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+
+<p>Parsing and Coarse Graining of Structures.
+<a href="#details">More...</a></p>
+
+<p><a href="RNAstruct_8h_source.html">Go to the source code of this file.</a></p>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a07b7e90e712559a1992fba3ac6d21bbd"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a07b7e90e712559a1992fba3ac6d21bbd">b2HIT</a> (const char *structure)</td></tr>
+<tr class="memdesc:a07b7e90e712559a1992fba3ac6d21bbd"><td class="mdescLeft"> </td><td class="mdescRight">Converts the full structure from bracket notation to the HIT notation including root. <a href="#a07b7e90e712559a1992fba3ac6d21bbd"></a><br/></td></tr>
+<tr class="memitem:a9c80d92391f2833549a8b6dac92233f0"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a9c80d92391f2833549a8b6dac92233f0">b2C</a> (const char *structure)</td></tr>
+<tr class="memdesc:a9c80d92391f2833549a8b6dac92233f0"><td class="mdescLeft"> </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>
+<tr class="memitem:a5cd2feb367feeacad0c03cb7ddba5f10"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a5cd2feb367feeacad0c03cb7ddba5f10">b2Shapiro</a> (const char *structure)</td></tr>
+<tr class="memdesc:a5cd2feb367feeacad0c03cb7ddba5f10"><td class="mdescLeft"> </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>
+<tr class="memitem:a880d33066dd95441e5fbb73c57ed1c3e"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a880d33066dd95441e5fbb73c57ed1c3e">add_root</a> (const char *structure)</td></tr>
+<tr class="memdesc:a880d33066dd95441e5fbb73c57ed1c3e"><td class="mdescLeft"> </td><td class="mdescRight">Adds a root to an un-rooted tree in any except bracket notation. <a href="#a880d33066dd95441e5fbb73c57ed1c3e"></a><br/></td></tr>
+<tr class="memitem:abe3d815b420dc4553bfb23511198b4c6"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#abe3d815b420dc4553bfb23511198b4c6">expand_Shapiro</a> (const char *coarse)</td></tr>
+<tr class="memdesc:abe3d815b420dc4553bfb23511198b4c6"><td class="mdescLeft"> </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 'H' 'B' ...">b2C()</a>. <a href="#abe3d815b420dc4553bfb23511198b4c6"></a><br/></td></tr>
+<tr class="memitem:a78d73cd54a068ef2812812771cdddc6f"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f">expand_Full</a> (const char *structure)</td></tr>
+<tr class="memdesc:a78d73cd54a068ef2812812771cdddc6f"><td class="mdescLeft"> </td><td class="mdescRight">Convert the full structure from bracket notation to the expanded notation including root. <a href="#a78d73cd54a068ef2812812771cdddc6f"></a><br/></td></tr>
+<tr class="memitem:a260c4b622093b76a883bf96628280de1"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a260c4b622093b76a883bf96628280de1">unexpand_Full</a> (const char *ffull)</td></tr>
+<tr class="memdesc:a260c4b622093b76a883bf96628280de1"><td class="mdescLeft"> </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>
+<tr class="memitem:a09a80253ac7b6bae606871ba7c6e5136"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a09a80253ac7b6bae606871ba7c6e5136">unweight</a> (const char *wcoarse)</td></tr>
+<tr class="memdesc:a09a80253ac7b6bae606871ba7c6e5136"><td class="mdescLeft"> </td><td class="mdescRight">Strip weights from any weighted tree. <a href="#a09a80253ac7b6bae606871ba7c6e5136"></a><br/></td></tr>
+<tr class="memitem:a1054c4477d53b31d79d4cb132100e87a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a">unexpand_aligned_F</a> (char *align[2])</td></tr>
+<tr class="memdesc:a1054c4477d53b31d79d4cb132100e87a"><td class="mdescLeft"> </td><td class="mdescRight">Converts two aligned structures in expanded notation. <a href="#a1054c4477d53b31d79d4cb132100e87a"></a><br/></td></tr>
+<tr class="memitem:a3c79042e6bf6f01706bf30ec9e69e8ac"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a3c79042e6bf6f01706bf30ec9e69e8ac">parse_structure</a> (const char *structure)</td></tr>
+<tr class="memdesc:a3c79042e6bf6f01706bf30ec9e69e8ac"><td class="mdescLeft"> </td><td class="mdescRight">Collects a statistic of structure elements of the full structure in bracket notation. <a href="#a3c79042e6bf6f01706bf30ec9e69e8ac"></a><br/></td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
+Variables</h2></td></tr>
+<tr class="memitem:a3f31e0e48125601bfa57b52f8b038e8e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a3f31e0e48125601bfa57b52f8b038e8e"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a3f31e0e48125601bfa57b52f8b038e8e">loop_size</a> [STRUC]</td></tr>
+<tr class="memdesc:a3f31e0e48125601bfa57b52f8b038e8e"><td class="mdescLeft"> </td><td class="mdescRight">contains a list of all loop sizes. loop_size[0] contains the number of external bases. <br/></td></tr>
+<tr class="memitem:a8218c0d581a3fba2a1a56a196abe19a5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a8218c0d581a3fba2a1a56a196abe19a5"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a8218c0d581a3fba2a1a56a196abe19a5">helix_size</a> [STRUC]</td></tr>
+<tr class="memdesc:a8218c0d581a3fba2a1a56a196abe19a5"><td class="mdescLeft"> </td><td class="mdescRight">contains a list of all stack sizes. <br/></td></tr>
+<tr class="memitem:aef14e2f8ab3f61e8e659ba6b9003b08a"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aef14e2f8ab3f61e8e659ba6b9003b08a"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#aef14e2f8ab3f61e8e659ba6b9003b08a">loop_degree</a> [STRUC]</td></tr>
+<tr class="memdesc:aef14e2f8ab3f61e8e659ba6b9003b08a"><td class="mdescLeft"> </td><td class="mdescRight">contains the corresponding list of loop degrees. <br/></td></tr>
+<tr class="memitem:a439fcb9f8d4f9f4d2227fde5fbfecb30"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a439fcb9f8d4f9f4d2227fde5fbfecb30"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a439fcb9f8d4f9f4d2227fde5fbfecb30">loops</a></td></tr>
+<tr class="memdesc:a439fcb9f8d4f9f4d2227fde5fbfecb30"><td class="mdescLeft"> </td><td class="mdescRight">contains the number of loops ( and therefore of stacks ). <br/></td></tr>
+<tr class="memitem:add2f952597e02d66e1116a9d11d252d6"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="add2f952597e02d66e1116a9d11d252d6"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#add2f952597e02d66e1116a9d11d252d6">unpaired</a></td></tr>
+<tr class="memdesc:add2f952597e02d66e1116a9d11d252d6"><td class="mdescLeft"> </td><td class="mdescRight">contains the number of unpaired bases. <br/></td></tr>
+<tr class="memitem:a6341cbb704924824e0236c1dce791032"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6341cbb704924824e0236c1dce791032"></a>
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="RNAstruct_8h.html#a6341cbb704924824e0236c1dce791032">pairs</a></td></tr>
+<tr class="memdesc:a6341cbb704924824e0236c1dce791032"><td class="mdescLeft"> </td><td class="mdescRight">contains the number of base pairs in the last parsed structure. <br/></td></tr>
+</table>
+<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<div class="textblock"><p>Parsing and Coarse Graining of Structures. </p>
+<pre class="fragment">Example:
+</pre> <pre class="fragment"> * .((..(((...)))..((..)))). is the bracket or full tree
+ * becomes expanded: - expand_Full() -
+ * ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)
+ * HIT: - b2HIT() -
+ * ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)
+ * Coarse: - b2C() -
+ * ((H)((H)M)R)
+ * becomes expanded: - expand_Shapiro() -
+ * (((((H)S)((H)S)M)S)R)
+ * weighted Shapiro: - b2Shapiro() -
+ * ((((((H3)S3)((H2)S2)M4)S2)E2)R)
+ * </pre> </div><hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a07b7e90e712559a1992fba3ac6d21bbd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* b2HIT </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>structure</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Converts the full structure from bracket notation to the HIT notation including root. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">structure</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a9c80d92391f2833549a8b6dac92233f0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* b2C </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>structure</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">structure</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a5cd2feb367feeacad0c03cb7ddba5f10"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* b2Shapiro </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>structure</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<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>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">structure</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a880d33066dd95441e5fbb73c57ed1c3e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* add_root </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>structure</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Adds a root to an un-rooted tree in any except bracket notation. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">structure</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="abe3d815b420dc4553bfb23511198b4c6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* expand_Shapiro </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>coarse</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<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 'H' 'B' ...">b2C()</a>. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">coarse</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a78d73cd54a068ef2812812771cdddc6f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* expand_Full </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>structure</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Convert the full structure from bracket notation to the expanded notation including root. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">structure</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a260c4b622093b76a883bf96628280de1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* unexpand_Full </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>ffull</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">ffull</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a09a80253ac7b6bae606871ba7c6e5136"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">char* unweight </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>wcoarse</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Strip weights from any weighted tree. </p>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">wcoarse</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
+<a class="anchor" id="a1054c4477d53b31d79d4cb132100e87a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">void unexpand_aligned_F </td>
+ <td>(</td>
+ <td class="paramtype">char * </td>
+ <td class="paramname"><em>align</em>[2]</td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Converts two aligned structures in expanded notation. </p>
+<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>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">align</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+
+</div>
+</div>
+<a class="anchor" id="a3c79042e6bf6f01706bf30ec9e69e8ac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">void parse_structure </td>
+ <td>(</td>
+ <td class="paramtype">const char * </td>
+ <td class="paramname"><em>structure</em></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+<p>Collects a statistic of structure elements of the full structure in bracket notation. </p>
+<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>
+<dl class="params"><dt>Parameters:</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">structure</td><td></td></tr>
+ </table>
+ </dd>
+</dl>
+<dl class="section return"><dt>Returns:</dt><dd></dd></dl>
+
+</div>
+</div>
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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>
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