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      <header>Boltzmann weight (partition function) interface</header>
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        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
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        <briefdescription>
        </briefdescription>
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        </detaileddescription>
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        </inbodydescription>
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<para>Energy evaluation of multibranch loops for MFE and partition function calculations. </para>
    </briefdescription>
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<para>, , </para>
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<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_EVAL_MULTIBRANCH_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_EVAL_MULTIBRANCH_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="utils_2basic_8h" kindref="compound">ViennaRNA/utils/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="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="array_8h" kindref="compound">ViennaRNA/datastructures/array.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><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="8"><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="9"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="eval_2basic_8h" kindref="compound">ViennaRNA/eval/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight></codeline>
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<codeline lineno="25"><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>__GNUC__</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>INLINE<sp/>inline</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="78"><highlight class="normal"></highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>basic<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight></codeline>
<codeline lineno="83"><highlight class="normal"></highlight></codeline>
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<codeline lineno="118"><highlight class="normal"></highlight></codeline>
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<codeline lineno="120"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>partition<sp/>function<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="122"><highlight class="normal"></highlight></codeline>
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<codeline lineno="155"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="156"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>E_MLstem(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="158"><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/>sj1,</highlight></codeline>
<codeline lineno="159"><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__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/>*P),</highlight></codeline>
<codeline lineno="160"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_E_multibranch_stem()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="161"><highlight class="normal"></highlight></codeline>
<codeline lineno="162"><highlight class="normal"></highlight></codeline>
<codeline lineno="163"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="164"><highlight class="normal">E_MLstem(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="165"><highlight class="normal"><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/>si1,</highlight></codeline>
<codeline lineno="166"><highlight class="normal"><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/>sj1,</highlight></codeline>
<codeline lineno="167"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*P)</highlight></codeline>
<codeline lineno="168"><highlight class="normal">{</highlight></codeline>
<codeline lineno="169"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>energy<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="170"><highlight class="normal"></highlight></codeline>
<codeline lineno="171"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(si1<sp/>&gt;=<sp/>0<sp/>&amp;&amp;<sp/>sj1<sp/>&gt;=<sp/>0)</highlight></codeline>
<codeline lineno="172"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;mismatchM[type][si1][sj1];</highlight></codeline>
<codeline lineno="173"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(si1<sp/>&gt;=<sp/>0)</highlight></codeline>
<codeline lineno="174"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;dangle5[type][si1];</highlight></codeline>
<codeline lineno="175"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sj1<sp/>&gt;=<sp/>0)</highlight></codeline>
<codeline lineno="176"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;dangle3[type][sj1];</highlight></codeline>
<codeline lineno="177"><highlight class="normal"></highlight></codeline>
<codeline lineno="178"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="179"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;TerminalAU;</highlight></codeline>
<codeline lineno="180"><highlight class="normal"></highlight></codeline>
<codeline lineno="181"><highlight class="normal"><sp/><sp/>energy<sp/>+=<sp/>P-&gt;MLintern[type];</highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="183"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy;</highlight></codeline>
<codeline lineno="184"><highlight class="normal">}</highlight></codeline>
<codeline lineno="185"><highlight class="normal"></highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="195"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="196"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exp_E_MLstem(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="197"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="198"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="199"><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/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/><sp/>*P),</highlight></codeline>
<codeline lineno="200"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_E_multibranch_stem()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="201"><highlight class="normal"></highlight></codeline>
<codeline lineno="202"><highlight class="normal"></highlight></codeline>
<codeline lineno="203"><highlight class="normal">PRIVATE<sp/>INLINE<sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="204"><highlight class="normal">exp_E_MLstem(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="205"><highlight class="normal"><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/>si1,</highlight></codeline>
<codeline lineno="206"><highlight class="normal"><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/>sj1,</highlight></codeline>
<codeline lineno="207"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*P)</highlight></codeline>
<codeline lineno="208"><highlight class="normal">{</highlight></codeline>
<codeline lineno="209"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>energy<sp/>=<sp/>1.0;</highlight></codeline>
<codeline lineno="210"><highlight class="normal"></highlight></codeline>
<codeline lineno="211"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(si1<sp/>&gt;=<sp/>0<sp/>&amp;&amp;<sp/>sj1<sp/>&gt;=<sp/>0)</highlight></codeline>
<codeline lineno="212"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;expmismatchM[type][si1][sj1];</highlight></codeline>
<codeline lineno="213"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(si1<sp/>&gt;=<sp/>0)</highlight></codeline>
<codeline lineno="214"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;expdangle5[type][si1];</highlight></codeline>
<codeline lineno="215"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sj1<sp/>&gt;=<sp/>0)</highlight></codeline>
<codeline lineno="216"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;expdangle3[type][sj1];</highlight></codeline>
<codeline lineno="217"><highlight class="normal"></highlight></codeline>
<codeline lineno="218"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="219"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>*=<sp/>P-&gt;expTermAU;</highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight></codeline>
<codeline lineno="221"><highlight class="normal"><sp/><sp/>energy<sp/>*=<sp/>P-&gt;expMLintern[type];</highlight></codeline>
<codeline lineno="222"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)energy;</highlight></codeline>
<codeline lineno="223"><highlight class="normal">}</highlight></codeline>
<codeline lineno="224"><highlight class="normal"></highlight></codeline>
<codeline lineno="225"><highlight class="normal"></highlight></codeline>
<codeline lineno="226"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="227"><highlight class="normal"></highlight></codeline>
<codeline lineno="231"><highlight class="normal"></highlight></codeline>
<codeline lineno="232"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/eval/multibranch.h"/>
  </compounddef>
</doxygen>
