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        <argsstring>[NBPAIRS+1][NBPAIRS+1][5][5][5][5]</argsstring>
        <name>int22_dH</name>
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        </briefdescription>
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        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>ML_BASE37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>ML_BASEdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <type>int</type>
        <definition>int ML_closing37</definition>
        <argsstring></argsstring>
        <name>ML_closing37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>ML_closingdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>ML_intern37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>ML_interndH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>TripleC37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <name>TripleCdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <name>MultipleCA37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <name>MultipleCAdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <name>MultipleCB37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <name>MultipleCBdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>MAX_NINIO</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="70" column="13" declfile="ViennaRNA/params/default.h" declline="70" declcolumn="13"/>
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        <argsstring></argsstring>
        <name>ninio37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="71" column="12" declfile="ViennaRNA/params/default.h" declline="71" declcolumn="12"/>
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        <type>int</type>
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        <argsstring></argsstring>
        <name>niniodH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="72" column="12" declfile="ViennaRNA/params/default.h" declline="72" declcolumn="12"/>
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        <argsstring></argsstring>
        <name>TerminalAU37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="74" column="12" declfile="ViennaRNA/params/default.h" declline="74" declcolumn="12"/>
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        <argsstring></argsstring>
        <name>TerminalAUdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <argsstring></argsstring>
        <name>DuplexInit37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="77" column="12" declfile="ViennaRNA/params/default.h" declline="77" declcolumn="12"/>
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        <argsstring></argsstring>
        <name>DuplexInitdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <type>char</type>
        <definition>char Tetraloops[281]</definition>
        <argsstring>[281]</argsstring>
        <name>Tetraloops</name>
        <briefdescription>
        </briefdescription>
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        </detaileddescription>
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        <argsstring>[40]</argsstring>
        <name>Tetraloop37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="81" column="13" declfile="ViennaRNA/params/default.h" declline="81" declcolumn="13"/>
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        <argsstring>[40]</argsstring>
        <name>TetraloopdH</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/default.h" line="82" column="13" declfile="ViennaRNA/params/default.h" declline="82" declcolumn="13"/>
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        <name>Triloops</name>
        <briefdescription>
        </briefdescription>
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        </detaileddescription>
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        <name>Triloop37</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
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        </inbodydescription>
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        <name>TriloopdH</name>
        <briefdescription>
        </briefdescription>
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        </detaileddescription>
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        </inbodydescription>
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        <name>Hexaloops</name>
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        </briefdescription>
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        <name>Hexaloop37</name>
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        </briefdescription>
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        </detaileddescription>
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        </briefdescription>
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        </detaileddescription>
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        <name>GQuadAlpha37</name>
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        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
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        </briefdescription>
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<codeline lineno="1"><highlight class="comment">/*</highlight></codeline>
<codeline lineno="2"><highlight class="comment"><sp/><sp/><sp/>prototypes<sp/>for<sp/>energy_par.c</highlight></codeline>
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<codeline lineno="4"><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PARAMS_DEFAULT_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PARAMS_DEFAULT_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="constants_8h" kindref="compound">ViennaRNA/params/constants.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>PUBLIC</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>lxc37;<sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>parameter<sp/>for<sp/>logarithmic<sp/>loop</highlight></codeline>
<codeline lineno="14"><highlight class="comment"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>energy<sp/>extrapolation<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="16"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>stack37[NBPAIRS+1][NBPAIRS+1];</highlight></codeline>
<codeline lineno="17"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>stackdH[NBPAIRS+1][NBPAIRS+1];<sp/></highlight><highlight class="comment">/*<sp/>stack<sp/>enthalpies<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="18"><highlight class="normal"></highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>hairpin37[31];</highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>hairpindH[31];</highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>bulge37[31];</highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>bulgedH[31];</highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>internal_loop37[31];</highlight></codeline>
<codeline lineno="24"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>internal_loopdH[31];</highlight></codeline>
<codeline lineno="25"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchI37[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>mismatches<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchIdH[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>mismatches<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatch1nI37[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>mismatches<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatch23I37[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>mismatches<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatch1nIdH[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>mismatches<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatch23IdH[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>internal<sp/>loop<sp/>mismatches<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchH37[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>same<sp/>for<sp/>hairpins<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchM37[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>same<sp/>for<sp/>multiloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchHdH[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>same<sp/>for<sp/>hairpins<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchMdH[NBPAIRS+1][5][5];<sp/><sp/></highlight><highlight class="comment">/*<sp/>same<sp/>for<sp/>multiloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="35"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchExt37[NBPAIRS+1][5][5];</highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>mismatchExtdH[NBPAIRS+1][5][5];</highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight></codeline>
<codeline lineno="38"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>dangle5_37[NBPAIRS+1][5];<sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>5&apos;<sp/>dangle<sp/>exterior<sp/>of<sp/>pair<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>dangle3_37[NBPAIRS+1][5];<sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>3&apos;<sp/>dangle<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>dangle3_dH[NBPAIRS+1][5];<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>corresponding<sp/>enthalpies<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>dangle5_dH[NBPAIRS+1][5];</highlight></codeline>
<codeline lineno="42"><highlight class="normal"></highlight></codeline>
<codeline lineno="43"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>int11_37[NBPAIRS+1][NBPAIRS+1][5][5];<sp/></highlight><highlight class="comment">/*<sp/>1x1<sp/>internal<sp/>loops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="44"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];</highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5];<sp/></highlight><highlight class="comment">/*<sp/>2x1<sp/>internal<sp/>loops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="47"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];</highlight></codeline>
<codeline lineno="48"><highlight class="normal"></highlight></codeline>
<codeline lineno="49"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5];<sp/></highlight><highlight class="comment">/*<sp/>2x2<sp/>internal<sp/>loops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="50"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5];</highlight></codeline>
<codeline lineno="51"><highlight class="normal"></highlight></codeline>
<codeline lineno="52"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>constants<sp/>for<sp/>linearly<sp/>destabilizing<sp/>contributions<sp/>for<sp/>multi-loops</highlight></codeline>
<codeline lineno="53"><highlight class="comment"><sp/><sp/><sp/>F<sp/>=<sp/>ML_closing<sp/>+<sp/>ML_intern*(k-1)<sp/>+<sp/>ML_BASE*u<sp/><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ML_BASE37;</highlight></codeline>
<codeline lineno="55"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ML_BASEdH;</highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ML_closing37;</highlight></codeline>
<codeline lineno="57"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ML_closingdH;</highlight></codeline>
<codeline lineno="58"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ML_intern37;</highlight></codeline>
<codeline lineno="59"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ML_interndH;</highlight></codeline>
<codeline lineno="60"><highlight class="normal"></highlight></codeline>
<codeline lineno="61"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>TripleC37;</highlight></codeline>
<codeline lineno="62"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>TripleCdH;</highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>MultipleCA37;</highlight></codeline>
<codeline lineno="64"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>MultipleCAdH;</highlight></codeline>
<codeline lineno="65"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>MultipleCB37;</highlight></codeline>
<codeline lineno="66"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>MultipleCBdH;</highlight></codeline>
<codeline lineno="67"><highlight class="normal"></highlight></codeline>
<codeline lineno="68"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>Ninio-correction<sp/>for<sp/>asymmetric<sp/>internal<sp/>loops<sp/>with<sp/>branches<sp/>n1<sp/>and<sp/>n2<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="69"><highlight class="normal"></highlight><highlight class="comment">/*<sp/><sp/><sp/><sp/>ninio_energy<sp/>=<sp/>min{max_ninio,<sp/>|n1-n2|*F_ninio[min{4.0,<sp/>n1,<sp/>n2}]<sp/>}<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="70"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>MAX_NINIO;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>maximum<sp/>correction<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="71"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>ninio37;</highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>niniodH;</highlight></codeline>
<codeline lineno="73"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>penalty<sp/>for<sp/>helices<sp/>terminated<sp/>by<sp/>AU<sp/>(actually<sp/>not<sp/>GC)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="74"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>TerminalAU37;</highlight></codeline>
<codeline lineno="75"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>TerminalAUdH;</highlight></codeline>
<codeline lineno="76"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>penalty<sp/>for<sp/>forming<sp/>bi-molecular<sp/>duplex<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>DuplexInit37;</highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>DuplexInitdH;</highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>stabilizing<sp/>contribution<sp/>due<sp/>to<sp/>special<sp/>hairpins<sp/>of<sp/>size<sp/>4<sp/>(tetraloops)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>Tetraloops[281];<sp/><sp/></highlight><highlight class="comment">/*<sp/>string<sp/>containing<sp/>the<sp/>special<sp/>tetraloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="81"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>Tetraloop37[40];<sp/><sp/></highlight><highlight class="comment">/*<sp/>Bonus<sp/>energy<sp/>for<sp/>special<sp/>tetraloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>TetraloopdH[40];</highlight></codeline>
<codeline lineno="83"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>Triloops[241];<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>string<sp/>containing<sp/>the<sp/>special<sp/>triloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>Triloop37[40];<sp/></highlight><highlight class="comment">/*<sp/>Bonus<sp/>energy<sp/>for<sp/>special<sp/>Triloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>TriloopdH[40];<sp/></highlight><highlight class="comment">/*<sp/>Bonus<sp/>energy<sp/>for<sp/>special<sp/>Triloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="86"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>Hexaloops[361];<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>string<sp/>containing<sp/>the<sp/>special<sp/>triloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="87"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>Hexaloop37[40];<sp/></highlight><highlight class="comment">/*<sp/>Bonus<sp/>energy<sp/>for<sp/>special<sp/>Triloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="88"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>HexaloopdH[40];<sp/></highlight><highlight class="comment">/*<sp/>Bonus<sp/>energy<sp/>for<sp/>special<sp/>Triloops<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="89"><highlight class="normal"></highlight></codeline>
<codeline lineno="90"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadAlpha37;</highlight></codeline>
<codeline lineno="91"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadAlphadH;</highlight></codeline>
<codeline lineno="92"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadBeta37;</highlight></codeline>
<codeline lineno="93"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadBetadH;</highlight></codeline>
<codeline lineno="94"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadLayerMismatch37;<sp/><sp/></highlight><highlight class="comment">/*<sp/>penalty<sp/>per<sp/>incompatible<sp/>gquad<sp/>layer<sp/>in<sp/>a<sp/>sub-alignment<sp/>(applied<sp/>twice<sp/>for<sp/>inner<sp/>layers)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadLayerMismatchH;</highlight></codeline>
<codeline lineno="96"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>GQuadLayerMismatchMax;<sp/></highlight><highlight class="comment">/*<sp/>maximum<sp/>number<sp/>of<sp/>mismatching<sp/>sequences<sp/>in<sp/>the<sp/>alignment<sp/>when<sp/>gquad<sp/>should<sp/>be<sp/>formed<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight></codeline>
<codeline lineno="98"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>Tmeasure;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>temperature<sp/>of<sp/>param<sp/>measurements<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="99"><highlight class="normal"></highlight></codeline>
<codeline lineno="100"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/params/default.h"/>
  </compounddef>
</doxygen>
