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    <sectiondef kind="user-defined">
      <header>Structure probability computations</header>
      <member refid="group__thermodynamics_1gad3f0c240512e6d43e2e4d4c2076021f5" kind="function"><name>vrna_mean_bp_distance_pr</name></member>
      <member refid="group__thermodynamics_1gafd9ef9f1a5f0ab31540e4c3d78addc82" kind="function"><name>vrna_mean_bp_distance</name></member>
      <member refid="group__thermodynamics_1ga20b7a56fa9e451461805fd968c6cd909" kind="function"><name>vrna_ensemble_defect_pt</name></member>
      <member refid="group__thermodynamics_1gaaf197722d1faa86af5e7b4240acafdee" kind="function"><name>vrna_ensemble_defect</name></member>
      <member refid="group__thermodynamics_1ga4ec346141028c7bcd15bc235c408b6e9" kind="function"><name>vrna_positional_entropy</name></member>
      <member refid="group__thermodynamics_1ga882c35d9dd775c1275593b3b6a966bec" kind="function"><name>vrna_pr_structure</name></member>
      <member refid="group__thermodynamics_1ga6a1e8a85e6fab2380ce235180beb85f8" kind="function"><name>vrna_pr_energy</name></member>
    </sectiondef>
    <briefdescription>
<para>Equilibrium Probabilities for structures and structure ensembles implementations. </para>
    </briefdescription>
    <detaileddescription>
<para>This file includes various implementations for equilibrium probability computations based on the partition function of an RNA sequence, two concatenated sequences, or a sequence alignment. </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_STRUCTURES_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_STRUCTURES_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">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><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="6"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="problist_8h" kindref="compound">ViennaRNA/structures/problist.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="params_2basic_8h" kindref="compound">ViennaRNA/params/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="21"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="22"><highlight class="comment"><sp/>#<sp/>BASE<sp/>PAIR<sp/>PROBABILITY<sp/>RELATED<sp/>FUNCTIONS<sp/><sp/><sp/><sp/><sp/><sp/><sp/>#</highlight></codeline>
<codeline lineno="23"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="24"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="25"><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight></codeline>
<codeline lineno="38"><highlight class="normal"></highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="57" refid="group__thermodynamics_1gad3f0c240512e6d43e2e4d4c2076021f5" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1gad3f0c240512e6d43e2e4d4c2076021f5" kindref="member">vrna_mean_bp_distance_pr</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</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/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>*<ref refid="fold__vars_8h_1ac98ec419070aee6831b44e5c700f090f" kindref="member">pr</ref>);</highlight></codeline>
<codeline lineno="59"><highlight class="normal"></highlight></codeline>
<codeline lineno="60"><highlight class="normal"></highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="78" refid="group__thermodynamics_1gafd9ef9f1a5f0ab31540e4c3d78addc82" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1gafd9ef9f1a5f0ab31540e4c3d78addc82" kindref="member">vrna_mean_bp_distance</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight></codeline>
<codeline lineno="105"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="106" refid="group__thermodynamics_1ga20b7a56fa9e451461805fd968c6cd909" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1ga20b7a56fa9e451461805fd968c6cd909" kindref="member">vrna_ensemble_defect_pt</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="107"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*pt);</highlight></codeline>
<codeline lineno="108"><highlight class="normal"></highlight></codeline>
<codeline lineno="109"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="136" refid="group__thermodynamics_1gaaf197722d1faa86af5e7b4240acafdee" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1gaaf197722d1faa86af5e7b4240acafdee" kindref="member">vrna_ensemble_defect</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="137"><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="138"><highlight class="normal"></highlight></codeline>
<codeline lineno="139"><highlight class="normal"></highlight></codeline>
<codeline lineno="164"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="165" refid="group__thermodynamics_1ga4ec346141028c7bcd15bc235c408b6e9" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1ga4ec346141028c7bcd15bc235c408b6e9" kindref="member">vrna_positional_entropy</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="166"><highlight class="normal"></highlight></codeline>
<codeline lineno="167"><highlight class="normal"></highlight></codeline>
<codeline lineno="194"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="195" refid="group__thermodynamics_1ga882c35d9dd775c1275593b3b6a966bec" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1ga882c35d9dd775c1275593b3b6a966bec" kindref="member">vrna_pr_structure</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="196"><highlight class="normal"><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/><sp/>*structure);</highlight></codeline>
<codeline lineno="197"><highlight class="normal"></highlight></codeline>
<codeline lineno="198"><highlight class="normal"></highlight></codeline>
<codeline lineno="199"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="200" refid="group__thermodynamics_1ga6a1e8a85e6fab2380ce235180beb85f8" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1ga6a1e8a85e6fab2380ce235180beb85f8" kindref="member">vrna_pr_energy</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="201"><highlight class="normal"><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/>e);</highlight></codeline>
<codeline lineno="202"><highlight class="normal"></highlight></codeline>
<codeline lineno="203"><highlight class="normal"></highlight></codeline>
<codeline lineno="204"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>structure<sp/>probability<sp/>related<sp/>functions<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="206"><highlight class="normal"></highlight></codeline>
<codeline lineno="207"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>thermodynamics<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="209"><highlight class="normal"></highlight></codeline>
<codeline lineno="210"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/probabilities/structures.h"/>
  </compounddef>
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