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    <innerclass refid="structvrna__pk__plex__result__s" prot="public">vrna_pk_plex_result_s</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="pk__plex_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/pk_plex.h" line="16" column="11" bodyfile="ViennaRNA/pk_plex.h" bodystart="16" bodyend="-1"/>
      </memberdef>
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    <sectiondef kind="typedef">
      <member refid="group__pseudoknots_1gaa3c616a490113feba261bed7a92981eb" kind="typedef"><name>vrna_pk_plex_score_f</name></member>
      <member refid="group__pseudoknots_1ga28c559c321ff78d351481fc0aa0a09b8" kind="typedef"><name>vrna_callback_pk_plex_score</name></member>
      <member refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" kind="typedef"><name>vrna_pk_plex_opt_t</name></member>
      <member refid="group__pseudoknots_1ga4b505034ccee4de966519afe8b3c120f" kind="typedef"><name>vrna_pk_plex_t</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__pseudoknots_1ga1d12c3e1affefec6339a15348b1bbdca" kind="function"><name>vrna_pk_plex</name></member>
      <member refid="group__pseudoknots_1gad3250f0443f875bba3c87c432356bc74" kind="function"><name>vrna_pk_plex_accessibility</name></member>
      <member refid="group__pseudoknots_1gaa6a5f5e20804ba729134eb8ad0c8da54" kind="function"><name>vrna_pk_plex_opt_defaults</name></member>
      <member refid="group__pseudoknots_1ga8f224a6aa666fd7444b225f676471992" kind="function"><name>vrna_pk_plex_opt</name></member>
      <member refid="group__pseudoknots_1ga7209e5212f611aa1c06b1609da696d35" kind="function"><name>vrna_pk_plex_opt_fun</name></member>
    </sectiondef>
    <briefdescription>
<para>Heuristics for two-step pseudoknot forming interaction predictions. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PK_PLEX_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PK_PLEX_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(DEPRECATED)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/><sp/>undef<sp/>DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><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="10"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><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="12"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><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="14"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight></codeline>
<codeline lineno="24"><highlight class="normal"></highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight></codeline>
<codeline lineno="58" refid="group__pseudoknots_1gaa3c616a490113feba261bed7a92981eb" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>int<sp/>(*<ref refid="group__pseudoknots_1gaa3c616a490113feba261bed7a92981eb" kindref="member">vrna_pk_plex_score_f</ref>)(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*pt,</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/><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>start_5,</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/><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>end_5,</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/><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>start_3,</highlight></codeline>
<codeline lineno="62"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>end_3,</highlight></codeline>
<codeline lineno="63"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data);</highlight></codeline>
<codeline lineno="64"><highlight class="normal"></highlight></codeline>
<codeline lineno="65"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>(vrna_callback_pk_plex_score)(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>*pt,</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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>start_5,</highlight></codeline>
<codeline lineno="67"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>end_5,</highlight></codeline>
<codeline lineno="68"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>start_3,</highlight></codeline>
<codeline lineno="69"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>end_3,</highlight></codeline>
<codeline lineno="70"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data),</highlight></codeline>
<codeline lineno="71"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pk_plex_score_f<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"></highlight></codeline>
<codeline lineno="80" refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" 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">vrna_pk_plex_option_s<sp/>*<ref refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" kindref="member">vrna_pk_plex_opt_t</ref>;</highlight></codeline>
<codeline lineno="81"><highlight class="normal"></highlight></codeline>
<codeline lineno="87" refid="group__pseudoknots_1ga4b505034ccee4de966519afe8b3c120f" 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__pk__plex__result__s" kindref="compound">vrna_pk_plex_result_s</ref><sp/><ref refid="group__pseudoknots_1ga4b505034ccee4de966519afe8b3c120f" kindref="member">vrna_pk_plex_t</ref>;</highlight></codeline>
<codeline lineno="88"><highlight class="normal"></highlight></codeline>
<codeline lineno="89"><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="90"><highlight class="normal"></highlight></codeline>
<codeline lineno="96" refid="structvrna__pk__plex__result__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__pk__plex__result__s" kindref="compound">vrna_pk_plex_result_s</ref><sp/>{</highlight></codeline>
<codeline lineno="97" refid="structvrna__pk__plex__result__s_1a31fe3dea3cb3799621cd111ab3e31629" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__pk__plex__result__s_1a31fe3dea3cb3799621cd111ab3e31629" kindref="member">structure</ref>;<sp/></highlight></codeline>
<codeline lineno="98" refid="structvrna__pk__plex__result__s_1a1a28780d20573e1e8e74137f74ebaa8b" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1a1a28780d20573e1e8e74137f74ebaa8b" kindref="member">energy</ref>;<sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="99" refid="structvrna__pk__plex__result__s_1ad229d6898ffdb195b6442defdec35171" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1ad229d6898ffdb195b6442defdec35171" kindref="member">dGpk</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="100" refid="structvrna__pk__plex__result__s_1abb999a7a5a80f71d57a801d83901a596" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1abb999a7a5a80f71d57a801d83901a596" kindref="member">dGint</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="101" refid="structvrna__pk__plex__result__s_1ad5c142b580ce0db3e2bb4ec7faa9cbdd" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1ad5c142b580ce0db3e2bb4ec7faa9cbdd" kindref="member">dG1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="102" refid="structvrna__pk__plex__result__s_1a3aaccf208713fe56d9a27d65062989cb" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1a3aaccf208713fe56d9a27d65062989cb" kindref="member">dG2</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="103" refid="structvrna__pk__plex__result__s_1aeebb3e74fb4390b23aefaa50b98e4672" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1aeebb3e74fb4390b23aefaa50b98e4672" kindref="member">start_5</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="104" refid="structvrna__pk__plex__result__s_1ae2a8ca7f4769a6595617649adbf6284f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1ae2a8ca7f4769a6595617649adbf6284f" kindref="member">end_5</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="105" refid="structvrna__pk__plex__result__s_1a364296aea56d85179a1576d83e5a4826" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1a364296aea56d85179a1576d83e5a4826" kindref="member">start_3</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="106" refid="structvrna__pk__plex__result__s_1a69f49f082cb148f0fbd5dd4fe84ab9bb" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__pk__plex__result__s_1a69f49f082cb148f0fbd5dd4fe84ab9bb" kindref="member">end_3</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="107"><highlight class="normal">};</highlight></codeline>
<codeline lineno="108"><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"><ref refid="group__pseudoknots_1ga4b505034ccee4de966519afe8b3c120f" kindref="member">vrna_pk_plex_t</ref><sp/>*</highlight></codeline>
<codeline lineno="139" refid="group__pseudoknots_1ga1d12c3e1affefec6339a15348b1bbdca" refkind="member"><highlight class="normal"><ref refid="group__pseudoknots_1ga1d12c3e1affefec6339a15348b1bbdca" kindref="member">vrna_pk_plex</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="140"><highlight class="normal"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**accessibility,</highlight></codeline>
<codeline lineno="141"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" kindref="member">vrna_pk_plex_opt_t</ref><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="142"><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"></highlight></codeline>
<codeline lineno="154"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>**</highlight></codeline>
<codeline lineno="155" refid="group__pseudoknots_1gad3250f0443f875bba3c87c432356bc74" refkind="member"><highlight class="normal"><ref refid="group__pseudoknots_1gad3250f0443f875bba3c87c432356bc74" kindref="member">vrna_pk_plex_accessibility</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="156"><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/></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/><ref refid="group__struct__utils__deprecated_1gadd2f952597e02d66e1116a9d11d252d6" kindref="member">unpaired</ref>,</highlight></codeline>
<codeline lineno="157"><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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>cutoff);</highlight></codeline>
<codeline lineno="158"><highlight class="normal"></highlight></codeline>
<codeline lineno="159"><highlight class="normal"></highlight></codeline>
<codeline lineno="167"><highlight class="normal"><ref refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" kindref="member">vrna_pk_plex_opt_t</ref></highlight></codeline>
<codeline lineno="168" refid="group__pseudoknots_1gaa6a5f5e20804ba729134eb8ad0c8da54" refkind="member"><highlight class="normal"><ref refid="group__pseudoknots_1gaa6a5f5e20804ba729134eb8ad0c8da54" kindref="member">vrna_pk_plex_opt_defaults</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="169"><highlight class="normal"></highlight></codeline>
<codeline lineno="170"><highlight class="normal"></highlight></codeline>
<codeline lineno="181"><highlight class="normal"><ref refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" kindref="member">vrna_pk_plex_opt_t</ref></highlight></codeline>
<codeline lineno="182" refid="group__pseudoknots_1ga8f224a6aa666fd7444b225f676471992" refkind="member"><highlight class="normal"><ref refid="group__pseudoknots_1ga8f224a6aa666fd7444b225f676471992" kindref="member">vrna_pk_plex_opt</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>delta,</highlight></codeline>
<codeline lineno="183"><highlight class="normal"><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/>max_interaction_length,</highlight></codeline>
<codeline lineno="184"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pk_penalty);</highlight></codeline>
<codeline lineno="185"><highlight class="normal"></highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="198"><highlight class="normal"><ref refid="group__pseudoknots_1gab5afc6c459727dbdc37257711f062090" kindref="member">vrna_pk_plex_opt_t</ref></highlight></codeline>
<codeline lineno="199" refid="group__pseudoknots_1ga7209e5212f611aa1c06b1609da696d35" refkind="member"><highlight class="normal"><ref refid="group__pseudoknots_1ga7209e5212f611aa1c06b1609da696d35" kindref="member">vrna_pk_plex_opt_fun</ref>(</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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>delta,</highlight></codeline>
<codeline lineno="200"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>max_interaction_length,</highlight></codeline>
<codeline lineno="201"><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__pseudoknots_1gaa3c616a490113feba261bed7a92981eb" kindref="member">vrna_pk_plex_score_f</ref><sp/><sp/>scoring_function,</highlight></codeline>
<codeline lineno="202"><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">void</highlight><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/>*scoring_data);</highlight></codeline>
<codeline lineno="203"><highlight class="normal"></highlight></codeline>
<codeline lineno="204"><highlight class="normal"></highlight></codeline>
<codeline lineno="208"><highlight class="normal"></highlight></codeline>
<codeline lineno="209"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/pk_plex.h"/>
  </compounddef>
</doxygen>
