<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.15.0" xml:lang="en-US">
  <compounddef id="RNAstruct_8h" kind="file" language="C++">
    <compoundname>RNAstruct.h</compoundname>
    <sectiondef kind="define">
      <memberdef kind="define" id="RNAstruct_8h_1aab347a3c03fbe8e7319551b9fa0cce4a" prot="public" static="no">
        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/RNAstruct.h" line="13" column="11" bodyfile="ViennaRNA/RNAstruct.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <member refid="group__struct__utils__deprecated_1gaa100f7d3ce0ad4f527a61c5764ebf277" kind="define"><name>STRUC</name></member>
    </sectiondef>
    <sectiondef kind="var">
      <member refid="group__struct__utils__deprecated_1ga3f31e0e48125601bfa57b52f8b038e8e" kind="variable"><name>loop_size</name></member>
      <member refid="group__struct__utils__deprecated_1ga8218c0d581a3fba2a1a56a196abe19a5" kind="variable"><name>helix_size</name></member>
      <member refid="group__struct__utils__deprecated_1gaef14e2f8ab3f61e8e659ba6b9003b08a" kind="variable"><name>loop_degree</name></member>
      <member refid="group__struct__utils__deprecated_1ga439fcb9f8d4f9f4d2227fde5fbfecb30" kind="variable"><name>loops</name></member>
      <member refid="group__struct__utils__deprecated_1gadd2f952597e02d66e1116a9d11d252d6" kind="variable"><name>unpaired</name></member>
      <member refid="group__struct__utils__deprecated_1ga6341cbb704924824e0236c1dce791032" kind="variable"><name>pairs</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__struct__utils__deprecated_1gab3fcb3ff7e9bcd86cd969093bdae0c8d" kind="function"><name>b2HIT</name></member>
      <member refid="group__struct__utils__deprecated_1gaab548531941f27c91108b89a8f570f95" kind="function"><name>b2C</name></member>
      <member refid="group__struct__utils__deprecated_1ga2baf1c3a2182f21a4384107df979cd67" kind="function"><name>b2Shapiro</name></member>
      <member refid="group__struct__utils__deprecated_1gaf3b80d1fe7485e69c6eb85965613a145" kind="function"><name>add_root</name></member>
      <member refid="group__struct__utils__deprecated_1ga04c7268dcc798f92290604a762c3ddf8" kind="function"><name>expand_Shapiro</name></member>
      <member refid="group__struct__utils__deprecated_1ga6eea10bca410a57aaffcdea7bcf89bda" kind="function"><name>expand_Full</name></member>
      <member refid="group__struct__utils__deprecated_1gad67c8ef662c147c5f55da3c233376e59" kind="function"><name>unexpand_Full</name></member>
      <member refid="group__struct__utils__deprecated_1ga4921d8967002f8e6e30a8ac046bbf557" kind="function"><name>unweight</name></member>
      <member refid="group__struct__utils__deprecated_1ga1054c4477d53b31d79d4cb132100e87a" kind="function"><name>unexpand_aligned_F</name></member>
      <member refid="group__struct__utils__deprecated_1ga3c79042e6bf6f01706bf30ec9e69e8ac" kind="function"><name>parse_structure</name></member>
    </sectiondef>
    <briefdescription>
<para>Parsing and Coarse Graining of Structures. </para>
    </briefdescription>
    <detaileddescription>
<para>Example: <verbatim>*   .((..(((...)))..((..)))).   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)
*  </verbatim> </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_RNASTRUCT_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_RNASTRUCT_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(&quot;&quot;,<sp/>msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>STRUC<sp/><sp/><sp/><sp/><sp/>2000</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight></codeline>
<codeline lineno="52"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1gab3fcb3ff7e9bcd86cd969093bdae0c8d" kindref="member">b2HIT</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="53" refid="group__struct__utils__deprecated_1gab3fcb3ff7e9bcd86cd969093bdae0c8d" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_db_to_tree_string()<sp/>instead!&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>Full<sp/><sp/><sp/>-&gt;<sp/>HIT<sp/><sp/><sp/><sp/>[incl.<sp/>root]<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"></highlight></codeline>
<codeline lineno="55"><highlight class="normal"></highlight></codeline>
<codeline lineno="66"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1gaab548531941f27c91108b89a8f570f95" kindref="member">b2C</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="67" refid="group__struct__utils__deprecated_1gaab548531941f27c91108b89a8f570f95" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_db_to_tree_string()<sp/>instead!&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>Full<sp/><sp/><sp/>-&gt;<sp/>Coarse<sp/>[incl.<sp/>root]<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight></codeline>
<codeline lineno="69"><highlight class="normal"></highlight></codeline>
<codeline lineno="81"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1ga2baf1c3a2182f21a4384107df979cd67" kindref="member">b2Shapiro</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="82" refid="group__struct__utils__deprecated_1ga2baf1c3a2182f21a4384107df979cd67" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_db_to_tree_string()<sp/>instead!&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>Full<sp/>-&gt;<sp/>weighted<sp/>Shapiro<sp/>[i.r.]<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="83"><highlight class="normal"></highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight></codeline>
<codeline lineno="91"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1gaf3b80d1fe7485e69c6eb85965613a145" kindref="member">add_root</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="92" refid="group__struct__utils__deprecated_1gaf3b80d1fe7485e69c6eb85965613a145" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>{Tree}<sp/>-&gt;<sp/>({Tree}R)<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="93"><highlight class="normal"></highlight></codeline>
<codeline lineno="94"><highlight class="normal"></highlight></codeline>
<codeline lineno="102"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1ga04c7268dcc798f92290604a762c3ddf8" kindref="member">expand_Shapiro</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*coarse),</highlight></codeline>
<codeline lineno="103" refid="group__struct__utils__deprecated_1ga04c7268dcc798f92290604a762c3ddf8" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_db_to_tree_string()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="104"><highlight class="normal"></highlight></codeline>
<codeline lineno="105"><highlight class="normal"></highlight></codeline>
<codeline lineno="106"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>add<sp/>S<sp/>for<sp/>stacks<sp/>to<sp/>coarse<sp/>struct<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="114"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1ga6eea10bca410a57aaffcdea7bcf89bda" kindref="member">expand_Full</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="115" refid="group__struct__utils__deprecated_1ga6eea10bca410a57aaffcdea7bcf89bda" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_db_to_tree_string()<sp/>instead!&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>Full<sp/><sp/><sp/>-&gt;<sp/>FFull<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="116"><highlight class="normal"></highlight></codeline>
<codeline lineno="117"><highlight class="normal"></highlight></codeline>
<codeline lineno="125"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1gad67c8ef662c147c5f55da3c233376e59" kindref="member">unexpand_Full</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*ffull),</highlight></codeline>
<codeline lineno="126" refid="group__struct__utils__deprecated_1gad67c8ef662c147c5f55da3c233376e59" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_tree_string_to_db()<sp/>instead!&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>FFull<sp/><sp/>-&gt;<sp/>Full<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="127"><highlight class="normal"></highlight></codeline>
<codeline lineno="128"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__struct__utils__deprecated_1ga4921d8967002f8e6e30a8ac046bbf557" kindref="member">unweight</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*wcoarse),</highlight></codeline>
<codeline lineno="136" refid="group__struct__utils__deprecated_1ga4921d8967002f8e6e30a8ac046bbf557" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_tree_string_unweight()<sp/>instead!&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>remove<sp/>weights<sp/>from<sp/>coarse<sp/>struct<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="137"><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"></highlight></codeline>
<codeline lineno="148"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="group__struct__utils__deprecated_1ga1054c4477d53b31d79d4cb132100e87a" kindref="member">unexpand_aligned_F</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*align[2]),</highlight></codeline>
<codeline lineno="149" refid="group__struct__utils__deprecated_1ga1054c4477d53b31d79d4cb132100e87a" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="150"><highlight class="normal"></highlight></codeline>
<codeline lineno="151"><highlight class="normal"></highlight></codeline>
<codeline lineno="161"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="group__struct__utils__deprecated_1ga3c79042e6bf6f01706bf30ec9e69e8ac" kindref="member">parse_structure</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure),</highlight></codeline>
<codeline lineno="162" refid="group__struct__utils__deprecated_1ga3c79042e6bf6f01706bf30ec9e69e8ac" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/></highlight><highlight class="comment">/*<sp/>make<sp/>structure<sp/>statistics<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="163"><highlight class="normal"></highlight></codeline>
<codeline lineno="164"><highlight class="normal"></highlight></codeline>
<codeline lineno="169"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__deprecated_1ga3f31e0e48125601bfa57b52f8b038e8e" kindref="member">loop_size</ref>[STRUC],</highlight></codeline>
<codeline lineno="170"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>loop<sp/>sizes<sp/>of<sp/>a<sp/>structure<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="171"><highlight class="normal"></highlight></codeline>
<codeline lineno="175"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__deprecated_1ga8218c0d581a3fba2a1a56a196abe19a5" kindref="member">helix_size</ref>[STRUC],</highlight></codeline>
<codeline lineno="176"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>helix<sp/>sizes<sp/>of<sp/>a<sp/>structure<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="177"><highlight class="normal"></highlight></codeline>
<codeline lineno="181"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__deprecated_1gaef14e2f8ab3f61e8e659ba6b9003b08a" kindref="member">loop_degree</ref>[STRUC],</highlight></codeline>
<codeline lineno="182"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>loop<sp/>degrees<sp/>of<sp/>a<sp/>structure<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="183"><highlight class="normal"></highlight></codeline>
<codeline lineno="187"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__deprecated_1ga439fcb9f8d4f9f4d2227fde5fbfecb30" kindref="member">loops</ref>,</highlight></codeline>
<codeline lineno="188"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>n<sp/>of<sp/>loops<sp/>and<sp/>stacks<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="189"><highlight class="normal"></highlight></codeline>
<codeline lineno="193"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__deprecated_1gadd2f952597e02d66e1116a9d11d252d6" kindref="member">unpaired</ref>,</highlight></codeline>
<codeline lineno="194"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="195"><highlight class="normal"></highlight></codeline>
<codeline lineno="199"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__deprecated_1ga6341cbb704924824e0236c1dce791032" kindref="member">pairs</ref>,</highlight></codeline>
<codeline lineno="200"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>n<sp/>of<sp/>unpaired<sp/>digits<sp/>and<sp/>pairs<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="201"><highlight class="normal"></highlight></codeline>
<codeline lineno="205"><highlight class="normal"></highlight></codeline>
<codeline lineno="206"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/RNAstruct.h"/>
  </compounddef>
</doxygen>
