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<para>, , </para>
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<codeline lineno="106"><highlight class="normal"><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="107"><highlight class="normal"><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="108"><highlight class="normal"><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/>sp1,</highlight></codeline>
<codeline lineno="109"><highlight class="normal"><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/>sq1,</highlight></codeline>
<codeline lineno="110"><highlight class="normal"><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="111"><highlight class="normal"></highlight></codeline>
<codeline lineno="112"><highlight class="normal"></highlight></codeline>
<codeline lineno="120"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="121" refid="group__eval__loops__int_1ga89b62e8fafa81514c6bd58a16e90d00a" refkind="member"><highlight class="normal"><ref refid="group__eval__loops__int_1ga89b62e8fafa81514c6bd58a16e90d00a" kindref="member">vrna_eval_internal</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="122"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="123"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="124"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k,</highlight></codeline>
<codeline lineno="125"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>l,</highlight></codeline>
<codeline lineno="126"><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">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="127"><highlight class="normal"></highlight></codeline>
<codeline lineno="128"><highlight class="normal"></highlight></codeline>
<codeline lineno="129"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="130"><highlight class="normal">vrna_eval_stack(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="131"><highlight class="normal"><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/>i,</highlight></codeline>
<codeline lineno="132"><highlight class="normal"><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/>j,</highlight></codeline>
<codeline lineno="133"><highlight class="normal"><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/>options);</highlight></codeline>
<codeline lineno="134"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal"></highlight></codeline>
<codeline lineno="136"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>basic<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"></highlight></codeline>
<codeline lineno="139"><highlight class="normal"></highlight></codeline>
<codeline lineno="144"><highlight class="normal"></highlight></codeline>
<codeline lineno="145"><highlight class="normal"></highlight></codeline>
<codeline lineno="146"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="147"><highlight class="normal">vrna_exp_E_internal(</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/>n1,</highlight></codeline>
<codeline lineno="148"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>n2,</highlight></codeline>
<codeline lineno="149"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="150"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>type_2,</highlight></codeline>
<codeline lineno="151"><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/>si1,</highlight></codeline>
<codeline lineno="152"><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/>sj1,</highlight></codeline>
<codeline lineno="153"><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/>sp1,</highlight></codeline>
<codeline lineno="154"><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/>sq1,</highlight></codeline>
<codeline lineno="155"><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_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/><sp/>*P);</highlight></codeline>
<codeline lineno="156"><highlight class="normal"></highlight></codeline>
<codeline lineno="157"><highlight class="normal"></highlight></codeline>
<codeline lineno="158"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="159"><highlight class="normal">vrna_exp_eval_internal(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="160"><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/></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/>i,</highlight></codeline>
<codeline lineno="161"><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/></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/>j,</highlight></codeline>
<codeline lineno="162"><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/></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/>k,</highlight></codeline>
<codeline lineno="163"><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/></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/>l,</highlight></codeline>
<codeline lineno="164"><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/></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="165"><highlight class="normal"></highlight></codeline>
<codeline lineno="166"><highlight class="normal"></highlight></codeline>
<codeline lineno="167"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>partition<sp/>function<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="169"><highlight class="normal"></highlight></codeline>
<codeline lineno="173"><highlight class="normal"></highlight></codeline>
<codeline lineno="174"><highlight class="normal"></highlight></codeline>
<codeline lineno="175"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="176"><highlight class="normal"></highlight></codeline>
<codeline lineno="181"><highlight class="normal"></highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="183"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>ON_SAME_STRAND</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="184"><highlight class="normal"></highlight><highlight class="preprocessor">#undef<sp/>ON_SAME_STRAND</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="185"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="187"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>ON_SAME_STRAND(I,<sp/>J,<sp/>C)<sp/><sp/>(((I)<sp/>&gt;=<sp/>(C))<sp/>||<sp/>((J)<sp/>&lt;<sp/>(C)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="188"><highlight class="normal"></highlight></codeline>
<codeline lineno="234"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="235"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>E_IntLoop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>n1,</highlight></codeline>
<codeline lineno="236"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>n2,</highlight></codeline>
<codeline lineno="237"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="238"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type_2,</highlight></codeline>
<codeline lineno="239"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="240"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="241"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="242"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="243"><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__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*P),</highlight></codeline>
<codeline lineno="244"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_E_internal()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="245"><highlight class="normal"></highlight></codeline>
<codeline lineno="246"><highlight class="normal"></highlight></codeline>
<codeline lineno="266"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="267"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exp_E_IntLoop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>u1,</highlight></codeline>
<codeline lineno="268"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>u2,</highlight></codeline>
<codeline lineno="269"><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/></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="270"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type2,</highlight></codeline>
<codeline lineno="271"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="272"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="273"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="274"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="275"><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__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*P),</highlight></codeline>
<codeline lineno="276"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_E_internal()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="277"><highlight class="normal"></highlight></codeline>
<codeline lineno="278"><highlight class="normal"></highlight></codeline>
<codeline lineno="279"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="280"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>E_IntLoop_Co(</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="281"><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/>type_2,</highlight></codeline>
<codeline lineno="282"><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/>i,</highlight></codeline>
<codeline lineno="283"><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/>j,</highlight></codeline>
<codeline lineno="284"><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/>p,</highlight></codeline>
<codeline lineno="285"><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/>q,</highlight></codeline>
<codeline lineno="286"><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/>cutpoint,</highlight></codeline>
<codeline lineno="287"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="288"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="289"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="290"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="291"><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/><ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="292"><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_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/>*P),</highlight></codeline>
<codeline lineno="293"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="294"><highlight class="normal"></highlight></codeline>
<codeline lineno="295"><highlight class="normal"></highlight></codeline>
<codeline lineno="296"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="297"><highlight class="normal">__E_IntLoop_Co(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="298"><highlight class="normal"><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/>type_2,</highlight></codeline>
<codeline lineno="299"><highlight class="normal"><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/>i,</highlight></codeline>
<codeline lineno="300"><highlight class="normal"><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/>j,</highlight></codeline>
<codeline lineno="301"><highlight class="normal"><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/>p,</highlight></codeline>
<codeline lineno="302"><highlight class="normal"><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/>q,</highlight></codeline>
<codeline lineno="303"><highlight class="normal"><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/>cutpoint,</highlight></codeline>
<codeline lineno="304"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="305"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="306"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="307"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="308"><highlight class="normal"><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/><ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="309"><highlight class="normal"><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/>*P);</highlight></codeline>
<codeline lineno="310"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="311"><highlight class="comment"><sp/>*<sp/><sp/>ugly<sp/>but<sp/>fast<sp/>internal<sp/>loop<sp/>evaluation</highlight></codeline>
<codeline lineno="312"><highlight class="comment"><sp/>*</highlight></codeline>
<codeline lineno="313"><highlight class="comment"><sp/>*<sp/><sp/>Avoid<sp/>including<sp/>this<sp/>function<sp/>in<sp/>your<sp/>own<sp/>code.<sp/>It<sp/>only<sp/>serves</highlight></codeline>
<codeline lineno="314"><highlight class="comment"><sp/>*<sp/><sp/>as<sp/>a<sp/>fast<sp/>inline<sp/>block<sp/>internally<sp/>re-used<sp/>throughout<sp/>the<sp/>RNAlib.<sp/>It</highlight></codeline>
<codeline lineno="315"><highlight class="comment"><sp/>*<sp/><sp/>evalutes<sp/>the<sp/>free<sp/>energy<sp/>of<sp/>internal<sp/>loops<sp/>in<sp/>single<sp/>sequences<sp/>or<sp/>sequence</highlight></codeline>
<codeline lineno="316"><highlight class="comment"><sp/>*<sp/><sp/>hybrids.<sp/>Soft<sp/>constraints<sp/>are<sp/>also<sp/>applied<sp/>if<sp/>available.</highlight></codeline>
<codeline lineno="317"><highlight class="comment"><sp/>*</highlight></codeline>
<codeline lineno="318"><highlight class="comment"><sp/>*<sp/><sp/>NOTE:<sp/>do<sp/>not<sp/>include<sp/>into<sp/>doxygen<sp/>reference<sp/>manual!</highlight></codeline>
<codeline lineno="319"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="320"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="321"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ubf_eval_int_loop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="322"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="323"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p,</highlight></codeline>
<codeline lineno="324"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q,</highlight></codeline>
<codeline lineno="325"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i1,</highlight></codeline>
<codeline lineno="326"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j1,</highlight></codeline>
<codeline lineno="327"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p1,</highlight></codeline>
<codeline lineno="328"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q1,</highlight></codeline>
<codeline lineno="329"><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="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si,</highlight></codeline>
<codeline lineno="330"><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="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj,</highlight></codeline>
<codeline lineno="331"><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="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp,</highlight></codeline>
<codeline lineno="332"><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="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq,</highlight></codeline>
<codeline lineno="333"><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="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>type,</highlight></codeline>
<codeline lineno="334"><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="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>type_2,</highlight></codeline>
<codeline lineno="335"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*rtype,</highlight></codeline>
<codeline lineno="336"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ij,</highlight></codeline>
<codeline lineno="337"><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="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>cp,</highlight></codeline>
<codeline lineno="338"><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/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/><sp/>*P,</highlight></codeline>
<codeline lineno="339"><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/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*sc),</highlight></codeline>
<codeline lineno="340"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="341"><highlight class="normal"></highlight></codeline>
<codeline lineno="342"><highlight class="normal"></highlight></codeline>
<codeline lineno="343"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="344"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ubf_eval_int_loop2(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="345"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="346"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p,</highlight></codeline>
<codeline lineno="347"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q,</highlight></codeline>
<codeline lineno="348"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i1,</highlight></codeline>
<codeline lineno="349"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j1,</highlight></codeline>
<codeline lineno="350"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p1,</highlight></codeline>
<codeline lineno="351"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q1,</highlight></codeline>
<codeline lineno="352"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si,</highlight></codeline>
<codeline lineno="353"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj,</highlight></codeline>
<codeline lineno="354"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp,</highlight></codeline>
<codeline lineno="355"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq,</highlight></codeline>
<codeline lineno="356"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>type,</highlight></codeline>
<codeline lineno="357"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>type_2,</highlight></codeline>
<codeline lineno="358"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*rtype,</highlight></codeline>
<codeline lineno="359"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ij,</highlight></codeline>
<codeline lineno="360"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>*sn,</highlight></codeline>
<codeline lineno="361"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>*ss,</highlight></codeline>
<codeline lineno="362"><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/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/>*P,</highlight></codeline>
<codeline lineno="363"><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/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/>*sc),</highlight></codeline>
<codeline lineno="364"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="365"><highlight class="normal"></highlight></codeline>
<codeline lineno="366"><highlight class="normal"></highlight></codeline>
<codeline lineno="367"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="368"><highlight class="comment"><sp/>*<sp/><sp/>ugly<sp/>but<sp/>fast<sp/>exterior<sp/>internal<sp/>loop<sp/>evaluation</highlight></codeline>
<codeline lineno="369"><highlight class="comment"><sp/>*</highlight></codeline>
<codeline lineno="370"><highlight class="comment"><sp/>*<sp/><sp/>Avoid<sp/>including<sp/>this<sp/>function<sp/>in<sp/>your<sp/>own<sp/>code.<sp/>It<sp/>only<sp/>serves</highlight></codeline>
<codeline lineno="371"><highlight class="comment"><sp/>*<sp/><sp/>as<sp/>a<sp/>fast<sp/>inline<sp/>block<sp/>internally<sp/>re-used<sp/>throughout<sp/>the<sp/>RNAlib.<sp/>It</highlight></codeline>
<codeline lineno="372"><highlight class="comment"><sp/>*<sp/><sp/>evalutes<sp/>the<sp/>free<sp/>energy<sp/>of<sp/>internal<sp/>loops<sp/>in<sp/>single<sp/>sequences<sp/>or<sp/>sequence</highlight></codeline>
<codeline lineno="373"><highlight class="comment"><sp/>*<sp/><sp/>hybrids.<sp/>Soft<sp/>constraints<sp/>are<sp/>also<sp/>applied<sp/>if<sp/>available.</highlight></codeline>
<codeline lineno="374"><highlight class="comment"><sp/>*</highlight></codeline>
<codeline lineno="375"><highlight class="comment"><sp/>*<sp/><sp/>NOTE:<sp/>do<sp/>not<sp/>include<sp/>into<sp/>doxygen<sp/>reference<sp/>manual!</highlight></codeline>
<codeline lineno="376"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="377"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="378"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ubf_eval_ext_int_loop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="379"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="380"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p,</highlight></codeline>
<codeline lineno="381"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q,</highlight></codeline>
<codeline lineno="382"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i1,</highlight></codeline>
<codeline lineno="383"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j1,</highlight></codeline>
<codeline lineno="384"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p1,</highlight></codeline>
<codeline lineno="385"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q1,</highlight></codeline>
<codeline lineno="386"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si,</highlight></codeline>
<codeline lineno="387"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj,</highlight></codeline>
<codeline lineno="388"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp,</highlight></codeline>
<codeline lineno="389"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq,</highlight></codeline>
<codeline lineno="390"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>type,</highlight></codeline>
<codeline lineno="391"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>type_2,</highlight></codeline>
<codeline lineno="392"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="393"><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/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/><sp/>*P,</highlight></codeline>
<codeline lineno="394"><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/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*sc),</highlight></codeline>
<codeline lineno="395"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="396"><highlight class="normal"></highlight></codeline>
<codeline lineno="397"><highlight class="normal"></highlight></codeline>
<codeline lineno="398"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="399"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__eval__deprecated_1gaab3547bfcdc39d89babbc7ed2a1a4b65" kindref="member">vrna_eval_int_loop</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="400"><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/></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/>i,</highlight></codeline>
<codeline lineno="401"><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/></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/>j,</highlight></codeline>
<codeline lineno="402"><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/></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/>k,</highlight></codeline>
<codeline lineno="403"><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/></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/>l),</highlight></codeline>
<codeline lineno="404" refid="group__eval__deprecated_1gaab3547bfcdc39d89babbc7ed2a1a4b65" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_internal()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="405"><highlight class="normal"></highlight></codeline>
<codeline lineno="406"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="407"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_E_stack(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="408"><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/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="409"><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/><sp/><sp/><sp/><sp/>j),</highlight></codeline>
<codeline lineno="410"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_stack()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="411"><highlight class="normal"></highlight></codeline>
<codeline lineno="412"><highlight class="normal"></highlight></codeline>
<codeline lineno="413"><highlight class="normal">DEPRECATED(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="414"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_exp_E_interior_loop(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="415"><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/></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/>i,</highlight></codeline>
<codeline lineno="416"><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/></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/>j,</highlight></codeline>
<codeline lineno="417"><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/></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/>k,</highlight></codeline>
<codeline lineno="418"><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/></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/>l),</highlight></codeline>
<codeline lineno="419"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_eval_internal()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="420"><highlight class="normal"></highlight></codeline>
<codeline lineno="421"><highlight class="normal"></highlight></codeline>
<codeline lineno="422"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="423"><highlight class="normal">ubf_eval_int_loop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="424"><highlight class="normal"><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/>j,</highlight></codeline>
<codeline lineno="425"><highlight class="normal"><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/>p,</highlight></codeline>
<codeline lineno="426"><highlight class="normal"><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/>q,</highlight></codeline>
<codeline lineno="427"><highlight class="normal"><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/>i1,</highlight></codeline>
<codeline lineno="428"><highlight class="normal"><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/>j1,</highlight></codeline>
<codeline lineno="429"><highlight class="normal"><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/>p1,</highlight></codeline>
<codeline lineno="430"><highlight class="normal"><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/>q1,</highlight></codeline>
<codeline lineno="431"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si,</highlight></codeline>
<codeline lineno="432"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj,</highlight></codeline>
<codeline lineno="433"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp,</highlight></codeline>
<codeline lineno="434"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq,</highlight></codeline>
<codeline lineno="435"><highlight class="normal"><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">char</highlight><highlight class="normal"><sp/>type,</highlight></codeline>
<codeline lineno="436"><highlight class="normal"><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">char</highlight><highlight class="normal"><sp/>type_2,</highlight></codeline>
<codeline lineno="437"><highlight class="normal"><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/>*rtype,</highlight></codeline>
<codeline lineno="438"><highlight class="normal"><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/>ij,</highlight></codeline>
<codeline lineno="439"><highlight class="normal"><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/>cp,</highlight></codeline>
<codeline lineno="440"><highlight class="normal"><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="441"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/>*sc)</highlight></codeline>
<codeline lineno="442"><highlight class="normal">{</highlight></codeline>
<codeline lineno="443"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>energy,<sp/>u1,<sp/>u2;</highlight></codeline>
<codeline lineno="444"><highlight class="normal"></highlight></codeline>
<codeline lineno="445"><highlight class="normal"><sp/><sp/>u1<sp/><sp/>=<sp/>p1<sp/>-<sp/>i;</highlight></codeline>
<codeline lineno="446"><highlight class="normal"><sp/><sp/>u2<sp/><sp/>=<sp/>j1<sp/>-<sp/>q;</highlight></codeline>
<codeline lineno="447"><highlight class="normal"></highlight></codeline>
<codeline lineno="448"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((cp<sp/>&lt;<sp/>0)<sp/>||<sp/>(ON_SAME_STRAND(i,<sp/>p,<sp/>cp)<sp/>&amp;&amp;<sp/>ON_SAME_STRAND(q,<sp/>j,<sp/>cp)))<sp/>{</highlight></codeline>
<codeline lineno="449"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>regular<sp/>internal<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="450"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/><ref refid="group__eval__loops__int_1gaaaa6eb5605d1c843af1269c6f23cb53c" kindref="member">vrna_E_internal</ref>(u1,<sp/>u2,<sp/>type,<sp/>type_2,<sp/>si,<sp/>sj,<sp/>sp,<sp/>sq,<sp/>P);</highlight></codeline>
<codeline lineno="451"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="452"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>like<sp/>cofold<sp/>structure<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="453"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>Si,<sp/>Sj;</highlight></codeline>
<codeline lineno="454"><highlight class="normal"><sp/><sp/><sp/><sp/>Si<sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>ON_SAME_STRAND(i,<sp/>i1,<sp/>cp)<sp/>?<sp/>si<sp/>:<sp/>-1;</highlight></codeline>
<codeline lineno="455"><highlight class="normal"><sp/><sp/><sp/><sp/>Sj<sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>ON_SAME_STRAND(j1,<sp/>j,<sp/>cp)<sp/>?<sp/>sj<sp/>:<sp/>-1;</highlight></codeline>
<codeline lineno="456"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/><sp/>=<sp/>__E_IntLoop_Co(rtype[type],<sp/>rtype[type_2],</highlight></codeline>
<codeline lineno="457"><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/>i,<sp/>j,<sp/>p,<sp/>q,</highlight></codeline>
<codeline lineno="458"><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/>cp,</highlight></codeline>
<codeline lineno="459"><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/>Si,<sp/>Sj,</highlight></codeline>
<codeline lineno="460"><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/>sq,</highlight></codeline>
<codeline lineno="461"><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/>P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1adcda4ff2ea77748ae0e8700288282efc" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="462"><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/>P);</highlight></codeline>
<codeline lineno="463"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="464"><highlight class="normal"></highlight></codeline>
<codeline lineno="465"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>add<sp/>soft<sp/>constraints<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="466"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc)<sp/>{</highlight></codeline>
<codeline lineno="467"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>)</highlight></codeline>
<codeline lineno="468"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[i1][u1]</highlight></codeline>
<codeline lineno="469"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[q1][u2];</highlight></codeline>
<codeline lineno="470"><highlight class="normal"></highlight></codeline>
<codeline lineno="471"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1ad139b8e06632e00cbcf3909815d0d03d" kindref="member">energy_bp</ref>)</highlight></codeline>
<codeline lineno="472"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ad139b8e06632e00cbcf3909815d0d03d" kindref="member">energy_bp</ref>[ij];</highlight></codeline>
<codeline lineno="473"><highlight class="normal"></highlight></codeline>
<codeline lineno="474"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>)</highlight></codeline>
<codeline lineno="475"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u1<sp/>+<sp/>u2<sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="476"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>a<sp/>=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[i]</highlight></codeline>
<codeline lineno="477"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[p]</highlight></codeline>
<codeline lineno="478"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[q]</highlight></codeline>
<codeline lineno="479"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[j];</highlight></codeline>
<codeline lineno="480"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>a;</highlight></codeline>
<codeline lineno="481"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="482"><highlight class="normal"></highlight></codeline>
<codeline lineno="483"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" kindref="member">f</ref>)</highlight></codeline>
<codeline lineno="484"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" kindref="member">f</ref>(i,<sp/>j,<sp/>p,<sp/>q,<sp/><ref refid="group__constraints_1gaeab04f34d7730cff2d651d782f95d857" kindref="member">VRNA_DECOMP_PAIR_IL</ref>,<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a7574680143df97b9029146c2150bf06d" kindref="member">data</ref>);</highlight></codeline>
<codeline lineno="485"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="486"><highlight class="normal"></highlight></codeline>
<codeline lineno="487"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy;</highlight></codeline>
<codeline lineno="488"><highlight class="normal">}</highlight></codeline>
<codeline lineno="489"><highlight class="normal"></highlight></codeline>
<codeline lineno="490"><highlight class="normal"></highlight></codeline>
<codeline lineno="491"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="492"><highlight class="normal">ubf_eval_int_loop2(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="493"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="494"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p,</highlight></codeline>
<codeline lineno="495"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q,</highlight></codeline>
<codeline lineno="496"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i1,</highlight></codeline>
<codeline lineno="497"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j1,</highlight></codeline>
<codeline lineno="498"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p1,</highlight></codeline>
<codeline lineno="499"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q1,</highlight></codeline>
<codeline lineno="500"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si,</highlight></codeline>
<codeline lineno="501"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj,</highlight></codeline>
<codeline lineno="502"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp,</highlight></codeline>
<codeline lineno="503"><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">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq,</highlight></codeline>
<codeline lineno="504"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>type,</highlight></codeline>
<codeline lineno="505"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>type_2,</highlight></codeline>
<codeline lineno="506"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*rtype,</highlight></codeline>
<codeline lineno="507"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ij,</highlight></codeline>
<codeline lineno="508"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>*sn,</highlight></codeline>
<codeline lineno="509"><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">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>*ss,</highlight></codeline>
<codeline lineno="510"><highlight class="normal"><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/><sp/>*P,</highlight></codeline>
<codeline lineno="511"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*sc)</highlight></codeline>
<codeline lineno="512"><highlight class="normal">{</highlight></codeline>
<codeline lineno="513"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>energy,<sp/>u1,<sp/>u2;</highlight></codeline>
<codeline lineno="514"><highlight class="normal"></highlight></codeline>
<codeline lineno="515"><highlight class="normal"><sp/><sp/>u1<sp/><sp/>=<sp/>p1<sp/>-<sp/>i;</highlight></codeline>
<codeline lineno="516"><highlight class="normal"><sp/><sp/>u2<sp/><sp/>=<sp/>j1<sp/>-<sp/>q;</highlight></codeline>
<codeline lineno="517"><highlight class="normal"></highlight></codeline>
<codeline lineno="518"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((sn[i]<sp/>==<sp/>sn[p])<sp/>&amp;&amp;<sp/>(sn[q]<sp/>==<sp/>sn[j]))<sp/>{</highlight></codeline>
<codeline lineno="519"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>regular<sp/>internal<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="520"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/><ref refid="group__eval__loops__int_1gaaaa6eb5605d1c843af1269c6f23cb53c" kindref="member">vrna_E_internal</ref>(u1,<sp/>u2,<sp/>type,<sp/>type_2,<sp/>si,<sp/>sj,<sp/>sp,<sp/>sq,<sp/>P);</highlight></codeline>
<codeline lineno="521"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="522"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>like<sp/>cofold<sp/>structure<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="523"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/>Si,<sp/>Sj;</highlight></codeline>
<codeline lineno="524"><highlight class="normal"><sp/><sp/><sp/><sp/>Si<sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>(sn[i1]<sp/>==<sp/>sn[i])<sp/>?<sp/>si<sp/>:<sp/>-1;</highlight></codeline>
<codeline lineno="525"><highlight class="normal"><sp/><sp/><sp/><sp/>Sj<sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>(sn[j]<sp/>==<sp/>sn[j1])<sp/>?<sp/>sj<sp/>:<sp/>-1;</highlight></codeline>
<codeline lineno="526"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/><sp/>=<sp/>__E_IntLoop_Co(rtype[type],<sp/>rtype[type_2],</highlight></codeline>
<codeline lineno="527"><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/>i,<sp/>j,<sp/>p,<sp/>q,</highlight></codeline>
<codeline lineno="528"><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/>ss[1],</highlight></codeline>
<codeline lineno="529"><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/>Si,<sp/>Sj,</highlight></codeline>
<codeline lineno="530"><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/>sq,</highlight></codeline>
<codeline lineno="531"><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/>P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1adcda4ff2ea77748ae0e8700288282efc" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="532"><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/>P);</highlight></codeline>
<codeline lineno="533"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="534"><highlight class="normal"></highlight></codeline>
<codeline lineno="535"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>add<sp/>soft<sp/>constraints<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="536"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc)<sp/>{</highlight></codeline>
<codeline lineno="537"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>)</highlight></codeline>
<codeline lineno="538"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[i1][u1]</highlight></codeline>
<codeline lineno="539"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[q1][u2];</highlight></codeline>
<codeline lineno="540"><highlight class="normal"></highlight></codeline>
<codeline lineno="541"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1ad139b8e06632e00cbcf3909815d0d03d" kindref="member">energy_bp</ref>)</highlight></codeline>
<codeline lineno="542"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ad139b8e06632e00cbcf3909815d0d03d" kindref="member">energy_bp</ref>[ij];</highlight></codeline>
<codeline lineno="543"><highlight class="normal"></highlight></codeline>
<codeline lineno="544"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>)</highlight></codeline>
<codeline lineno="545"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u1<sp/>+<sp/>u2<sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="546"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>a<sp/>=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[i]</highlight></codeline>
<codeline lineno="547"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[p]</highlight></codeline>
<codeline lineno="548"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[q]</highlight></codeline>
<codeline lineno="549"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[j];</highlight></codeline>
<codeline lineno="550"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>a;</highlight></codeline>
<codeline lineno="551"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="552"><highlight class="normal"></highlight></codeline>
<codeline lineno="553"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" kindref="member">f</ref>)</highlight></codeline>
<codeline lineno="554"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" kindref="member">f</ref>(i,<sp/>j,<sp/>p,<sp/>q,<sp/><ref refid="group__constraints_1gaeab04f34d7730cff2d651d782f95d857" kindref="member">VRNA_DECOMP_PAIR_IL</ref>,<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a7574680143df97b9029146c2150bf06d" kindref="member">data</ref>);</highlight></codeline>
<codeline lineno="555"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="556"><highlight class="normal"></highlight></codeline>
<codeline lineno="557"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy;</highlight></codeline>
<codeline lineno="558"><highlight class="normal">}</highlight></codeline>
<codeline lineno="559"><highlight class="normal"></highlight></codeline>
<codeline lineno="560"><highlight class="normal"></highlight></codeline>
<codeline lineno="561"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="562"><highlight class="normal">ubf_eval_ext_int_loop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="563"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="564"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p,</highlight></codeline>
<codeline lineno="565"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q,</highlight></codeline>
<codeline lineno="566"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i1,</highlight></codeline>
<codeline lineno="567"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j1,</highlight></codeline>
<codeline lineno="568"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>p1,</highlight></codeline>
<codeline lineno="569"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q1,</highlight></codeline>
<codeline lineno="570"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si,</highlight></codeline>
<codeline lineno="571"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj,</highlight></codeline>
<codeline lineno="572"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp,</highlight></codeline>
<codeline lineno="573"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq,</highlight></codeline>
<codeline lineno="574"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>type,</highlight></codeline>
<codeline lineno="575"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>type_2,</highlight></codeline>
<codeline lineno="576"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="577"><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/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/>*P,</highlight></codeline>
<codeline lineno="578"><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/><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref><sp/><sp/><sp/><sp/><sp/>*sc)</highlight></codeline>
<codeline lineno="579"><highlight class="normal">{</highlight></codeline>
<codeline lineno="580"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>energy,<sp/>u1,<sp/>u2,<sp/>u3;</highlight></codeline>
<codeline lineno="581"><highlight class="normal"></highlight></codeline>
<codeline lineno="582"><highlight class="normal"><sp/><sp/>u1<sp/><sp/>=<sp/>i1;</highlight></codeline>
<codeline lineno="583"><highlight class="normal"><sp/><sp/>u2<sp/><sp/>=<sp/>p1<sp/>-<sp/>j;</highlight></codeline>
<codeline lineno="584"><highlight class="normal"><sp/><sp/>u3<sp/><sp/>=<sp/>length<sp/>-<sp/>q;</highlight></codeline>
<codeline lineno="585"><highlight class="normal"></highlight></codeline>
<codeline lineno="586"><highlight class="normal"><sp/><sp/>energy<sp/>=<sp/><ref refid="group__eval__loops__int_1gaaaa6eb5605d1c843af1269c6f23cb53c" kindref="member">vrna_E_internal</ref>(u2,<sp/>u1<sp/>+<sp/>u3,<sp/>type,<sp/>type_2,<sp/>si,<sp/>sj,<sp/>sp,<sp/>sq,<sp/>P);</highlight></codeline>
<codeline lineno="587"><highlight class="normal"></highlight></codeline>
<codeline lineno="588"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>add<sp/>soft<sp/>constraints<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="589"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc)<sp/>{</highlight></codeline>
<codeline lineno="590"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>)<sp/>{</highlight></codeline>
<codeline lineno="591"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[j1][u2]</highlight></codeline>
<codeline lineno="592"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>((u3<sp/>&gt;<sp/>0)<sp/>?<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[q1][u3]<sp/>:<sp/>0)</highlight></codeline>
<codeline lineno="593"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>((u1<sp/>&gt;<sp/>0)<sp/>?<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" kindref="member">energy_up</ref>[1][u1]<sp/>:<sp/>0);</highlight></codeline>
<codeline lineno="594"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="595"><highlight class="normal"></highlight></codeline>
<codeline lineno="596"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>)</highlight></codeline>
<codeline lineno="597"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u1<sp/>+<sp/>u2<sp/>+<sp/>u3<sp/>==<sp/>0)</highlight></codeline>
<codeline lineno="598"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[i]</highlight></codeline>
<codeline lineno="599"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[p]</highlight></codeline>
<codeline lineno="600"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[q]</highlight></codeline>
<codeline lineno="601"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>+<sp/>sc-&gt;<ref refid="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" kindref="member">energy_stack</ref>[j];</highlight></codeline>
<codeline lineno="602"><highlight class="normal"></highlight></codeline>
<codeline lineno="603"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(sc-&gt;<ref refid="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" kindref="member">f</ref>)</highlight></codeline>
<codeline lineno="604"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" kindref="member">f</ref>(i,<sp/>j,<sp/>p,<sp/>q,<sp/><ref refid="group__constraints_1gaeab04f34d7730cff2d651d782f95d857" kindref="member">VRNA_DECOMP_PAIR_IL</ref>,<sp/>sc-&gt;<ref refid="structvrna__sc__s_1a7574680143df97b9029146c2150bf06d" kindref="member">data</ref>);</highlight></codeline>
<codeline lineno="605"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="606"><highlight class="normal"></highlight></codeline>
<codeline lineno="607"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy;</highlight></codeline>
<codeline lineno="608"><highlight class="normal">}</highlight></codeline>
<codeline lineno="609"><highlight class="normal"></highlight></codeline>
<codeline lineno="610"><highlight class="normal"></highlight></codeline>
<codeline lineno="611"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="612"><highlight class="normal">E_IntLoop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>n1,</highlight></codeline>
<codeline lineno="613"><highlight class="normal"><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/>n2,</highlight></codeline>
<codeline lineno="614"><highlight class="normal"><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/>type,</highlight></codeline>
<codeline lineno="615"><highlight class="normal"><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/>type_2,</highlight></codeline>
<codeline lineno="616"><highlight class="normal"><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="617"><highlight class="normal"><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="618"><highlight class="normal"><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/>sp1,</highlight></codeline>
<codeline lineno="619"><highlight class="normal"><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/>sq1,</highlight></codeline>
<codeline lineno="620"><highlight class="normal"><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="621"><highlight class="normal">{</highlight></codeline>
<codeline lineno="622"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>compute<sp/>energy<sp/>of<sp/>degree<sp/>2<sp/>loop<sp/>(stack<sp/>bulge<sp/>or<sp/>internal)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="623"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>nl,<sp/>ns,<sp/>u,<sp/>energy,<sp/>salt_stack_correction,<sp/>salt_loop_correction,<sp/>backbones;</highlight></codeline>
<codeline lineno="624"><highlight class="normal"></highlight></codeline>
<codeline lineno="625"><highlight class="normal"><sp/><sp/>salt_stack_correction<sp/>=<sp/>P-&gt;SaltStack;</highlight></codeline>
<codeline lineno="626"><highlight class="normal"><sp/><sp/>salt_loop_correction<sp/><sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="627"><highlight class="normal"></highlight></codeline>
<codeline lineno="628"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(n1<sp/>&gt;<sp/>n2)<sp/>{</highlight></codeline>
<codeline lineno="629"><highlight class="normal"><sp/><sp/><sp/><sp/>nl<sp/><sp/>=<sp/>n1;</highlight></codeline>
<codeline lineno="630"><highlight class="normal"><sp/><sp/><sp/><sp/>ns<sp/><sp/>=<sp/>n2;</highlight></codeline>
<codeline lineno="631"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="632"><highlight class="normal"><sp/><sp/><sp/><sp/>nl<sp/><sp/>=<sp/>n2;</highlight></codeline>
<codeline lineno="633"><highlight class="normal"><sp/><sp/><sp/><sp/>ns<sp/><sp/>=<sp/>n1;</highlight></codeline>
<codeline lineno="634"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="635"><highlight class="normal"></highlight></codeline>
<codeline lineno="636"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(nl<sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="637"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>P-&gt;stack[type][type_2]<sp/>+<sp/>salt_stack_correction;<sp/><sp/></highlight><highlight class="comment">/*<sp/>stack<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="638"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="639"><highlight class="normal"></highlight></codeline>
<codeline lineno="640"><highlight class="normal"><sp/><sp/>backbones<sp/>=<sp/>nl<sp/>+<sp/>ns<sp/>+<sp/>2;</highlight></codeline>
<codeline lineno="641"><highlight class="normal"></highlight></codeline>
<codeline lineno="642"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref><sp/>!=<sp/><ref refid="group__model__details_1gaa68703da9ccc5ae6da508bfda36b533f" kindref="member">VRNA_MODEL_DEFAULT_SALT</ref>)<sp/>{</highlight></codeline>
<codeline lineno="643"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>salt<sp/>correction<sp/>for<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="644"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(backbones<sp/>&lt;=<sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1)</highlight></codeline>
<codeline lineno="645"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_loop_correction<sp/>=<sp/>P-&gt;SaltLoop[backbones];</highlight></codeline>
<codeline lineno="646"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="647"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_loop_correction<sp/>=</highlight></codeline>
<codeline lineno="648"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters__salt_1ga79eb7c0dcb7e08dd37437c19be4a7751" kindref="member">vrna_salt_loop_int</ref>(backbones,<sp/>P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref>,<sp/>P-&gt;<ref refid="structvrna__param__s_1aeed2cd83713012bcb52e431041e037c8" kindref="member">temperature</ref><sp/>+<sp/>K0,</highlight></codeline>
<codeline lineno="649"><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/>P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.backbone_length);</highlight></codeline>
<codeline lineno="650"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="651"><highlight class="normal"></highlight></codeline>
<codeline lineno="652"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ns<sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="653"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>bulge<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="654"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>(nl<sp/>&lt;=<sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref>)<sp/>?<sp/>P-&gt;bulge[nl]<sp/>:</highlight></codeline>
<codeline lineno="655"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(P-&gt;bulge[30]<sp/>+<sp/>(int)(P-&gt;lxc<sp/>*<sp/>log(nl<sp/>/<sp/>30.)));</highlight></codeline>
<codeline lineno="656"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(nl<sp/>==<sp/>1)<sp/>{</highlight></codeline>
<codeline lineno="657"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;stack[type][type_2];</highlight></codeline>
<codeline lineno="658"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="659"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="660"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;TerminalAU;</highlight></codeline>
<codeline lineno="661"><highlight class="normal"></highlight></codeline>
<codeline lineno="662"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type_2<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="663"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;TerminalAU;</highlight></codeline>
<codeline lineno="664"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="665"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="666"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="667"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ns<sp/>==<sp/>1)<sp/>{</highlight></codeline>
<codeline lineno="668"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(nl<sp/>==<sp/>1)<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>1x1<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="669"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>P-&gt;int11[type][type_2][si1][sj1]<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="670"><highlight class="normal"></highlight></codeline>
<codeline lineno="671"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(nl<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="672"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>2x1<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="673"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(n1<sp/>==<sp/>1)</highlight></codeline>
<codeline lineno="674"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;int21[type][type_2][si1][sq1][sj1];</highlight></codeline>
<codeline lineno="675"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="676"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;int21[type_2][type][sq1][si1][sp1];</highlight></codeline>
<codeline lineno="677"><highlight class="normal"></highlight></codeline>
<codeline lineno="678"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="679"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="680"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>1xn<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="681"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>=</highlight></codeline>
<codeline lineno="682"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(nl<sp/>+<sp/>1<sp/>&lt;=</highlight></codeline>
<codeline lineno="683"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref>)<sp/>?<sp/>(P-&gt;internal_loop[nl<sp/>+<sp/>1])<sp/>:<sp/>(P-&gt;internal_loop[30]<sp/>+</highlight></codeline>
<codeline lineno="684"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(int)(P-&gt;lxc<sp/>*<sp/>log((nl<sp/>+<sp/>1)<sp/>/<sp/>30.)));</highlight></codeline>
<codeline lineno="685"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(MAX_NINIO,<sp/>(nl<sp/>-<sp/>ns)<sp/>*<sp/>P-&gt;ninio[2]);</highlight></codeline>
<codeline lineno="686"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>P-&gt;mismatch1nI[type][si1][sj1]<sp/>+<sp/>P-&gt;mismatch1nI[type_2][sq1][sp1];</highlight></codeline>
<codeline lineno="687"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="688"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="689"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ns<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="690"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(nl<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="691"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>2x2<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="692"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>P-&gt;int22[type][type_2][si1][sp1][sq1][sj1]<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="693"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(nl<sp/>==<sp/>3)<sp/>{</highlight></codeline>
<codeline lineno="694"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>2x3<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="695"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>=<sp/>P-&gt;internal_loop[5]<sp/>+<sp/>P-&gt;ninio[2];</highlight></codeline>
<codeline lineno="696"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>P-&gt;mismatch23I[type][si1][sj1]<sp/>+<sp/>P-&gt;mismatch23I[type_2][sq1][sp1];</highlight></codeline>
<codeline lineno="697"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="698"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="699"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="700"><highlight class="normal"></highlight></codeline>
<codeline lineno="701"><highlight class="normal"><sp/><sp/><sp/><sp/>{</highlight></codeline>
<codeline lineno="702"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>generic<sp/>internal<sp/>loop<sp/>(no<sp/>else<sp/>here!)*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="703"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>u<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>nl<sp/>+<sp/>ns;</highlight></codeline>
<codeline lineno="704"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>=</highlight></codeline>
<codeline lineno="705"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(u<sp/>&lt;=</highlight></codeline>
<codeline lineno="706"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref>)<sp/>?<sp/>(P-&gt;internal_loop[u])<sp/>:<sp/>(P-&gt;internal_loop[30]<sp/>+<sp/>(int)(P-&gt;lxc<sp/>*<sp/>log((u)<sp/>/<sp/>30.)));</highlight></codeline>
<codeline lineno="707"><highlight class="normal"></highlight></codeline>
<codeline lineno="708"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(MAX_NINIO,<sp/>(nl<sp/>-<sp/>ns)<sp/>*<sp/>P-&gt;ninio[2]);</highlight></codeline>
<codeline lineno="709"><highlight class="normal"></highlight></codeline>
<codeline lineno="710"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;mismatchI[type][si1][sj1]<sp/>+<sp/>P-&gt;mismatchI[type_2][sq1][sp1];</highlight></codeline>
<codeline lineno="711"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="712"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="713"><highlight class="normal"></highlight></codeline>
<codeline lineno="714"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="715"><highlight class="normal">}</highlight></codeline>
<codeline lineno="716"><highlight class="normal"></highlight></codeline>
<codeline lineno="717"><highlight class="normal"></highlight></codeline>
<codeline lineno="718"><highlight class="normal">PRIVATE<sp/>INLINE<sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="719"><highlight class="normal">exp_E_IntLoop(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>u1,</highlight></codeline>
<codeline lineno="720"><highlight class="normal"><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/>u2,</highlight></codeline>
<codeline lineno="721"><highlight class="normal"><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/>type,</highlight></codeline>
<codeline lineno="722"><highlight class="normal"><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/>type2,</highlight></codeline>
<codeline lineno="723"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="724"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="725"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="726"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="727"><highlight class="normal"><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="728"><highlight class="normal">{</highlight></codeline>
<codeline lineno="729"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>ul,<sp/>us,<sp/>no_close<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="730"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>z<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>0.;</highlight></codeline>
<codeline lineno="731"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>noGUclosure<sp/>=<sp/>P-&gt;<ref refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a7e883db1f33f8f3baa5c9b140350c78e" kindref="member">noGUclosure</ref>;</highlight></codeline>
<codeline lineno="732"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>backbones;</highlight></codeline>
<codeline lineno="733"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>salt_stack_correction<sp/>=<sp/>P-&gt;expSaltStack;</highlight></codeline>
<codeline lineno="734"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>salt_loop_correction<sp/><sp/>=<sp/>1.;</highlight></codeline>
<codeline lineno="735"><highlight class="normal"></highlight></codeline>
<codeline lineno="736"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((noGUclosure)<sp/>&amp;&amp;<sp/>((type2<sp/>==<sp/>3)<sp/>||<sp/>(type2<sp/>==<sp/>4)<sp/>||<sp/>(type<sp/>==<sp/>3)<sp/>||<sp/>(type<sp/>==<sp/>4)))</highlight></codeline>
<codeline lineno="737"><highlight class="normal"><sp/><sp/><sp/><sp/>no_close<sp/>=<sp/>1;</highlight></codeline>
<codeline lineno="738"><highlight class="normal"></highlight></codeline>
<codeline lineno="739"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u1<sp/>&gt;<sp/>u2)<sp/>{</highlight></codeline>
<codeline lineno="740"><highlight class="normal"><sp/><sp/><sp/><sp/>ul<sp/><sp/>=<sp/>u1;</highlight></codeline>
<codeline lineno="741"><highlight class="normal"><sp/><sp/><sp/><sp/>us<sp/><sp/>=<sp/>u2;</highlight></codeline>
<codeline lineno="742"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="743"><highlight class="normal"><sp/><sp/><sp/><sp/>ul<sp/><sp/>=<sp/>u2;</highlight></codeline>
<codeline lineno="744"><highlight class="normal"><sp/><sp/><sp/><sp/>us<sp/><sp/>=<sp/>u1;</highlight></codeline>
<codeline lineno="745"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="746"><highlight class="normal"></highlight></codeline>
<codeline lineno="747"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>salt<sp/>correction<sp/>for<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="748"><highlight class="normal"><sp/><sp/>backbones<sp/>=<sp/>ul<sp/>+<sp/>us<sp/>+<sp/>2;</highlight></codeline>
<codeline lineno="749"><highlight class="normal"></highlight></codeline>
<codeline lineno="750"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(P-&gt;<ref refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref><sp/>!=<sp/><ref refid="group__model__details_1gaa68703da9ccc5ae6da508bfda36b533f" kindref="member">VRNA_MODEL_DEFAULT_SALT</ref>)<sp/>{</highlight></codeline>
<codeline lineno="751"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(backbones<sp/>&lt;=<sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1)</highlight></codeline>
<codeline lineno="752"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_loop_correction<sp/>=<sp/>P-&gt;expSaltLoop[backbones];</highlight></codeline>
<codeline lineno="753"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="754"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_loop_correction<sp/>=</highlight></codeline>
<codeline lineno="755"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exp(-<ref refid="group__energy__parameters__salt_1ga79eb7c0dcb7e08dd37437c19be4a7751" kindref="member">vrna_salt_loop_int</ref>(backbones,<sp/>P-&gt;<ref refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref>,<sp/>P-&gt;<ref refid="structvrna__exp__param__s_1a674656d65ea957ddbeff8bd146b7fc16" kindref="member">temperature</ref><sp/>+<sp/>K0,</highlight></codeline>
<codeline lineno="756"><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/>P-&gt;<ref refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" kindref="member">model_details</ref>.backbone_length)<sp/>*<sp/>10.<sp/>/<sp/>P-&gt;kT);</highlight></codeline>
<codeline lineno="757"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="758"><highlight class="normal"></highlight></codeline>
<codeline lineno="759"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ul<sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="760"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>stack<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="761"><highlight class="normal"><sp/><sp/><sp/><sp/>z<sp/>=<sp/>P-&gt;expstack[type][type2]<sp/>*<sp/>salt_stack_correction;</highlight></codeline>
<codeline lineno="762"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(!no_close)<sp/>{</highlight></codeline>
<codeline lineno="763"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(us<sp/>==<sp/>0)<sp/>{</highlight></codeline>
<codeline lineno="764"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>bulge<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="765"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>z<sp/>=<sp/>P-&gt;expbulge[ul];</highlight></codeline>
<codeline lineno="766"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ul<sp/>==<sp/>1)<sp/>{</highlight></codeline>
<codeline lineno="767"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>z<sp/>*=<sp/>P-&gt;expstack[type][type2];</highlight></codeline>
<codeline lineno="768"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="769"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="770"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>z<sp/>*=<sp/>P-&gt;expTermAU;</highlight></codeline>
<codeline lineno="771"><highlight class="normal"></highlight></codeline>
<codeline lineno="772"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type2<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="773"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>z<sp/>*=<sp/>P-&gt;expTermAU;</highlight></codeline>
<codeline lineno="774"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="775"><highlight class="normal"></highlight></codeline>
<codeline lineno="776"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(z<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="777"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(us<sp/>==<sp/>1)<sp/>{</highlight></codeline>
<codeline lineno="778"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ul<sp/>==<sp/>1)<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>1x1<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="779"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(P-&gt;expint11[type][type2][si1][sj1]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="780"><highlight class="normal"></highlight></codeline>
<codeline lineno="781"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ul<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="782"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>2x1<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="783"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u1<sp/>==<sp/>1)</highlight></codeline>
<codeline lineno="784"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(P-&gt;expint21[type][type2][si1][sq1][sj1]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="785"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="786"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(P-&gt;expint21[type2][type][sq1][si1][sp1]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="787"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="788"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>1xn<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="789"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>z<sp/>=<sp/>P-&gt;expinternal[ul<sp/>+<sp/>us]<sp/>*<sp/>P-&gt;expmismatch1nI[type][si1][sj1]<sp/>*</highlight></codeline>
<codeline lineno="790"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>P-&gt;expmismatch1nI[type2][sq1][sp1];</highlight></codeline>
<codeline lineno="791"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(z<sp/>*<sp/>P-&gt;expninio[2][ul<sp/>-<sp/>us]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="792"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="793"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(us<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="794"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ul<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="795"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>2x2<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="796"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(P-&gt;expint22[type][type2][si1][sp1][sq1][sj1]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="797"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(ul<sp/>==<sp/>3)<sp/>{</highlight></codeline>
<codeline lineno="798"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>2x3<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="799"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>z<sp/>=<sp/>P-&gt;expinternal[5]<sp/>*<sp/>P-&gt;expmismatch23I[type][si1][sj1]<sp/>*</highlight></codeline>
<codeline lineno="800"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>P-&gt;expmismatch23I[type2][sq1][sp1];</highlight></codeline>
<codeline lineno="801"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(z<sp/>*<sp/>P-&gt;expninio[2][1]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="802"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="803"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="804"><highlight class="normal"></highlight></codeline>
<codeline lineno="805"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>generic<sp/>internal<sp/>loop<sp/>(no<sp/>else<sp/>here!)*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="806"><highlight class="normal"><sp/><sp/><sp/><sp/>z<sp/>=<sp/>P-&gt;expinternal[ul<sp/>+<sp/>us]<sp/>*<sp/>P-&gt;expmismatchI[type][si1][sj1]<sp/>*</highlight></codeline>
<codeline lineno="807"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>P-&gt;expmismatchI[type2][sq1][sp1];</highlight></codeline>
<codeline lineno="808"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref>)(z<sp/>*<sp/>P-&gt;expninio[2][ul<sp/>-<sp/>us]<sp/>*<sp/>salt_loop_correction);</highlight></codeline>
<codeline lineno="809"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="810"><highlight class="normal"></highlight></codeline>
<codeline lineno="811"><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>)z;</highlight></codeline>
<codeline lineno="812"><highlight class="normal">}</highlight></codeline>
<codeline lineno="813"><highlight class="normal"></highlight></codeline>
<codeline lineno="814"><highlight class="normal"></highlight></codeline>
<codeline lineno="815"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="816"><highlight class="normal">E_IntLoop_Co(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="817"><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/>type_2,</highlight></codeline>
<codeline lineno="818"><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/>i,</highlight></codeline>
<codeline lineno="819"><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/>j,</highlight></codeline>
<codeline lineno="820"><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/>p,</highlight></codeline>
<codeline lineno="821"><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/>q,</highlight></codeline>
<codeline lineno="822"><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/>cutpoint,</highlight></codeline>
<codeline lineno="823"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="824"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="825"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="826"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="827"><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/><ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="828"><highlight class="normal"><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/>*P)</highlight></codeline>
<codeline lineno="829"><highlight class="normal">{</highlight></codeline>
<codeline lineno="830"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>__E_IntLoop_Co(type,</highlight></codeline>
<codeline lineno="831"><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/>type_2,</highlight></codeline>
<codeline lineno="832"><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/>i,</highlight></codeline>
<codeline lineno="833"><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/>j,</highlight></codeline>
<codeline lineno="834"><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/>p,</highlight></codeline>
<codeline lineno="835"><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/>q,</highlight></codeline>
<codeline lineno="836"><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/>cutpoint,</highlight></codeline>
<codeline lineno="837"><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/>si1,</highlight></codeline>
<codeline lineno="838"><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/>sj1,</highlight></codeline>
<codeline lineno="839"><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/>sp1,</highlight></codeline>
<codeline lineno="840"><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/>sq1,</highlight></codeline>
<codeline lineno="841"><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__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="842"><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/>P);</highlight></codeline>
<codeline lineno="843"><highlight class="normal">}</highlight></codeline>
<codeline lineno="844"><highlight class="normal"></highlight></codeline>
<codeline lineno="845"><highlight class="normal"></highlight></codeline>
<codeline lineno="846"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="847"><highlight class="normal">__E_IntLoop_Co(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="848"><highlight class="normal"><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/>type_2,</highlight></codeline>
<codeline lineno="849"><highlight class="normal"><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/>i,</highlight></codeline>
<codeline lineno="850"><highlight class="normal"><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/>j,</highlight></codeline>
<codeline lineno="851"><highlight class="normal"><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/>p,</highlight></codeline>
<codeline lineno="852"><highlight class="normal"><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/>q,</highlight></codeline>
<codeline lineno="853"><highlight class="normal"><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/>cutpoint,</highlight></codeline>
<codeline lineno="854"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="855"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="856"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="857"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sq1,</highlight></codeline>
<codeline lineno="858"><highlight class="normal"><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/><ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="859"><highlight class="normal"><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/>*P)</highlight></codeline>
<codeline lineno="860"><highlight class="normal">{</highlight></codeline>
<codeline lineno="861"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>e,<sp/>energy,<sp/>ci,<sp/>cj,<sp/>cp,<sp/>cq,<sp/>d3,<sp/>d5,<sp/>d5_2,<sp/>d3_2,<sp/>tmm,<sp/>tmm_2;</highlight></codeline>
<codeline lineno="862"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>salt_loop_correction,<sp/>backbones;</highlight></codeline>
<codeline lineno="863"><highlight class="normal"></highlight></codeline>
<codeline lineno="864"><highlight class="normal"><sp/><sp/>salt_loop_correction<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="865"><highlight class="normal"></highlight></codeline>
<codeline lineno="866"><highlight class="normal"><sp/><sp/>backbones<sp/>=<sp/>p<sp/>-<sp/>i<sp/>+<sp/>j<sp/>-<sp/>q;</highlight></codeline>
<codeline lineno="867"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>salt<sp/>correction<sp/>for<sp/>loop<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="868"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref><sp/>!=<sp/><ref refid="group__model__details_1gaa68703da9ccc5ae6da508bfda36b533f" kindref="member">VRNA_MODEL_DEFAULT_SALT</ref>)<sp/>{</highlight></codeline>
<codeline lineno="869"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(backbones<sp/>&lt;=<sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1)</highlight></codeline>
<codeline lineno="870"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_loop_correction<sp/>=<sp/>P-&gt;SaltLoop[backbones];</highlight></codeline>
<codeline lineno="871"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="872"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_loop_correction<sp/>=</highlight></codeline>
<codeline lineno="873"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters__salt_1ga79eb7c0dcb7e08dd37437c19be4a7751" kindref="member">vrna_salt_loop_int</ref>(backbones,<sp/>P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref>,<sp/>P-&gt;<ref refid="structvrna__param__s_1aeed2cd83713012bcb52e431041e037c8" kindref="member">temperature</ref><sp/>+<sp/>K0,</highlight></codeline>
<codeline lineno="874"><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/>P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.backbone_length);</highlight></codeline>
<codeline lineno="875"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="876"><highlight class="normal"></highlight></codeline>
<codeline lineno="877"><highlight class="normal"><sp/><sp/>energy<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="878"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="879"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;TerminalAU;</highlight></codeline>
<codeline lineno="880"><highlight class="normal"></highlight></codeline>
<codeline lineno="881"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type_2<sp/>&gt;<sp/>2)</highlight></codeline>
<codeline lineno="882"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>P-&gt;TerminalAU;</highlight></codeline>
<codeline lineno="883"><highlight class="normal"></highlight></codeline>
<codeline lineno="884"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(!<ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>)</highlight></codeline>
<codeline lineno="885"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="886"><highlight class="normal"></highlight></codeline>
<codeline lineno="887"><highlight class="normal"><sp/><sp/>ci<sp/><sp/>=<sp/>ON_SAME_STRAND(i,<sp/>i<sp/>+<sp/>1,<sp/>cutpoint);</highlight></codeline>
<codeline lineno="888"><highlight class="normal"><sp/><sp/>cj<sp/><sp/>=<sp/>ON_SAME_STRAND(j<sp/>-<sp/>1,<sp/>j,<sp/>cutpoint);</highlight></codeline>
<codeline lineno="889"><highlight class="normal"><sp/><sp/>cp<sp/><sp/>=<sp/>ON_SAME_STRAND(p<sp/>-<sp/>1,<sp/>p,<sp/>cutpoint);</highlight></codeline>
<codeline lineno="890"><highlight class="normal"><sp/><sp/>cq<sp/><sp/>=<sp/>ON_SAME_STRAND(q,<sp/>q<sp/>+<sp/>1,<sp/>cutpoint);</highlight></codeline>
<codeline lineno="891"><highlight class="normal"></highlight></codeline>
<codeline lineno="892"><highlight class="normal"><sp/><sp/>d3<sp/><sp/><sp/><sp/>=<sp/>ci<sp/><sp/>?<sp/>P-&gt;dangle3[type][si1]<sp/><sp/><sp/>:<sp/>0;</highlight></codeline>
<codeline lineno="893"><highlight class="normal"><sp/><sp/>d5<sp/><sp/><sp/><sp/>=<sp/>cj<sp/><sp/>?<sp/>P-&gt;dangle5[type][sj1]<sp/><sp/><sp/>:<sp/>0;</highlight></codeline>
<codeline lineno="894"><highlight class="normal"><sp/><sp/>d5_2<sp/><sp/>=<sp/>cp<sp/><sp/>?<sp/>P-&gt;dangle5[type_2][sp1]<sp/>:<sp/>0;</highlight></codeline>
<codeline lineno="895"><highlight class="normal"><sp/><sp/>d3_2<sp/><sp/>=<sp/>cq<sp/><sp/>?<sp/>P-&gt;dangle3[type_2][sq1]<sp/>:<sp/>0;</highlight></codeline>
<codeline lineno="896"><highlight class="normal"></highlight></codeline>
<codeline lineno="897"><highlight class="normal"><sp/><sp/>tmm<sp/><sp/><sp/>=<sp/>(cj<sp/>&amp;&amp;<sp/>ci)<sp/>?<sp/>P-&gt;mismatchExt[type][sj1][si1]<sp/><sp/><sp/>:<sp/>d5<sp/>+<sp/>d3;</highlight></codeline>
<codeline lineno="898"><highlight class="normal"><sp/><sp/>tmm_2<sp/>=<sp/>(cp<sp/>&amp;&amp;<sp/>cq)<sp/>?<sp/>P-&gt;mismatchExt[type_2][sp1][sq1]<sp/>:<sp/>d5_2<sp/>+<sp/>d3_2;</highlight></codeline>
<codeline lineno="899"><highlight class="normal"></highlight></codeline>
<codeline lineno="900"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(<ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref><sp/>==<sp/>2)</highlight></codeline>
<codeline lineno="901"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>tmm<sp/>+<sp/>tmm_2<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="902"><highlight class="normal"></highlight></codeline>
<codeline lineno="903"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>now<sp/>we<sp/>may<sp/>have<sp/>non-double<sp/>dangles<sp/>only<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="904"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(p<sp/>-<sp/>i<sp/>&gt;<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="905"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(j<sp/>-<sp/>q<sp/>&gt;<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="906"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>all<sp/>degrees<sp/>of<sp/>freedom<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="907"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(tmm,<sp/>d5);</highlight></codeline>
<codeline lineno="908"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3);</highlight></codeline>
<codeline lineno="909"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>e;</highlight></codeline>
<codeline lineno="910"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(tmm_2,<sp/>d5_2);</highlight></codeline>
<codeline lineno="911"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3_2);</highlight></codeline>
<codeline lineno="912"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>e;</highlight></codeline>
<codeline lineno="913"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(j<sp/>-<sp/>q<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="914"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>all<sp/>degrees<sp/>of<sp/>freedom<sp/>in<sp/>5&apos;<sp/>part<sp/>between<sp/>i<sp/>and<sp/>p<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="915"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(tmm<sp/>+<sp/>d5_2,<sp/>d3<sp/>+<sp/>d5_2);</highlight></codeline>
<codeline lineno="916"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5<sp/>+<sp/>d5_2);</highlight></codeline>
<codeline lineno="917"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3<sp/>+<sp/>tmm_2);</highlight></codeline>
<codeline lineno="918"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3<sp/>+<sp/>d3_2);</highlight></codeline>
<codeline lineno="919"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>tmm_2);<sp/></highlight><highlight class="comment">/*<sp/>no<sp/>dangles<sp/>on<sp/>enclosing<sp/>pair<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="920"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5_2);<sp/><sp/></highlight><highlight class="comment">/*<sp/>no<sp/>dangles<sp/>on<sp/>enclosing<sp/>pair<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="921"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3_2);<sp/><sp/></highlight><highlight class="comment">/*<sp/>no<sp/>dangles<sp/>on<sp/>enclosing<sp/>pair<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="922"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>e;</highlight></codeline>
<codeline lineno="923"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="924"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>no<sp/>unpaired<sp/>base<sp/>between<sp/>q<sp/>and<sp/>j<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="925"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>d3<sp/>+<sp/>d5_2;</highlight></codeline>
<codeline lineno="926"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="927"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(p<sp/>-<sp/>i<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="928"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(j<sp/>-<sp/>q<sp/>&gt;<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="929"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>all<sp/>degrees<sp/>of<sp/>freedom<sp/>in<sp/>3&apos;<sp/>part<sp/>between<sp/>q<sp/>and<sp/>j<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="930"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(tmm<sp/>+<sp/>d3_2,<sp/>d5<sp/>+<sp/>d3_2);</highlight></codeline>
<codeline lineno="931"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5<sp/>+<sp/>d3_2);</highlight></codeline>
<codeline lineno="932"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3<sp/>+<sp/>d3_2);</highlight></codeline>
<codeline lineno="933"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5<sp/>+<sp/>tmm_2);</highlight></codeline>
<codeline lineno="934"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>tmm_2);</highlight></codeline>
<codeline lineno="935"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5_2);</highlight></codeline>
<codeline lineno="936"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3_2);</highlight></codeline>
<codeline lineno="937"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>e;</highlight></codeline>
<codeline lineno="938"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(j<sp/>-<sp/>q<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="939"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>one<sp/>possible<sp/>dangling<sp/>base<sp/>between<sp/>either<sp/>side<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="940"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(tmm,<sp/>tmm_2);</highlight></codeline>
<codeline lineno="941"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3);</highlight></codeline>
<codeline lineno="942"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5);</highlight></codeline>
<codeline lineno="943"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5_2);</highlight></codeline>
<codeline lineno="944"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3_2);</highlight></codeline>
<codeline lineno="945"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d3<sp/>+<sp/>d3_2);</highlight></codeline>
<codeline lineno="946"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>e<sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(e,<sp/>d5<sp/>+<sp/>d5_2);</highlight></codeline>
<codeline lineno="947"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/><sp/>+=<sp/>e;</highlight></codeline>
<codeline lineno="948"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="949"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>one<sp/>unpaired<sp/>base<sp/>between<sp/>i<sp/>and<sp/>p<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="950"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(d3,<sp/>d5_2);</highlight></codeline>
<codeline lineno="951"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="952"><highlight class="normal"><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="953"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>no<sp/>unpaired<sp/>base<sp/>between<sp/>i<sp/>and<sp/>p<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="954"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(j<sp/>-<sp/>q<sp/>&gt;<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="955"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>all<sp/>degrees<sp/>of<sp/>freedom<sp/>in<sp/>3&apos;<sp/>part<sp/>between<sp/>q<sp/>and<sp/>j<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="956"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/>d5<sp/>+<sp/>d3_2;</highlight></codeline>
<codeline lineno="957"><highlight class="normal"><sp/><sp/><sp/><sp/>}<sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(j<sp/>-<sp/>q<sp/>==<sp/>2)<sp/>{</highlight></codeline>
<codeline lineno="958"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>one<sp/>unpaired<sp/>base<sp/>between<sp/>q<sp/>and<sp/>j<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="959"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>+=<sp/><ref refid="group__utils_1gae0b9cd0ce090bd69b951aa73e8fa4f7d" kindref="member">MIN2</ref>(d5,<sp/>d3_2);</highlight></codeline>
<codeline lineno="960"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="961"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="962"><highlight class="normal"></highlight></codeline>
<codeline lineno="963"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>salt_loop_correction;</highlight></codeline>
<codeline lineno="964"><highlight class="normal">}</highlight></codeline>
<codeline lineno="968"><highlight class="normal"></highlight></codeline>
<codeline lineno="969"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="970"><highlight class="normal"></highlight></codeline>
<codeline lineno="971"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/eval/internal.h"/>
  </compounddef>
</doxygen>
