e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Adds a root to an un-rooted tree in any except bracket notation.  <a href="#a880d33066dd95441e5fbb73c57ed1c3e"></a><br/></td></tr>
  87 <tr class="memitem:abe3d815b420dc4553bfb23511198b4c6"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#abe3d815b420dc4553bfb23511198b4c6">expand_Shapiro</a> (const char *coarse)</td></tr>
  88 <tr class="memdesc:abe3d815b420dc4553bfb23511198b4c6"><td class="mdescLeft">&#160;</td><td class="mdescRight">Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from <a class="el" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0" title="Converts the full structure from bracket notation to the a coarse grained notation using the &#39;H&#39; &#39;B&#39; ...">b2C()</a>.  <a href="#abe3d815b420dc4553bfb23511198b4c6"></a><br/></td></tr>
  89 <tr class="memitem:a78d73cd54a068ef2812812771cdddc6f"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f">expand_Full</a> (const char *structure)</td></tr>
  90 <tr class="memdesc:a78d73cd54a068ef2812812771cdddc6f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Convert the full structure from bracket notation to the expanded notation including root.  <a href="#a78d73cd54a068ef2812812771cdddc6f"></a><br/></td></tr>
  91 <tr class="memitem:a260c4b622093b76a883bf96628280de1"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a260c4b622093b76a883bf96628280de1">unexpand_Full</a> (const char *ffull)</td></tr>
  92 <tr class="memdesc:a260c4b622093b76a883bf96628280de1"><td class="mdescLeft">&#160;</td><td class="mdescRight">Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'.  <a href="#a260c4b622093b76a883bf96628280de1"></a><br/></td></tr>
  93 <tr class="memitem:a09a80253ac7b6bae606871ba7c6e5136"><td class="memItemLeft" align="right" valign="top">char *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a09a80253ac7b6bae606871ba7c6e5136">unweight</a> (const char *wcoarse)</td></tr>
  94 <tr class="memdesc:a09a80253ac7b6bae606871ba7c6e5136"><td class="mdescLeft">&#160;</td><td class="mdescRight">Strip weights from any weighted tree.  <a href="#a09a80253ac7b6bae606871ba7c6e5136"></a><br/></td></tr>
  95 <tr class="memitem:a1054c4477d53b31d79d4cb132100e87a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a">unexpand_aligned_F</a> (char *align[2])</td></tr>
  96 <tr class="memdesc:a1054c4477d53b31d79d4cb132100e87a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Converts two aligned structures in expanded notation.  <a href="#a1054c4477d53b31d79d4cb132100e87a"></a><br/></td></tr>
  97 <tr class="memitem:a3c79042e6bf6f01706bf30ec9e69e8ac"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a3c79042e6bf6f01706bf30ec9e69e8ac">parse_structure</a> (const char *structure)</td></tr>
  98 <tr class="memdesc:a3c79042e6bf6f01706bf30ec9e69e8ac"><td class="mdescLeft">&#160;</td><td class="mdescRight">Collects a statistic of structure elements of the full structure in bracket notation.  <a href="#a3c79042e6bf6f01706bf30ec9e69e8ac"></a><br/></td></tr>
  99 </table><table class="memberdecls">
 100 <tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
 101 Variables</h2></td></tr>
 102 <tr class="memitem:a3f31e0e48125601bfa57b52f8b038e8e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3f31e0e48125601bfa57b52f8b038e8e"></a>
 103 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a3f31e0e48125601bfa57b52f8b038e8e">loop_size</a> [STRUC]</td></tr>
 104 <tr class="memdesc:a3f31e0e48125601bfa57b52f8b038e8e"><td class="mdescLeft">&#160;</td><td class="mdescRight">contains a list of all loop sizes. loop_size[0] contains the number of external bases. <br/></td></tr>
 105 <tr class="memitem:a8218c0d581a3fba2a1a56a196abe19a5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a8218c0d581a3fba2a1a56a196abe19a5"></a>
 106 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a8218c0d581a3fba2a1a56a196abe19a5">helix_size</a> [STRUC]</td></tr>
 107 <tr class="memdesc:a8218c0d581a3fba2a1a56a196abe19a5"><td class="mdescLeft">&#160;</td><td class="mdescRight">contains a list of all stack sizes. <br/></td></tr>
 108 <tr class="memitem:aef14e2f8ab3f61e8e659ba6b9003b08a"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aef14e2f8ab3f61e8e659ba6b9003b08a"></a>
 109 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#aef14e2f8ab3f61e8e659ba6b9003b08a">loop_degree</a> [STRUC]</td></tr>
 110 <tr class="memdesc:aef14e2f8ab3f61e8e659ba6b9003b08a"><td class="mdescLeft">&#160;</td><td class="mdescRight">contains the corresponding list of loop degrees. <br/></td></tr>
 111 <tr class="memitem:a439fcb9f8d4f9f4d2227fde5fbfecb30"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a439fcb9f8d4f9f4d2227fde5fbfecb30"></a>
 112 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a439fcb9f8d4f9f4d2227fde5fbfecb30">loops</a></td></tr>
 113 <tr class="memdesc:a439fcb9f8d4f9f4d2227fde5fbfecb30"><td class="mdescLeft">&#160;</td><td class="mdescRight">contains the number of loops ( and therefore of stacks ). <br/></td></tr>
 114 <tr class="memitem:add2f952597e02d66e1116a9d11d252d6"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="add2f952597e02d66e1116a9d11d252d6"></a>
 115 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#add2f952597e02d66e1116a9d11d252d6">unpaired</a></td></tr>
 116 <tr class="memdesc:add2f952597e02d66e1116a9d11d252d6"><td class="mdescLeft">&#160;</td><td class="mdescRight">contains the number of unpaired bases. <br/></td></tr>
 117 <tr class="memitem:a6341cbb704924824e0236c1dce791032"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6341cbb704924824e0236c1dce791032"></a>
 118 int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a6341cbb704924824e0236c1dce791032">pairs</a></td></tr>
 119 <tr class="memdesc:a6341cbb704924824e0236c1dce791032"><td class="mdescLeft">&#160;</td><td class="mdescRight">contains the number of base pairs in the last parsed structure. <br/></td></tr>
 120 </table>
 121 <hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
 122 <div class="textblock"><p>Parsing and Coarse Graining of Structures. </p>
 123 <pre class="fragment">Example:
 124 </pre> <pre class="fragment"> *   .((..(((...)))..((..)))).   is the bracket or full tree
 125  *   becomes expanded:   - expand_Full() -
 126  *   ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)
 127  *   HIT:                - b2HIT() -
 128  *   ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)
 129  *   Coarse:             - b2C() -
 130  *   ((H)((H)M)R)
 131  *   becomes expanded:   - expand_Shapiro() -
 132  *   (((((H)S)((H)S)M)S)R)
 133  *   weighted Shapiro:   - b2Shapiro() -
 134  *   ((((((H3)S3)((H2)S2)M4)S2)E2)R)
 135  *  </pre> </div><hr/><h2>Function Documentation</h2>
 136 <a class="anchor" id="a07b7e90e712559a1992fba3ac6d21bbd"></a>
 137 <div class="memitem">
 138 <div class="memproto">
 139       <table class="memname">
 140         <tr>
 141           <td class="memname">char* b2HIT </td>
 142           <td>(</td>
 143           <td class="paramtype">const char *&#160;</td>
 144           <td class="paramname"><em>structure</em></td><td>)</td>
 145           <td></td>
 146         </tr>
 147       </table>
 148 </div><div class="memdoc">
 149
 150 <p>Converts the full structure from bracket notation to the HIT notation including root. </p>
 151 <dl class="params"><dt>Parameters:</dt><dd>
 152   <table class="params">
 153     <tr><td class="paramname">structure</td><td></td></tr>
 154   </table>
 155   </dd>
 156 </dl>
 157 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 158
 159 </div>
 160 </div>
 161 <a class="anchor" id="a9c80d92391f2833549a8b6dac92233f0"></a>
 162 <div class="memitem">
 163 <div class="memproto">
 164       <table class="memname">
 165         <tr>
 166           <td class="memname">char* b2C </td>
 167           <td>(</td>
 168           <td class="paramtype">const char *&#160;</td>
 169           <td class="paramname"><em>structure</em></td><td>)</td>
 170           <td></td>
 171         </tr>
 172       </table>
 173 </div><div class="memdoc">
 174
 175 <p>Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. </p>
 176 <dl class="params"><dt>Parameters:</dt><dd>
 177   <table class="params">
 178     <tr><td class="paramname">structure</td><td></td></tr>
 179   </table>
 180   </dd>
 181 </dl>
 182 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 183
 184 </div>
 185 </div>
 186 <a class="anchor" id="a5cd2feb367feeacad0c03cb7ddba5f10"></a>
 187 <div class="memitem">
 188 <div class="memproto">
 189       <table class="memname">
 190         <tr>
 191           <td class="memname">char* b2Shapiro </td>
 192           <td>(</td>
 193           <td class="paramtype">const char *&#160;</td>
 194           <td class="paramname"><em>structure</em></td><td>)</td>
 195           <td></td>
 196         </tr>
 197       </table>
 198 </div><div class="memdoc">
 199
 200 <p>Converts the full structure from bracket notation to the <em>weighted</em> coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers. </p>
 201 <dl class="params"><dt>Parameters:</dt><dd>
 202   <table class="params">
 203     <tr><td class="paramname">structure</td><td></td></tr>
 204   </table>
 205   </dd>
 206 </dl>
 207 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 208
 209 </div>
 210 </div>
 211 <a class="anchor" id="a880d33066dd95441e5fbb73c57ed1c3e"></a>
 212 <div class="memitem">
 213 <div class="memproto">
 214       <table class="memname">
 215         <tr>
 216           <td class="memname">char* add_root </td>
 217           <td>(</td>
 218           <td class="paramtype">const char *&#160;</td>
 219           <td class="paramname"><em>structure</em></td><td>)</td>
 220           <td></td>
 221         </tr>
 222       </table>
 223 </div><div class="memdoc">
 224
 225 <p>Adds a root to an un-rooted tree in any except bracket notation. </p>
 226 <dl class="params"><dt>Parameters:</dt><dd>
 227   <table class="params">
 228     <tr><td class="paramname">structure</td><td></td></tr>
 229   </table>
 230   </dd>
 231 </dl>
 232 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 233
 234 </div>
 235 </div>
 236 <a class="anchor" id="abe3d815b420dc4553bfb23511198b4c6"></a>
 237 <div class="memitem">
 238 <div class="memproto">
 239       <table class="memname">
 240         <tr>
 241           <td class="memname">char* expand_Shapiro </td>
 242           <td>(</td>
 243           <td class="paramtype">const char *&#160;</td>
 244           <td class="paramname"><em>coarse</em></td><td>)</td>
 245           <td></td>
 246         </tr>
 247       </table>
 248 </div><div class="memdoc">
 249
 250 <p>Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from <a class="el" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0" title="Converts the full structure from bracket notation to the a coarse grained notation using the &#39;H&#39; &#39;B&#39; ...">b2C()</a>. </p>
 251 <dl class="params"><dt>Parameters:</dt><dd>
 252   <table class="params">
 253     <tr><td class="paramname">coarse</td><td></td></tr>
 254   </table>
 255   </dd>
 256 </dl>
 257 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 258
 259 </div>
 260 </div>
 261 <a class="anchor" id="a78d73cd54a068ef2812812771cdddc6f"></a>
 262 <div class="memitem">
 263 <div class="memproto">
 264       <table class="memname">
 265         <tr>
 266           <td class="memname">char* expand_Full </td>
 267           <td>(</td>
 268           <td class="paramtype">const char *&#160;</td>
 269           <td class="paramname"><em>structure</em></td><td>)</td>
 270           <td></td>
 271         </tr>
 272       </table>
 273 </div><div class="memdoc">
 274
 275 <p>Convert the full structure from bracket notation to the expanded notation including root. </p>
 276 <dl class="params"><dt>Parameters:</dt><dd>
 277   <table class="params">
 278     <tr><td class="paramname">structure</td><td></td></tr>
 279   </table>
 280   </dd>
 281 </dl>
 282 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 283
 284 </div>
 285 </div>
 286 <a class="anchor" id="a260c4b622093b76a883bf96628280de1"></a>
 287 <div class="memitem">
 288 <div class="memproto">
 289       <table class="memname">
 290         <tr>
 291           <td class="memname">char* unexpand_Full </td>
 292           <td>(</td>
 293           <td class="paramtype">const char *&#160;</td>
 294           <td class="paramname"><em>ffull</em></td><td>)</td>
 295           <td></td>
 296         </tr>
 297       </table>
 298 </div><div class="memdoc">
 299
 300 <p>Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'. </p>
 301 <dl class="params"><dt>Parameters:</dt><dd>
 302   <table class="params">
 303     <tr><td class="paramname">ffull</td><td></td></tr>
 304   </table>
 305   </dd>
 306 </dl>
 307 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 308
 309 </div>
 310 </div>
 311 <a class="anchor" id="a09a80253ac7b6bae606871ba7c6e5136"></a>
 312 <div class="memitem">
 313 <div class="memproto">
 314       <table class="memname">
 315         <tr>
 316           <td class="memname">char* unweight </td>
 317           <td>(</td>
 318           <td class="paramtype">const char *&#160;</td>
 319           <td class="paramname"><em>wcoarse</em></td><td>)</td>
 320           <td></td>
 321         </tr>
 322       </table>
 323 </div><div class="memdoc">
 324
 325 <p>Strip weights from any weighted tree. </p>
 326 <dl class="params"><dt>Parameters:</dt><dd>
 327   <table class="params">
 328     <tr><td class="paramname">wcoarse</td><td></td></tr>
 329   </table>
 330   </dd>
 331 </dl>
 332 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 333
 334 </div>
 335 </div>
 336 <a class="anchor" id="a1054c4477d53b31d79d4cb132100e87a"></a>
 337 <div class="memitem">
 338 <div class="memproto">
 339       <table class="memname">
 340         <tr>
 341           <td class="memname">void unexpand_aligned_F </td>
 342           <td>(</td>
 343           <td class="paramtype">char *&#160;</td>
 344           <td class="paramname"><em>align</em>[2]</td><td>)</td>
 345           <td></td>
 346         </tr>
 347       </table>
 348 </div><div class="memdoc">
 349
 350 <p>Converts two aligned structures in expanded notation. </p>
 351 <p>Takes two aligned structures as produced by <a class="el" href="treedist_8h.html#a3b21f1925f7071f46d93431a835217bb" title="Calculates the edit distance of the two trees.">tree_edit_distance()</a> function back to bracket notation with '_' as the gap character. The result overwrites the input.</p>
 352 <dl class="params"><dt>Parameters:</dt><dd>
 353   <table class="params">
 354     <tr><td class="paramname">align</td><td></td></tr>
 355   </table>
 356   </dd>
 357 </dl>
 358
 359 </div>
 360 </div>
 361 <a class="anchor" id="a3c79042e6bf6f01706bf30ec9e69e8ac"></a>
 362 <div class="memitem">
 363 <div class="memproto">
 364       <table class="memname">
 365         <tr>
 366           <td class="memname">void parse_structure </td>
 367           <td>(</td>
 368           <td class="paramtype">const char *&#160;</td>
 369           <td class="paramname"><em>structure</em></td><td>)</td>
 370           <td></td>
 371         </tr>
 372       </table>
 373 </div><div class="memdoc">
 374
 375 <p>Collects a statistic of structure elements of the full structure in bracket notation. </p>
 376 <p>The function writes to the following global variables: <a class="el" href="RNAstruct_8h.html#a3f31e0e48125601bfa57b52f8b038e8e" title="contains a list of all loop sizes. loop_size[0] contains the number of external bases.">loop_size</a>, <a class="el" href="RNAstruct_8h.html#aef14e2f8ab3f61e8e659ba6b9003b08a" title="contains the corresponding list of loop degrees.">loop_degree</a>, <a class="el" href="RNAstruct_8h.html#a8218c0d581a3fba2a1a56a196abe19a5" title="contains a list of all stack sizes.">helix_size</a>, <a class="el" href="RNAstruct_8h.html#a439fcb9f8d4f9f4d2227fde5fbfecb30" title="contains the number of loops ( and therefore of stacks ).">loops</a>, <a class="el" href="RNAstruct_8h.html#a6341cbb704924824e0236c1dce791032" title="contains the number of base pairs in the last parsed structure.">pairs</a>, <a class="el" href="RNAstruct_8h.html#add2f952597e02d66e1116a9d11d252d6" title="contains the number of unpaired bases.">unpaired</a></p>
 377 <dl class="params"><dt>Parameters:</dt><dd>
 378   <table class="params">
 379     <tr><td class="paramname">structure</td><td></td></tr>
 380   </table>
 381   </dd>
 382 </dl>
 383 <dl class="section return"><dt>Returns:</dt><dd></dd></dl>
 384
 385 </div>
 386 </div>
 387 </div><!-- contents -->
 388 </div><!-- doc-content -->
 389 <!-- start footer part -->
 390 <div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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 394     <a href="http://www.doxygen.org/index.html">
 395     <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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