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    <innerclass refid="structvrna__sc__motif__s" prot="public">vrna_sc_motif_s</innerclass>
    <sectiondef kind="typedef">
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    <sectiondef kind="func">
      <member refid="group__constraints__ligand_1ga2bd49930c9695b2f4b85989d1daa62d3" kind="function"><name>vrna_sc_add_hi_motif</name></member>
      <member refid="group__constraints__ligand_1ga07bd6a7f23a2d559bcec021e03805daa" kind="function"><name>vrna_sc_ligand_detect_motifs</name></member>
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    <briefdescription>
<para>Functions for incorporation of ligands binding to hairpin and internal loop motifs using the soft constraints framework. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_LIGAND_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_LIGAND_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="17" refid="group__constraints__ligand_1ga56615bc45d2aa4d6d3326fb74183c9ac" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__sc__motif__s" kindref="compound">vrna_sc_motif_s</ref><sp/><ref refid="group__constraints__ligand_1ga56615bc45d2aa4d6d3326fb74183c9ac" kindref="member">vrna_sc_motif_t</ref>;</highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="22" refid="structvrna__sc__motif__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__sc__motif__s" kindref="compound">vrna_sc_motif_s</ref><sp/>{</highlight></codeline>
<codeline lineno="23"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>i;</highlight></codeline>
<codeline lineno="24"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>j;</highlight></codeline>
<codeline lineno="25"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>k;</highlight></codeline>
<codeline lineno="26"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>l;</highlight></codeline>
<codeline lineno="27"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>number;</highlight></codeline>
<codeline lineno="28"><highlight class="normal">};</highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="57" refid="group__constraints__ligand_1ga2bd49930c9695b2f4b85989d1daa62d3" refkind="member"><highlight class="normal"><ref refid="group__constraints__ligand_1ga2bd49930c9695b2f4b85989d1daa62d3" kindref="member">vrna_sc_add_hi_motif</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="58"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*seq,</highlight></codeline>
<codeline lineno="59"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="60"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy,</highlight></codeline>
<codeline lineno="61"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="62"><highlight class="normal"></highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight></codeline>
<codeline lineno="64"><highlight class="normal"><ref refid="group__constraints__ligand_1ga56615bc45d2aa4d6d3326fb74183c9ac" kindref="member">vrna_sc_motif_t</ref><sp/>*</highlight></codeline>
<codeline lineno="65"><highlight class="normal">vrna_sc_ligand_detect_motifs(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="66"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure);</highlight></codeline>
<codeline lineno="67"><highlight class="normal"></highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight></codeline>
<codeline lineno="69"><highlight class="normal"><ref refid="group__constraints__ligand_1ga56615bc45d2aa4d6d3326fb74183c9ac" kindref="member">vrna_sc_motif_t</ref><sp/>*</highlight></codeline>
<codeline lineno="70"><highlight class="normal">vrna_sc_ligand_get_all_motifs(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="71"><highlight class="normal"></highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight></codeline>
<codeline lineno="76"><highlight class="normal"></highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
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    <location file="ViennaRNA/constraints/ligand.h"/>
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