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-<div class="title">RNAstruct.h</div> </div>
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-<div class="contents">
-<a href="RNAstruct_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_RNASTRUCT_H__</span></div>
-<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_RNASTRUCT_H__</span></div>
-<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#define STRUC 2000</span></div>
-<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor"></span></div>
-<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a07b7e90e712559a1992fba3ac6d21bbd" title="Converts the full structure from bracket notation to the HIT notation including root.">b2HIT</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> HIT [incl. root] */</span></div>
-<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
-<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0" title="Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' ...">b2C</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> Coarse [incl. root] */</span></div>
-<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div>
-<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a5cd2feb367feeacad0c03cb7ddba5f10" title="Converts the full structure from bracket notation to the weighted coarse grained notation using the '...">b2Shapiro</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> weighted Shapiro [i.r.] */</span></div>
-<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div>
-<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a880d33066dd95441e5fbb73c57ed1c3e" title="Adds a root to an un-rooted tree in any except bracket notation.">add_root</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* {Tree} -> ({Tree}R) */</span></div>
-<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div>
-<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#abe3d815b420dc4553bfb23511198b4c6" title="Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C()...">expand_Shapiro</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *coarse);</div>
-<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
-<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="comment">/* add S for stacks to coarse struct */</span></div>
-<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f" title="Convert the full structure from bracket notation to the expanded notation including root...">expand_Full</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> FFull */</span></div>
-<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
-<div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a260c4b622093b76a883bf96628280de1" title="Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifi...">unexpand_Full</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *ffull); <span class="comment">/* FFull -> Full */</span></div>
-<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
-<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a09a80253ac7b6bae606871ba7c6e5136" title="Strip weights from any weighted tree.">unweight</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *wcoarse); <span class="comment">/* remove weights from coarse struct */</span></div>
-<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
-<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> <span class="keywordtype">void</span> <a class="code" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a" title="Converts two aligned structures in expanded notation.">unexpand_aligned_F</a>(<span class="keywordtype">char</span> *align[2]);</div>
-<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
-<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="keywordtype">void</span> <a class="code" href="RNAstruct_8h.html#a3c79042e6bf6f01706bf30ec9e69e8ac" title="Collects a statistic of structure elements of the full structure in bracket notation.">parse_structure</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* make structure statistics */</span></div>
-<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
-<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" 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>[STRUC]; <span class="comment">/* loop sizes of a structure */</span></div>
-<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
-<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#a8218c0d581a3fba2a1a56a196abe19a5" title="contains a list of all stack sizes.">helix_size</a>[STRUC]; <span class="comment">/* helix sizes of a structure */</span></div>
-<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
-<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#aef14e2f8ab3f61e8e659ba6b9003b08a" title="contains the corresponding list of loop degrees.">loop_degree</a>[STRUC]; <span class="comment">/* loop degrees of a structure */</span></div>
-<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
-<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#a439fcb9f8d4f9f4d2227fde5fbfecb30" title="contains the number of loops ( and therefore of stacks ).">loops</a>; <span class="comment">/* n of loops and stacks */</span></div>
-<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div>
-<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#add2f952597e02d66e1116a9d11d252d6" title="contains the number of unpaired bases.">unpaired</a>;</div>
-<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> </div>
-<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#a6341cbb704924824e0236c1dce791032" title="contains the number of base pairs in the last parsed structure.">pairs</a>; <span class="comment">/* n of unpaired digits and pairs */</span></div>
-<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
-<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="preprocessor">#endif</span></div>
-</div><!-- fragment --></div><!-- contents -->
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- <li class="navelem"><a class="el" href="dir_d72344b28b4f2089ce25682c4e6eba22.html">H</a></li><li class="navelem"><a class="el" href="RNAstruct_8h.html">RNAstruct.h</a></li>
- <li class="footer">Generated on Wed Jul 24 2013 13:38:56 for RNAlib-2.1.2 by
- <a href="http://www.doxygen.org/index.html">
- <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.1.1 </li>
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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/RNAstruct.h</h1><a href="RNAstruct_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef __VIENNA_RNA_PACKAGE_RNASTRUCT_H__</span>
+<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define __VIENNA_RNA_PACKAGE_RNASTRUCT_H__</span>
+<a name="l00003"></a>00003 <span class="preprocessor"></span>
+<a name="l00024"></a>00024 <span class="preprocessor">#define STRUC 2000</span>
+<a name="l00025"></a>00025 <span class="preprocessor"></span>
+<a name="l00033"></a>00033 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a07b7e90e712559a1992fba3ac6d21bbd" title="Converts the full structure from bracket notation to the HIT notation including root...">b2HIT</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> HIT [incl. root] */</span>
+<a name="l00034"></a>00034
+<a name="l00042"></a>00042 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0" title="Converts the full structure from bracket notation to the a coarse grained notation...">b2C</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> Coarse [incl. root] */</span>
+<a name="l00043"></a>00043
+<a name="l00052"></a>00052 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a5cd2feb367feeacad0c03cb7ddba5f10" title="Converts the full structure from bracket notation to the weighted coarse grained...">b2Shapiro</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> weighted Shapiro [i.r.] */</span>
+<a name="l00053"></a>00053
+<a name="l00060"></a>00060 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a880d33066dd95441e5fbb73c57ed1c3e" title="Adds a root to an un-rooted tree in any except bracket notation.">add_root</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* {Tree} -> ({Tree}R) */</span>
+<a name="l00061"></a>00061
+<a name="l00069"></a>00069 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#abe3d815b420dc4553bfb23511198b4c6" title="Inserts missing &#39;S&#39; identifiers in unweighted coarse grained structures as...">expand_Shapiro</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *coarse);
+<a name="l00070"></a>00070
+<a name="l00071"></a>00071 <span class="comment">/* add S for stacks to coarse struct */</span>
+<a name="l00079"></a>00079 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f" title="Convert the full structure from bracket notation to the expanded notation including...">expand_Full</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* Full -> FFull */</span>
+<a name="l00080"></a>00080
+<a name="l00088"></a>00088 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a260c4b622093b76a883bf96628280de1" title="Restores the bracket notation from an expanded full or HIT tree, that is any tree...">unexpand_Full</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *ffull); <span class="comment">/* FFull -> Full */</span>
+<a name="l00089"></a>00089
+<a name="l00096"></a>00096 <span class="keywordtype">char</span> *<a class="code" href="RNAstruct_8h.html#a09a80253ac7b6bae606871ba7c6e5136" title="Strip weights from any weighted tree.">unweight</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *wcoarse); <span class="comment">/* remove weights from coarse struct */</span>
+<a name="l00097"></a>00097
+<a name="l00107"></a>00107 <span class="keywordtype">void</span> <a class="code" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a" title="Converts two aligned structures in expanded notation.">unexpand_aligned_F</a>(<span class="keywordtype">char</span> *align[2]);
+<a name="l00108"></a>00108
+<a name="l00119"></a>00119 <span class="keywordtype">void</span> <a class="code" href="RNAstruct_8h.html#a3c79042e6bf6f01706bf30ec9e69e8ac" title="Collects a statistic of structure elements of the full structure in bracket notation...">parse_structure</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *structure); <span class="comment">/* make structure statistics */</span>
+<a name="l00120"></a>00120
+<a name="l00125"></a>00125 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" 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>[STRUC]; <span class="comment">/* loop sizes of a structure */</span>
+<a name="l00126"></a>00126
+<a name="l00130"></a>00130 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#a8218c0d581a3fba2a1a56a196abe19a5" title="contains a list of all stack sizes.">helix_size</a>[STRUC]; <span class="comment">/* helix sizes of a structure */</span>
+<a name="l00131"></a>00131
+<a name="l00135"></a>00135 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#aef14e2f8ab3f61e8e659ba6b9003b08a" title="contains the corresponding list of loop degrees.">loop_degree</a>[STRUC]; <span class="comment">/* loop degrees of a structure */</span>
+<a name="l00136"></a>00136
+<a name="l00140"></a>00140 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#a439fcb9f8d4f9f4d2227fde5fbfecb30" title="contains the number of loops ( and therefore of stacks ).">loops</a>; <span class="comment">/* n of loops and stacks */</span>
+<a name="l00141"></a>00141
+<a name="l00145"></a>00145 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#add2f952597e02d66e1116a9d11d252d6" title="contains the number of unpaired bases.">unpaired</a>;
+<a name="l00146"></a>00146
+<a name="l00150"></a>00150 <span class="keyword">extern</span> <span class="keywordtype">int</span> <a class="code" href="RNAstruct_8h.html#a6341cbb704924824e0236c1dce791032" title="contains the number of base pairs in the last parsed structure.">pairs</a>; <span class="comment">/* n of unpaired digits and pairs */</span>
+<a name="l00151"></a>00151
+<a name="l00152"></a>00152 <span class="preprocessor">#endif</span>
+</pre></div></div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
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