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<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_LOOPS_HAIRPIN_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
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<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
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<codeline lineno="12"><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight></codeline>
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<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"></highlight></codeline>
<codeline lineno="48"><highlight class="normal"></highlight></codeline>
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<codeline lineno="99"><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>
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<codeline lineno="139"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="140"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="141"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="142"><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"></highlight></codeline>
<codeline lineno="144"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>basic<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="146"><highlight class="normal"></highlight></codeline>
<codeline lineno="147"><highlight class="normal"></highlight></codeline>
<codeline lineno="152"><highlight class="normal"></highlight></codeline>
<codeline lineno="153"><highlight class="normal"></highlight></codeline>
<codeline lineno="174"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="175" refid="group__eval__loops__hp_1ga847c34387b29b06448c7c843156bca91" refkind="member"><highlight class="normal"><ref refid="group__eval__loops__hp_1ga847c34387b29b06448c7c843156bca91" kindref="member">vrna_exp_E_hairpin</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>size,</highlight></codeline>
<codeline lineno="176"><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/>type,</highlight></codeline>
<codeline lineno="177"><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/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="178"><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/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="179"><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="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="180"><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_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*P);</highlight></codeline>
<codeline lineno="181"><highlight class="normal"></highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="214"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="215" refid="group__eval__loops__hp_1ga4997b7ebab4b1d8a34dee8365b28d03e" refkind="member"><highlight class="normal"><ref refid="group__eval__loops__hp_1ga4997b7ebab4b1d8a34dee8365b28d03e" kindref="member">vrna_exp_eval_hairpin</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="216"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="217"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="218"><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">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="219"><highlight class="normal"></highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight></codeline>
<codeline lineno="221"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>partition<sp/>function<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="223"><highlight class="normal"></highlight></codeline>
<codeline lineno="224"><highlight class="normal"></highlight></codeline>
<codeline lineno="228"><highlight class="normal"></highlight></codeline>
<codeline lineno="229"><highlight class="normal"></highlight></codeline>
<codeline lineno="230"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="231"><highlight class="normal"></highlight></codeline>
<codeline lineno="236"><highlight class="normal"></highlight></codeline>
<codeline lineno="271"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="272"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>E_Hairpin(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>size,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="276"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="277"><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="278"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_E_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="279"><highlight class="normal"></highlight></codeline>
<codeline lineno="280"><highlight class="normal"></highlight></codeline>
<codeline lineno="281"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="282"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_E_hp_loop(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</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/><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="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/><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="285"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="286"><highlight class="normal"></highlight></codeline>
<codeline lineno="287"><highlight class="normal"></highlight></codeline>
<codeline lineno="288"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="289"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_E_ext_hp_loop(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</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/><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="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/><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="292"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="293"><highlight class="normal"></highlight></codeline>
<codeline lineno="294"><highlight class="normal"></highlight></codeline>
<codeline lineno="295"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="296"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__eval__deprecated_1gad0bb844f8dc704c71737ae1d7e32b975" kindref="member">vrna_eval_hp_loop</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="297"><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/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="298"><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/><sp/><sp/><sp/><sp/><sp/><sp/>j),</highlight></codeline>
<codeline lineno="299" refid="group__eval__deprecated_1gad0bb844f8dc704c71737ae1d7e32b975" 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_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="300"><highlight class="normal"></highlight></codeline>
<codeline lineno="301"><highlight class="normal"></highlight></codeline>
<codeline lineno="302"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="303"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_eval_ext_hp_loop(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="304"><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/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="305"><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/><sp/><sp/><sp/><sp/><sp/><sp/>j),</highlight></codeline>
<codeline lineno="306"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_eval_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="307"><highlight class="normal"></highlight></codeline>
<codeline lineno="308"><highlight class="normal"></highlight></codeline>
<codeline lineno="327"><highlight class="normal">DEPRECATED(PRIVATE<sp/>INLINE<sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="328"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exp_E_Hairpin(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>u,</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/></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="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/></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="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/></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="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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</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/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*P),</highlight></codeline>
<codeline lineno="334"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_E_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="335"><highlight class="normal"></highlight></codeline>
<codeline lineno="336"><highlight class="normal"></highlight></codeline>
<codeline lineno="337"><highlight class="normal">DEPRECATED(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="338"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_exp_E_hp_loop(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</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/><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="340"><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="341"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_eval_hairpin()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="342"><highlight class="normal"></highlight></codeline>
<codeline lineno="343"><highlight class="normal"></highlight></codeline>
<codeline lineno="344"><highlight class="normal">PRIVATE<sp/>INLINE<sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="345"><highlight class="normal">E_Hairpin(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>size,</highlight></codeline>
<codeline lineno="346"><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="347"><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="348"><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="349"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="350"><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="351"><highlight class="normal">{</highlight></codeline>
<codeline lineno="352"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>energy,<sp/>salt_correction;</highlight></codeline>
<codeline lineno="353"><highlight class="normal"></highlight></codeline>
<codeline lineno="354"><highlight class="normal"><sp/><sp/>salt_correction<sp/>=<sp/>0;</highlight></codeline>
<codeline lineno="355"><highlight class="normal"></highlight></codeline>
<codeline lineno="356"><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="357"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(size<sp/>&lt;=<sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref>)</highlight></codeline>
<codeline lineno="358"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_correction<sp/>=<sp/>P-&gt;SaltLoop[size<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="359"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="360"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_correction<sp/>=<sp/><ref refid="group__energy__parameters__salt_1ga79eb7c0dcb7e08dd37437c19be4a7751" kindref="member">vrna_salt_loop_int</ref>(size<sp/>+<sp/>1,</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/><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_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref>,</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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>P-&gt;<ref refid="structvrna__param__s_1aeed2cd83713012bcb52e431041e037c8" kindref="member">temperature</ref><sp/>+<sp/>K0,</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/><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="364"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="365"><highlight class="normal"></highlight></codeline>
<codeline lineno="366"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(size<sp/>&lt;=<sp/>30)</highlight></codeline>
<codeline lineno="367"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;hairpin[size];</highlight></codeline>
<codeline lineno="368"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="369"><highlight class="normal"><sp/><sp/><sp/><sp/>energy<sp/>=<sp/>P-&gt;hairpin[30]<sp/>+<sp/>(int)(P-&gt;lxc<sp/>*<sp/>log((size)<sp/>/<sp/>30.));</highlight></codeline>
<codeline lineno="370"><highlight class="normal"></highlight></codeline>
<codeline lineno="371"><highlight class="normal"><sp/><sp/>energy<sp/>+=<sp/>salt_correction;</highlight></codeline>
<codeline lineno="372"><highlight class="normal"></highlight></codeline>
<codeline lineno="373"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(size<sp/>&lt;<sp/>3)</highlight></codeline>
<codeline lineno="374"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>should<sp/>only<sp/>be<sp/>the<sp/>case<sp/>when<sp/>folding<sp/>alignments<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="375"><highlight class="normal"></highlight></codeline>
<codeline lineno="376"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">)<sp/>&amp;&amp;<sp/>(P-&gt;<ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1add64a96d23e77ef1d0ddf8dfc5228143" kindref="member">special_hp</ref>))<sp/>{</highlight></codeline>
<codeline lineno="377"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(size<sp/>==<sp/>4)<sp/>{</highlight></codeline>
<codeline lineno="378"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>check<sp/>for<sp/>tetraloop<sp/>bonus<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="379"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>tl[7]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="380"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight></codeline>
<codeline lineno="381"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>},<sp/>*ts;</highlight></codeline>
<codeline lineno="382"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>memcpy(tl,<sp/></highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,<sp/></highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal">)<sp/>*<sp/>6);</highlight></codeline>
<codeline lineno="383"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>tl[6]<sp/>=<sp/></highlight><highlight class="charliteral">&apos;\0&apos;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="384"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((ts<sp/>=<sp/>strstr(P-&gt;Tetraloops,<sp/>tl)))</highlight></codeline>
<codeline lineno="385"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>P-&gt;Tetraloop_E[(ts<sp/>-<sp/>P-&gt;Tetraloops)<sp/>/<sp/>7]<sp/>+<sp/>salt_correction;</highlight></codeline>
<codeline lineno="386"><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/>(size<sp/>==<sp/>6)<sp/>{</highlight></codeline>
<codeline lineno="387"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>tl[9]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="388"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight></codeline>
<codeline lineno="389"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>},<sp/>*ts;</highlight></codeline>
<codeline lineno="390"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>memcpy(tl,<sp/></highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,<sp/></highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal">)<sp/>*<sp/>8);</highlight></codeline>
<codeline lineno="391"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>tl[8]<sp/>=<sp/></highlight><highlight class="charliteral">&apos;\0&apos;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="392"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((ts<sp/>=<sp/>strstr(P-&gt;Hexaloops,<sp/>tl)))</highlight></codeline>
<codeline lineno="393"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>P-&gt;Hexaloop_E[(ts<sp/>-<sp/>P-&gt;Hexaloops)<sp/>/<sp/>9]<sp/>+<sp/>salt_correction;</highlight></codeline>
<codeline lineno="394"><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/>(size<sp/>==<sp/>3)<sp/>{</highlight></codeline>
<codeline lineno="395"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>tl[6]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="396"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight></codeline>
<codeline lineno="397"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>},<sp/>*ts;</highlight></codeline>
<codeline lineno="398"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>memcpy(tl,<sp/></highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,<sp/></highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal">)<sp/>*<sp/>5);</highlight></codeline>
<codeline lineno="399"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>tl[5]<sp/>=<sp/></highlight><highlight class="charliteral">&apos;\0&apos;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="400"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((ts<sp/>=<sp/>strstr(P-&gt;Triloops,<sp/>tl)))</highlight></codeline>
<codeline lineno="401"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>P-&gt;Triloop_E[(ts<sp/>-<sp/>P-&gt;Triloops)<sp/>/<sp/>6]<sp/>+<sp/>salt_correction;</highlight></codeline>
<codeline lineno="402"><highlight class="normal"></highlight></codeline>
<codeline lineno="403"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy<sp/>+<sp/>(type<sp/>&gt;<sp/>2<sp/>?<sp/>P-&gt;TerminalAU<sp/>:<sp/>0);</highlight></codeline>
<codeline lineno="404"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="405"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="406"><highlight class="normal"></highlight></codeline>
<codeline lineno="407"><highlight class="normal"><sp/><sp/>energy<sp/>+=<sp/>P-&gt;mismatchH[type][si1][sj1];</highlight></codeline>
<codeline lineno="408"><highlight class="normal"></highlight></codeline>
<codeline lineno="409"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">return</highlight><highlight class="normal"><sp/>energy;</highlight></codeline>
<codeline lineno="410"><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">PRIVATE<sp/>INLINE<sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="414"><highlight class="normal">exp_E_Hairpin(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>u,</highlight></codeline>
<codeline lineno="415"><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="416"><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="417"><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="418"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,</highlight></codeline>
<codeline lineno="419"><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="420"><highlight class="normal">{</highlight></codeline>
<codeline lineno="421"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>q,<sp/>kT,<sp/>salt_correction;</highlight></codeline>
<codeline lineno="422"><highlight class="normal"></highlight></codeline>
<codeline lineno="423"><highlight class="normal"><sp/><sp/>kT<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>=<sp/>P-&gt;kT;<sp/></highlight><highlight class="comment">/*<sp/>kT<sp/>in<sp/>cal/mol<sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="424"><highlight class="normal"><sp/><sp/>salt_correction<sp/>=<sp/>1.;</highlight></codeline>
<codeline lineno="425"><highlight class="normal"></highlight></codeline>
<codeline lineno="426"><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="427"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u<sp/>&lt;=<sp/><ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref>)</highlight></codeline>
<codeline lineno="428"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_correction<sp/>=<sp/>P-&gt;expSaltLoop[u<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="429"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="430"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>salt_correction<sp/>=</highlight></codeline>
<codeline lineno="431"><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>(u<sp/>+<sp/>1,<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="432"><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/>kT);</highlight></codeline>
<codeline lineno="433"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="434"><highlight class="normal"></highlight></codeline>
<codeline lineno="435"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u<sp/>&lt;=<sp/>30)</highlight></codeline>
<codeline lineno="436"><highlight class="normal"><sp/><sp/><sp/><sp/>q<sp/>=<sp/>P-&gt;exphairpin[u];</highlight></codeline>
<codeline lineno="437"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="438"><highlight class="normal"><sp/><sp/><sp/><sp/>q<sp/>=<sp/>P-&gt;exphairpin[30]<sp/>*<sp/>exp(-(P-&gt;lxc<sp/>*<sp/>log(u<sp/>/<sp/>30.))<sp/>*<sp/>10.<sp/>/<sp/>kT);</highlight></codeline>
<codeline lineno="439"><highlight class="normal"></highlight></codeline>
<codeline lineno="440"><highlight class="normal"><sp/><sp/>q<sp/>*=<sp/>salt_correction;</highlight></codeline>
<codeline lineno="441"><highlight class="normal"></highlight></codeline>
<codeline lineno="442"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u<sp/>&lt;<sp/>3)</highlight></codeline>
<codeline lineno="443"><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>)q;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>should<sp/>only<sp/>be<sp/>the<sp/>case<sp/>when<sp/>folding<sp/>alignments<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="444"><highlight class="normal"></highlight></codeline>
<codeline lineno="445"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">)<sp/>&amp;&amp;<sp/>(P-&gt;<ref refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" kindref="member">model_details</ref>.<ref refid="structvrna__md__s_1add64a96d23e77ef1d0ddf8dfc5228143" kindref="member">special_hp</ref>))<sp/>{</highlight></codeline>
<codeline lineno="446"><highlight class="normal"><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(u<sp/>==<sp/>4)<sp/>{</highlight></codeline>
<codeline lineno="447"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>tl[7]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="448"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight></codeline>
<codeline lineno="449"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>},<sp/>*ts;</highlight></codeline>
<codeline lineno="450"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>memcpy(tl,<sp/></highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,<sp/></highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal">)<sp/>*<sp/>6);</highlight></codeline>
<codeline lineno="451"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>tl[6]<sp/>=<sp/></highlight><highlight class="charliteral">&apos;\0&apos;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="452"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((ts<sp/>=<sp/>strstr(P-&gt;Tetraloops,<sp/>tl)))<sp/>{</highlight></codeline>
<codeline lineno="453"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>(type<sp/>!=<sp/>7)</highlight></codeline>
<codeline lineno="454"><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;exptetra[(ts<sp/>-<sp/>P-&gt;Tetraloops)<sp/>/<sp/>7]<sp/>*<sp/>salt_correction);</highlight></codeline>
<codeline lineno="455"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="456"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>q<sp/>*=<sp/>P-&gt;exptetra[(ts<sp/>-<sp/>P-&gt;Tetraloops)<sp/>/<sp/>7];</highlight></codeline>
<codeline lineno="457"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="458"><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/>(u<sp/>==<sp/>6)<sp/>{</highlight></codeline>
<codeline lineno="459"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>tl[9]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="460"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight></codeline>
<codeline lineno="461"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>},<sp/>*ts;</highlight></codeline>
<codeline lineno="462"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>memcpy(tl,<sp/></highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,<sp/></highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal">)<sp/>*<sp/>8);</highlight></codeline>
<codeline lineno="463"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>tl[8]<sp/>=<sp/></highlight><highlight class="charliteral">&apos;\0&apos;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="464"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((ts<sp/>=<sp/>strstr(P-&gt;Hexaloops,<sp/>tl)))</highlight></codeline>
<codeline lineno="465"><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;exphex[(ts<sp/>-<sp/>P-&gt;Hexaloops)<sp/>/<sp/>9]<sp/>*<sp/>salt_correction);</highlight></codeline>
<codeline lineno="466"><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/>(u<sp/>==<sp/>3)<sp/>{</highlight></codeline>
<codeline lineno="467"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>tl[6]<sp/>=<sp/>{</highlight></codeline>
<codeline lineno="468"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight></codeline>
<codeline lineno="469"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>},<sp/>*ts;</highlight></codeline>
<codeline lineno="470"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>memcpy(tl,<sp/></highlight><highlight class="keywordtype">string</highlight><highlight class="normal">,<sp/></highlight><highlight class="keyword">sizeof</highlight><highlight class="normal">(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal">)<sp/>*<sp/>5);</highlight></codeline>
<codeline lineno="471"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>tl[5]<sp/>=<sp/></highlight><highlight class="charliteral">&apos;\0&apos;</highlight><highlight class="normal">;</highlight></codeline>
<codeline lineno="472"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">if</highlight><highlight class="normal"><sp/>((ts<sp/>=<sp/>strstr(P-&gt;Triloops,<sp/>tl)))</highlight></codeline>
<codeline lineno="473"><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;exptri[(ts<sp/>-<sp/>P-&gt;Triloops)<sp/>/<sp/>6]<sp/>*<sp/>salt_correction);</highlight></codeline>
<codeline lineno="474"><highlight class="normal"></highlight></codeline>
<codeline lineno="475"><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="476"><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>)(q<sp/>*<sp/>P-&gt;expTermAU);</highlight></codeline>
<codeline lineno="477"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordflow">else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="478"><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>)q;</highlight></codeline>
<codeline lineno="479"><highlight class="normal"><sp/><sp/><sp/><sp/>}</highlight></codeline>
<codeline lineno="480"><highlight class="normal"><sp/><sp/>}</highlight></codeline>
<codeline lineno="481"><highlight class="normal"></highlight></codeline>
<codeline lineno="482"><highlight class="normal"><sp/><sp/>q<sp/>*=<sp/>P-&gt;expmismatchH[type][si1][sj1];</highlight></codeline>
<codeline lineno="483"><highlight class="normal"></highlight></codeline>
<codeline lineno="484"><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>)q;</highlight></codeline>
<codeline lineno="485"><highlight class="normal">}</highlight></codeline>
<codeline lineno="486"><highlight class="normal"></highlight></codeline>
<codeline lineno="487"><highlight class="normal"></highlight></codeline>
<codeline lineno="489"><highlight class="normal"></highlight></codeline>
<codeline lineno="490"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="491"><highlight class="normal"></highlight></codeline>
<codeline lineno="492"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/eval/hairpin.h"/>
  </compounddef>
</doxygen>
