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    <includes refid="array_8h" local="yes">ViennaRNA/datastructures/array.h</includes>
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        <label>time.h</label>
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    <innerclass refid="structvrna__sc__mod__param__s" prot="public">vrna_sc_mod_param_s</innerclass>
    <innerclass refid="structenergy__corrections" prot="public">energy_corrections</innerclass>
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        <name>MOD_PARAMS_STACK_dG</name>
        <initializer>(1 &lt;&lt; 0)</initializer>
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        <name>MOD_PARAMS_MISMATCH_dG</name>
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        <briefdescription>
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        <name>MOD_PARAMS_DANGLES_dG</name>
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        <name>MAX_ALPHABET</name>
        <initializer>(6)</initializer>
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        <name>MAX_PAIRS</name>
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        </detaileddescription>
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        </inbodydescription>
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<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_INTERN_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_INTERN_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&quot;<ref refid="array_8h" kindref="compound">ViennaRNA/datastructures/array.h</ref>&quot;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_STACK_dG<sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>0)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_STACK_dH<sp/><sp/><sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>1)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_MISMATCH_dG<sp/><sp/>(1<sp/>&lt;&lt;<sp/>2)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_MISMATCH_dH<sp/><sp/>(1<sp/>&lt;&lt;<sp/>3)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_TERMINAL_dG<sp/><sp/>(1<sp/>&lt;&lt;<sp/>4)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_TERMINAL_dH<sp/><sp/>(1<sp/>&lt;&lt;<sp/>5)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_DANGLES_dG<sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>6)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MOD_PARAMS_DANGLES_dH<sp/><sp/><sp/>(1<sp/>&lt;&lt;<sp/>7)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MAX_ALPHABET<sp/><sp/>(6)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MAX_PAIRS<sp/><sp/><sp/><sp/><sp/>(NBPAIRS<sp/>+<sp/>1<sp/>+<sp/>25)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>a<sp/>container<sp/>to<sp/>store<sp/>the<sp/>data<sp/>read<sp/>from<sp/>a<sp/>json<sp/>parameter<sp/>file<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="20" refid="structvrna__sc__mod__param__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__sc__mod__param__s" kindref="compound">vrna_sc_mod_param_s</ref><sp/>{</highlight></codeline>
<codeline lineno="21"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>available;</highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*name;</highlight></codeline>
<codeline lineno="24"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>one_letter_code;</highlight></codeline>
<codeline lineno="25"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>unmodified;</highlight></codeline>
<codeline lineno="26"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>fallback;</highlight></codeline>
<codeline lineno="27"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pairing_partners[7];</highlight></codeline>
<codeline lineno="28"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>pairing_partners_encoding[7];</highlight></codeline>
<codeline lineno="29"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>unmodified_encoding;</highlight></codeline>
<codeline lineno="30"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>fallback_encoding;</highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">size_t</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>num_ptypes;</highlight></codeline>
<codeline lineno="33"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">size_t</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>ptypes[MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="35"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>stack_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="36"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>stack_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight></codeline>
<codeline lineno="38"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>dangle5_dG[MAX_PAIRS][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="39"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>dangle5_dH[MAX_PAIRS][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="40"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>dangle3_dG[MAX_PAIRS][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="41"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>dangle3_dH[MAX_PAIRS][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="42"><highlight class="normal"></highlight></codeline>
<codeline lineno="43"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>mismatch_dG[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="44"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>mismatch_dH[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>terminal_dG[MAX_PAIRS];</highlight></codeline>
<codeline lineno="47"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>terminal_dH[MAX_PAIRS];</highlight></codeline>
<codeline lineno="48"><highlight class="normal">};</highlight></codeline>
<codeline lineno="49"><highlight class="normal"></highlight></codeline>
<codeline lineno="50"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>the<sp/>actual<sp/>data<sp/>structure<sp/>passed<sp/>around<sp/>while<sp/>evaluating<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="51" refid="structenergy__corrections" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="52"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/>*enc;</highlight></codeline>
<codeline lineno="53"><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">size_t</highlight><highlight class="normal"><sp/><sp/>strands;</highlight></codeline>
<codeline lineno="55"><highlight class="normal"><sp/><sp/><ref refid="group__array__utils_1ga97302e41c5c33faae998eb956c8f1f91" kindref="member">vrna_array</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>*)<sp/><sp/>modification_sites;</highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight></codeline>
<codeline lineno="57"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">size_t</highlight><highlight class="normal"><sp/><sp/>ptypes[MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="58"><highlight class="normal"></highlight></codeline>
<codeline lineno="59"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>stack_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="60"><highlight class="normal"></highlight></codeline>
<codeline lineno="61"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>dangle5_diff[MAX_PAIRS][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="62"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>dangle3_diff[MAX_PAIRS][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight></codeline>
<codeline lineno="64"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>mismatch_diff[MAX_PAIRS][MAX_ALPHABET][MAX_ALPHABET];</highlight></codeline>
<codeline lineno="65"><highlight class="normal"></highlight></codeline>
<codeline lineno="66"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>terminal_diff[MAX_PAIRS];</highlight></codeline>
<codeline lineno="67"><highlight class="normal">}<sp/><ref refid="structenergy__corrections" kindref="compound">energy_corrections</ref>;</highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight></codeline>
<codeline lineno="69"><highlight class="normal"></highlight></codeline>
<codeline lineno="70"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
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    <location file="ViennaRNA/constraints/sc_cb_intern.h"/>
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