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    <sectiondef kind="user-defined">
      <header>Base pair probabilities and derived computations</header>
      <member refid="group__thermodynamics_1gaf3733c2244379f9954365d021b50ef4c" kind="function"><name>vrna_pairing_probs</name></member>
      <member refid="group__thermodynamics_1ga39bbe73ccb7685b6521cfa5c1c64ae78" kind="function"><name>vrna_stack_prob</name></member>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Multimer probabilities computations</header>
      <member refid="group__thermodynamics_1gaa1e39e73afb51fbaf4ae38f0c066c46b" kind="function"><name>vrna_pf_dimer_probs</name></member>
    </sectiondef>
    <briefdescription>
<para>Equilibrium Probability 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_BASEPAIRS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_BASEPAIRS_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><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal">vrna_pairing_probs(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="40"><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="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure);</highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight></codeline>
<codeline lineno="42"><highlight class="normal"></highlight></codeline>
<codeline lineno="53"><highlight class="normal"><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>*</highlight></codeline>
<codeline lineno="54" refid="group__thermodynamics_1ga39bbe73ccb7685b6521cfa5c1c64ae78" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1ga39bbe73ccb7685b6521cfa5c1c64ae78" kindref="member">vrna_stack_prob</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="55"><highlight class="normal"><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/><sp/>cutoff);</highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight></codeline>
<codeline lineno="57"><highlight class="normal"></highlight></codeline>
<codeline lineno="58"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>base<sp/>pair<sp/>related<sp/>functions<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="60"><highlight class="normal"></highlight></codeline>
<codeline lineno="65"><highlight class="normal"></highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="85" refid="group__thermodynamics_1gaa1e39e73afb51fbaf4ae38f0c066c46b" refkind="member"><highlight class="normal"><ref refid="group__thermodynamics_1gaa1e39e73afb51fbaf4ae38f0c066c46b" kindref="member">vrna_pf_dimer_probs</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FAB,</highlight></codeline>
<codeline lineno="86"><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="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FA,</highlight></codeline>
<codeline lineno="87"><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="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>FB,</highlight></codeline>
<codeline lineno="88"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*prAB,</highlight></codeline>
<codeline lineno="89"><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="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*prA,</highlight></codeline>
<codeline lineno="90"><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="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*prB,</highlight></codeline>
<codeline lineno="91"><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="keywordtype">int</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/>Alength,</highlight></codeline>
<codeline lineno="92"><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="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/><sp/>*exp_params);</highlight></codeline>
<codeline lineno="93"><highlight class="normal"></highlight></codeline>
<codeline lineno="94"><highlight class="normal"></highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>multimer<sp/>probability<sp/>related<sp/>functions<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight></codeline>
<codeline lineno="98"><highlight class="normal"></highlight></codeline>
<codeline lineno="99"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>thermodynamics<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="101"><highlight class="normal"></highlight></codeline>
<codeline lineno="102"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/probabilities/basepairs.h"/>
  </compounddef>
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