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        <label>ViennaRNA/structures/centroid.h</label>
        <link refid="structures_2centroid_8h"/>
        <childnode refid="108" relation="include">
        </childnode>
      </node>
      <node id="138">
        <label>ViennaRNA/structures/mea.h</label>
        <link refid="mea_8h_source"/>
        <childnode refid="139" relation="include">
        </childnode>
      </node>
      <node id="111">
        <label>ViennaRNA/subopt.h</label>
        <link refid="subopt_8h"/>
      </node>
      <node id="109">
        <label>ViennaRNA/subopt/gquad.h</label>
        <link refid="subopt_2gquad_8h"/>
      </node>
      <node id="110">
        <label>ViennaRNA/subopt/wuchty.h</label>
        <link refid="wuchty_8h"/>
        <childnode refid="111" relation="include">
        </childnode>
      </node>
      <node id="112">
        <label>ViennaRNA/subopt/zuker.h</label>
        <link refid="zuker_8h_source"/>
        <childnode refid="113" relation="include">
        </childnode>
      </node>
      <node id="113">
        <label>ViennaRNA/subopt_zuker.h</label>
        <link refid="subopt__zuker_8h"/>
      </node>
      <node id="114">
        <label>ViennaRNA/unstructured_domains.h</label>
        <link refid="unstructured__domains_8h"/>
        <childnode refid="16" relation="include">
        </childnode>
        <childnode refid="37" relation="include">
        </childnode>
      </node>
      <node id="104">
        <label>ViennaRNA/utils.h</label>
        <link refid="utils_8h"/>
      </node>
      <node id="101">
        <label>ViennaRNA/utils/alignments.h</label>
        <link refid="utils_2alignments_8h"/>
      </node>
      <node id="140">
        <label>ViennaRNA/utils/basic.h</label>
        <link refid="utils_2basic_8h"/>
        <childnode refid="25" relation="include">
        </childnode>
        <childnode refid="28" relation="include">
        </childnode>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="49" relation="include">
        </childnode>
        <childnode refid="36" relation="include">
        </childnode>
        <childnode refid="50" relation="include">
        </childnode>
        <childnode refid="69" relation="include">
        </childnode>
        <childnode refid="73" relation="include">
        </childnode>
        <childnode refid="118" relation="include">
        </childnode>
        <childnode refid="141" relation="include">
        </childnode>
        <childnode refid="43" relation="include">
        </childnode>
        <childnode refid="81" relation="include">
        </childnode>
        <childnode refid="104" relation="include">
        </childnode>
      </node>
      <node id="142">
        <label>ViennaRNA/utils/strings.h</label>
        <link refid="strings_8h"/>
        <childnode refid="143" relation="include">
        </childnode>
        <childnode refid="104" relation="include">
        </childnode>
      </node>
      <node id="137">
        <label>ViennaRNA/utils/structures.h</label>
        <link refid="utils_2structures_8h"/>
        <childnode refid="104" relation="include">
        </childnode>
      </node>
      <node id="63">
        <label>ViennaRNA/walk.h</label>
        <link refid="walk_8h"/>
      </node>
    </invincdepgraph>
    <innerclass refid="structvrna__param__s" prot="public">vrna_param_s</innerclass>
    <innerclass refid="structvrna__exp__param__s" prot="public">vrna_exp_param_s</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="params_2basic_8h_1aab347a3c03fbe8e7319551b9fa0cce4a" prot="public" static="no">
        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/basic.h" line="13" column="11" bodyfile="ViennaRNA/params/basic.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <member refid="group__energy__parameters_1gab7b5159125a90babbd3b81319305f35f" kind="define"><name>VRNA_GQUAD_MAX_STACK_SIZE</name></member>
      <member refid="group__energy__parameters_1gae24794ad38d2bf86d4c1e2f24cf35230" kind="define"><name>VRNA_GQUAD_MIN_STACK_SIZE</name></member>
      <member refid="group__energy__parameters_1gaabc251a60f6dbe927dd3a3881a161fb7" kind="define"><name>VRNA_GQUAD_MAX_LINKER_LENGTH</name></member>
      <member refid="group__energy__parameters_1gab0e3cb58bc3a7e3fb08cc05f8e58ddab" kind="define"><name>VRNA_GQUAD_MIN_LINKER_LENGTH</name></member>
      <member refid="group__energy__parameters_1gad7bdd880afca461f97763d79ee57a347" kind="define"><name>VRNA_GQUAD_MIN_BOX_SIZE</name></member>
      <member refid="group__energy__parameters_1ga56cafabad2f8a7db83f2d5d3b0e8d313" kind="define"><name>VRNA_GQUAD_MAX_BOX_SIZE</name></member>
    </sectiondef>
    <sectiondef kind="typedef">
      <member refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kind="typedef"><name>vrna_param_t</name></member>
      <member refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kind="typedef"><name>vrna_exp_param_t</name></member>
      <member refid="group__energy__parameters_1ga857dde86357d306cc902f0d8b2797659" kind="typedef"><name>paramT</name></member>
      <member refid="group__energy__parameters_1ga8bffe1828e2cbec101769f5cc0b1535b" kind="typedef"><name>pf_paramT</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__energy__parameters_1ga51839957423a01c8613f5a978b37a514" kind="function"><name>vrna_params</name></member>
      <member refid="group__energy__parameters_1ga2cb17f57d4de820b034a9d46f115ea49" kind="function"><name>vrna_params_copy</name></member>
      <member refid="group__energy__parameters_1ga049c8196ed6b9af9f13c633f0fe7acc0" kind="function"><name>vrna_exp_params</name></member>
      <member refid="group__energy__parameters_1ga71255857b629f2c5b86adc75c78df13e" kind="function"><name>vrna_exp_params_comparative</name></member>
      <member refid="group__energy__parameters_1ga47828f98665c57d9b8bc954b5769e484" kind="function"><name>vrna_exp_params_copy</name></member>
      <member refid="group__energy__parameters_1ga9202b803da6f5364f91db89ab3d8b048" kind="function"><name>vrna_params_subst</name></member>
      <member refid="group__energy__parameters_1ga4abbca93defd54fa0dc797ceca36d2f0" kind="function"><name>vrna_exp_params_subst</name></member>
      <member refid="group__energy__parameters_1gac377cdd18c3a6da4e04683742fda3b7a" kind="function"><name>vrna_exp_params_rescale</name></member>
      <member refid="group__energy__parameters_1ga033fea3322aeac71a260241e8ba6e773" kind="function"><name>vrna_params_reset</name></member>
      <member refid="group__energy__parameters_1ga7740b358409b339f0db7b99d7c20e693" kind="function"><name>vrna_exp_params_reset</name></member>
      <member refid="group__energy__parameters_1ga06befb1f7beed0b4014cc07628636bc3" kind="function"><name>vrna_params_prepare</name></member>
      <member refid="group__energy__parameters_1ga92879f2a9bc4cfc4e700d7f9222853bc" kind="function"><name>get_parameter_copy</name></member>
      <member refid="group__energy__parameters_1ga1007b70b7176f7cc78ed224460b89bbe" kind="function"><name>get_scaled_pf_parameters</name></member>
      <member refid="group__energy__parameters_1gaf05b50c0e8d29511941203554daf2919" kind="function"><name>get_boltzmann_factors</name></member>
      <member refid="group__energy__parameters_1ga356800d32f664d455af4676850638f99" kind="function"><name>get_boltzmann_factor_copy</name></member>
      <member refid="group__energy__parameters_1ga1c9a23ef63e80859776eac8a0beda437" kind="function"><name>get_scaled_alipf_parameters</name></member>
      <member refid="group__energy__parameters_1ga010ff3879cb0a053ce2547948315a10c" kind="function"><name>get_boltzmann_factors_ali</name></member>
      <member refid="group__energy__parameters_1ga5fe3524fd6d2a297099238f117254c13" kind="function"><name>scale_parameters</name></member>
      <member refid="group__energy__parameters_1gacdbcef8d5022d9e2eaac347374f5b3a9" kind="function"><name>get_scaled_parameters</name></member>
      <member refid="group__energy__parameters_1ga8e44a24c8277d2dcca5694c30fb3a8b7" kind="function"><name>copy_parameters</name></member>
      <member refid="group__energy__parameters_1gab29c16026009b5e2b1f4e70d18b75cb1" kind="function"><name>set_parameters</name></member>
      <member refid="group__energy__parameters_1ga1309d1982122772d185b86f85ccb5fa5" kind="function"><name>scale_pf_parameters</name></member>
      <member refid="group__energy__parameters_1gaf2095e2c08146b61ec17a34366b3128d" kind="function"><name>copy_pf_param</name></member>
      <member refid="group__energy__parameters_1ga9ee3f54406bb566ee8f11db4f803937a" kind="function"><name>set_pf_param</name></member>
    </sectiondef>
    <briefdescription>
<para>Functions to deal with sets of energy parameters. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PARAMS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PARAMS_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">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(&quot;&quot;,<sp/>msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight></codeline>
<codeline lineno="28" refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/><sp/></highlight><highlight class="normal"><ref refid="structvrna__param__s" kindref="compound">vrna_param_s</ref><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref>;</highlight></codeline>
<codeline lineno="30" refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/><sp/></highlight><highlight class="normal"><ref refid="structvrna__exp__param__s" kindref="compound">vrna_exp_param_s</ref><sp/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref>;</highlight></codeline>
<codeline lineno="31"><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><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="33"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="35"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="model_8h" kindref="compound">ViennaRNA/model.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>VRNA_GQUAD_MAX_STACK_SIZE<sp/><sp/><sp/><sp/><sp/>7</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="38"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>VRNA_GQUAD_MIN_STACK_SIZE<sp/><sp/><sp/><sp/><sp/>2</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>VRNA_GQUAD_MAX_LINKER_LENGTH<sp/><sp/>15</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>VRNA_GQUAD_MIN_LINKER_LENGTH<sp/><sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="41"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>VRNA_GQUAD_MIN_BOX_SIZE<sp/><sp/><sp/><sp/><sp/><sp/><sp/>((4<sp/>*<sp/>VRNA_GQUAD_MIN_STACK_SIZE)<sp/>+<sp/>\</highlight></codeline>
<codeline lineno="42"><highlight class="preprocessor"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(3<sp/>*<sp/>VRNA_GQUAD_MIN_LINKER_LENGTH))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="43"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/><sp/><sp/>VRNA_GQUAD_MAX_BOX_SIZE<sp/><sp/><sp/><sp/><sp/><sp/><sp/>((4<sp/>*<sp/>VRNA_GQUAD_MAX_STACK_SIZE)<sp/>+<sp/>\</highlight></codeline>
<codeline lineno="44"><highlight class="preprocessor"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(3<sp/>*<sp/>VRNA_GQUAD_MAX_LINKER_LENGTH))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="49" refid="structvrna__param__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__param__s" kindref="compound">vrna_param_s</ref><sp/>{</highlight></codeline>
<codeline lineno="50"><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/>id;</highlight></codeline>
<codeline lineno="51"><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[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="52"><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/>hairpin[31];</highlight></codeline>
<codeline lineno="53"><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/>bulge[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="54"><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/>internal_loop[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="55"><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/>mismatchExt[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="56"><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/>mismatchI[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="57"><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/>mismatch1nI[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="58"><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/>mismatch23I[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="59"><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/>mismatchH[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="60"><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/>mismatchM[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="61"><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[NBPAIRS<sp/>+<sp/>1][5];</highlight></codeline>
<codeline lineno="62"><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[NBPAIRS<sp/>+<sp/>1][5];</highlight></codeline>
<codeline lineno="63"><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/>int11[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="64"><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/>int21[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1][5][5][5];</highlight></codeline>
<codeline lineno="65"><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/>int22[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1][5][5][5][5];</highlight></codeline>
<codeline lineno="66"><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/>ninio[5];</highlight></codeline>
<codeline lineno="67"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>lxc;</highlight></codeline>
<codeline lineno="68"><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/>MLbase;</highlight></codeline>
<codeline lineno="69"><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/>MLintern[NBPAIRS<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="70"><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/>MLclosing;</highlight></codeline>
<codeline lineno="71"><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/>TerminalAU;</highlight></codeline>
<codeline lineno="72"><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/>DuplexInit;</highlight></codeline>
<codeline lineno="73"><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/>Tetraloop_E[200];</highlight></codeline>
<codeline lineno="74"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Tetraloops[1401];</highlight></codeline>
<codeline lineno="75"><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/>Triloop_E[40];</highlight></codeline>
<codeline lineno="76"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Triloops[241];</highlight></codeline>
<codeline lineno="77"><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/>Hexaloop_E[40];</highlight></codeline>
<codeline lineno="78"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Hexaloops[1801];</highlight></codeline>
<codeline lineno="79"><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/>TripleC;</highlight></codeline>
<codeline lineno="80"><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/>MultipleCA;</highlight></codeline>
<codeline lineno="81"><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/>MultipleCB;</highlight></codeline>
<codeline lineno="82"><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/>gquad[VRNA_GQUAD_MAX_STACK_SIZE<sp/>+<sp/>1][3<sp/>*<sp/>VRNA_GQUAD_MAX_LINKER_LENGTH<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="83"><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/>gquadLayerMismatch;</highlight></codeline>
<codeline lineno="84"><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/>gquadLayerMismatchMax;</highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="86" refid="structvrna__param__s_1aeed2cd83713012bcb52e431041e037c8" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__param__s_1aeed2cd83713012bcb52e431041e037c8" kindref="member">temperature</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="87"><highlight class="normal"></highlight></codeline>
<codeline lineno="88" refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__param__s_1a7b84353eb9075c595bad4ceb871bcae7" kindref="member">model_details</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="89" refid="structvrna__param__s_1ace10aa4aacffcbf6de92349f2ee0d66a" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__param__s_1ace10aa4aacffcbf6de92349f2ee0d66a" kindref="member">param_file</ref>[256];<sp/><sp/></highlight></codeline>
<codeline lineno="90"><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/>SaltStack;</highlight></codeline>
<codeline lineno="91"><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/>SaltLoop[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>2];</highlight></codeline>
<codeline lineno="92"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>SaltLoopDbl[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>2];</highlight></codeline>
<codeline lineno="93"><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/>SaltMLbase;</highlight></codeline>
<codeline lineno="94"><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/>SaltMLintern;</highlight></codeline>
<codeline lineno="95"><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/>SaltMLclosing;</highlight></codeline>
<codeline lineno="96"><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/>SaltDPXInit;</highlight></codeline>
<codeline lineno="97"><highlight class="normal">};</highlight></codeline>
<codeline lineno="98"><highlight class="normal"></highlight></codeline>
<codeline lineno="102" refid="structvrna__exp__param__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__exp__param__s" kindref="compound">vrna_exp_param_s</ref><sp/>{</highlight></codeline>
<codeline lineno="103" refid="structvrna__exp__param__s_1a378d5bcf2bae1f3ec84c912c7d3908d2" refkind="member"><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/><ref refid="structvrna__exp__param__s_1a378d5bcf2bae1f3ec84c912c7d3908d2" kindref="member">id</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="106"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expstack[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="107"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exphairpin[31];</highlight></codeline>
<codeline lineno="108"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expbulge[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="109"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expinternal[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="110"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expmismatchExt[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="111"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expmismatchI[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="112"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expmismatch23I[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="113"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expmismatch1nI[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="114"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expmismatchH[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="115"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expmismatchM[NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="116"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expdangle5[NBPAIRS<sp/>+<sp/>1][5];</highlight></codeline>
<codeline lineno="117"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expdangle3[NBPAIRS<sp/>+<sp/>1][5];</highlight></codeline>
<codeline lineno="118"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expint11[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1][5][5];</highlight></codeline>
<codeline lineno="119"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expint21[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1][5][5][5];</highlight></codeline>
<codeline lineno="120"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expint22[NBPAIRS<sp/>+<sp/>1][NBPAIRS<sp/>+<sp/>1][5][5][5][5];</highlight></codeline>
<codeline lineno="121"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expninio[5][<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="122"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>lxc;</highlight></codeline>
<codeline lineno="123"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expMLbase;</highlight></codeline>
<codeline lineno="124"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expMLintern[NBPAIRS<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="125"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expMLclosing;</highlight></codeline>
<codeline lineno="126"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expTermAU;</highlight></codeline>
<codeline lineno="127"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expDuplexInit;</highlight></codeline>
<codeline lineno="128"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exptetra[40];</highlight></codeline>
<codeline lineno="129"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exptri[40];</highlight></codeline>
<codeline lineno="130"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>exphex[40];</highlight></codeline>
<codeline lineno="131"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Tetraloops[1401];</highlight></codeline>
<codeline lineno="132"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expTriloop[40];</highlight></codeline>
<codeline lineno="133"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Triloops[241];</highlight></codeline>
<codeline lineno="134"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Hexaloops[1801];</highlight></codeline>
<codeline lineno="135"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expTripleC;</highlight></codeline>
<codeline lineno="136"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expMultipleCA;</highlight></codeline>
<codeline lineno="137"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expMultipleCB;</highlight></codeline>
<codeline lineno="138"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expgquad[VRNA_GQUAD_MAX_STACK_SIZE<sp/>+<sp/>1][3<sp/>*<sp/>VRNA_GQUAD_MAX_LINKER_LENGTH<sp/>+<sp/>1];</highlight></codeline>
<codeline lineno="139"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expgquadLayerMismatch;</highlight></codeline>
<codeline lineno="140"><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/>gquadLayerMismatchMax;</highlight></codeline>
<codeline lineno="141"><highlight class="normal"></highlight></codeline>
<codeline lineno="142"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>kT;</highlight></codeline>
<codeline lineno="143" refid="structvrna__exp__param__s_1a53c12f0d74f94ce371e0471a8ab5a377" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__exp__param__s_1a53c12f0d74f94ce371e0471a8ab5a377" kindref="member">pf_scale</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="144"><highlight class="normal"></highlight></codeline>
<codeline lineno="145" refid="structvrna__exp__param__s_1a674656d65ea957ddbeff8bd146b7fc16" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__exp__param__s_1a674656d65ea957ddbeff8bd146b7fc16" kindref="member">temperature</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="146" refid="structvrna__exp__param__s_1a77145830b7bb01b36c3217b363310ef0" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__exp__param__s_1a77145830b7bb01b36c3217b363310ef0" kindref="member">alpha</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="152"><highlight class="normal"></highlight></codeline>
<codeline lineno="153" refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__exp__param__s_1ac18055127bccc27c1223f1d2f3b01b53" kindref="member">model_details</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="154" refid="structvrna__exp__param__s_1a8e1b02a4753a9b64c3c9ae8529b9d75c" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__exp__param__s_1a8e1b02a4753a9b64c3c9ae8529b9d75c" kindref="member">param_file</ref>[256];<sp/><sp/></highlight></codeline>
<codeline lineno="155"><highlight class="normal"></highlight></codeline>
<codeline lineno="156"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expSaltStack;</highlight></codeline>
<codeline lineno="157"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>expSaltLoop[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>2];</highlight></codeline>
<codeline lineno="158"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>SaltLoopDbl[<ref refid="constants_8h_1ad1bd6eabac419670ddd3c9ed82145988" kindref="member">MAXLOOP</ref><sp/>+<sp/>2];</highlight></codeline>
<codeline lineno="159"><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/>SaltMLbase;</highlight></codeline>
<codeline lineno="160"><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/>SaltMLintern;</highlight></codeline>
<codeline lineno="161"><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/>SaltMLclosing;</highlight></codeline>
<codeline lineno="162"><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/>SaltDPXInit;</highlight></codeline>
<codeline lineno="163"><highlight class="normal">};</highlight></codeline>
<codeline lineno="164"><highlight class="normal"></highlight></codeline>
<codeline lineno="165"><highlight class="normal"></highlight></codeline>
<codeline lineno="177"><highlight class="normal"><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*</highlight></codeline>
<codeline lineno="178" refid="group__energy__parameters_1ga51839957423a01c8613f5a978b37a514" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga51839957423a01c8613f5a978b37a514" kindref="member">vrna_params</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md);</highlight></codeline>
<codeline lineno="179"><highlight class="normal"></highlight></codeline>
<codeline lineno="180"><highlight class="normal"></highlight></codeline>
<codeline lineno="192"><highlight class="normal"><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*</highlight></codeline>
<codeline lineno="193" refid="group__energy__parameters_1ga2cb17f57d4de820b034a9d46f115ea49" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga2cb17f57d4de820b034a9d46f115ea49" kindref="member">vrna_params_copy</ref>(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*par);</highlight></codeline>
<codeline lineno="194"><highlight class="normal"></highlight></codeline>
<codeline lineno="195"><highlight class="normal"></highlight></codeline>
<codeline lineno="218"><highlight class="normal"><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*</highlight></codeline>
<codeline lineno="219" refid="group__energy__parameters_1ga049c8196ed6b9af9f13c633f0fe7acc0" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga049c8196ed6b9af9f13c633f0fe7acc0" kindref="member">vrna_exp_params</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md);</highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight></codeline>
<codeline lineno="221"><highlight class="normal"></highlight></codeline>
<codeline lineno="235"><highlight class="normal"><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*</highlight></codeline>
<codeline lineno="236" refid="group__energy__parameters_1ga71255857b629f2c5b86adc75c78df13e" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga71255857b629f2c5b86adc75c78df13e" kindref="member">vrna_exp_params_comparative</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>n_seq,</highlight></codeline>
<codeline lineno="237"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/>*md);</highlight></codeline>
<codeline lineno="238"><highlight class="normal"></highlight></codeline>
<codeline lineno="239"><highlight class="normal"></highlight></codeline>
<codeline lineno="251"><highlight class="normal"><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*</highlight></codeline>
<codeline lineno="252" refid="group__energy__parameters_1ga47828f98665c57d9b8bc954b5769e484" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga47828f98665c57d9b8bc954b5769e484" kindref="member">vrna_exp_params_copy</ref>(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*par);</highlight></codeline>
<codeline lineno="253"><highlight class="normal"></highlight></codeline>
<codeline lineno="254"><highlight class="normal"></highlight></codeline>
<codeline lineno="267"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="268" refid="group__energy__parameters_1ga9202b803da6f5364f91db89ab3d8b048" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga9202b803da6f5364f91db89ab3d8b048" kindref="member">vrna_params_subst</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="269"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*par);</highlight></codeline>
<codeline lineno="270"><highlight class="normal"></highlight></codeline>
<codeline lineno="271"><highlight class="normal"></highlight></codeline>
<codeline lineno="289"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="290" refid="group__energy__parameters_1ga4abbca93defd54fa0dc797ceca36d2f0" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga4abbca93defd54fa0dc797ceca36d2f0" kindref="member">vrna_exp_params_subst</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</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/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*params);</highlight></codeline>
<codeline lineno="292"><highlight class="normal"></highlight></codeline>
<codeline lineno="293"><highlight class="normal"></highlight></codeline>
<codeline lineno="331"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="332" refid="group__energy__parameters_1gac377cdd18c3a6da4e04683742fda3b7a" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1gac377cdd18c3a6da4e04683742fda3b7a" kindref="member">vrna_exp_params_rescale</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*mfe);</highlight></codeline>
<codeline lineno="334"><highlight class="normal"></highlight></codeline>
<codeline lineno="335"><highlight class="normal"></highlight></codeline>
<codeline lineno="350"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="351" refid="group__energy__parameters_1ga033fea3322aeac71a260241e8ba6e773" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga033fea3322aeac71a260241e8ba6e773" kindref="member">vrna_params_reset</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="352"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*md);</highlight></codeline>
<codeline lineno="353"><highlight class="normal"></highlight></codeline>
<codeline lineno="354"><highlight class="normal"></highlight></codeline>
<codeline lineno="370"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="371" refid="group__energy__parameters_1ga7740b358409b339f0db7b99d7c20e693" refkind="member"><highlight class="normal"><ref refid="group__energy__parameters_1ga7740b358409b339f0db7b99d7c20e693" kindref="member">vrna_exp_params_reset</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="372"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*md);</highlight></codeline>
<codeline lineno="373"><highlight class="normal"></highlight></codeline>
<codeline lineno="374"><highlight class="normal"></highlight></codeline>
<codeline lineno="375"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="376"><highlight class="normal">vrna_params_prepare(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="377"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="378"><highlight class="normal"></highlight></codeline>
<codeline lineno="379"><highlight class="normal"></highlight></codeline>
<codeline lineno="380"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="381"><highlight class="normal"></highlight></codeline>
<codeline lineno="386" refid="group__energy__parameters_1ga857dde86357d306cc902f0d8b2797659" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__param__s" kindref="compound">vrna_param_s</ref><sp/><ref refid="group__energy__parameters_1ga857dde86357d306cc902f0d8b2797659" kindref="member">paramT</ref>;</highlight></codeline>
<codeline lineno="387"><highlight class="normal"></highlight></codeline>
<codeline lineno="392" refid="group__energy__parameters_1ga8bffe1828e2cbec101769f5cc0b1535b" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__exp__param__s" kindref="compound">vrna_exp_param_s</ref><sp/><ref refid="group__energy__parameters_1ga8bffe1828e2cbec101769f5cc0b1535b" kindref="member">pf_paramT</ref>;</highlight></codeline>
<codeline lineno="393"><highlight class="normal"></highlight></codeline>
<codeline lineno="394"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*get_parameter_copy(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*par),</highlight></codeline>
<codeline lineno="395"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_params_copy()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="396"><highlight class="normal"></highlight></codeline>
<codeline lineno="406"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*<ref refid="group__energy__parameters_1ga1007b70b7176f7cc78ed224460b89bbe" kindref="member">get_scaled_pf_parameters</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="407" refid="group__energy__parameters_1ga1007b70b7176f7cc78ed224460b89bbe" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_params()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="408"><highlight class="normal"></highlight></codeline>
<codeline lineno="434"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*<ref refid="group__energy__parameters_1gaf05b50c0e8d29511941203554daf2919" kindref="member">get_boltzmann_factors</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gab4b11c8d9c758430960896bc3fe82ead" kindref="member">temperature</ref>,</highlight></codeline>
<codeline lineno="435"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>betaScale,</highlight></codeline>
<codeline lineno="436"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>md,</highlight></codeline>
<codeline lineno="437"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gad3b22044065acc6dee0af68931b52cfd" kindref="member">pf_scale</ref>),</highlight></codeline>
<codeline lineno="438" refid="group__energy__parameters_1gaf05b50c0e8d29511941203554daf2919" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="439"><highlight class="normal"></highlight></codeline>
<codeline lineno="450"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*<ref refid="group__energy__parameters_1ga356800d32f664d455af4676850638f99" kindref="member">get_boltzmann_factor_copy</ref>(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*parameters),</highlight></codeline>
<codeline lineno="451" refid="group__energy__parameters_1ga356800d32f664d455af4676850638f99" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params_copy()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="452"><highlight class="normal"></highlight></codeline>
<codeline lineno="460"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*<ref refid="group__energy__parameters_1ga1c9a23ef63e80859776eac8a0beda437" kindref="member">get_scaled_alipf_parameters</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n_seq),</highlight></codeline>
<codeline lineno="461" refid="group__energy__parameters_1ga1c9a23ef63e80859776eac8a0beda437" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params_comparative()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="462"><highlight class="normal"></highlight></codeline>
<codeline lineno="471"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*<ref refid="group__energy__parameters_1ga010ff3879cb0a053ce2547948315a10c" kindref="member">get_boltzmann_factors_ali</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>n_seq,</highlight></codeline>
<codeline lineno="472"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gab4b11c8d9c758430960896bc3fe82ead" kindref="member">temperature</ref>,</highlight></codeline>
<codeline lineno="473"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>betaScale,</highlight></codeline>
<codeline lineno="474"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/>md,</highlight></codeline>
<codeline lineno="475"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gad3b22044065acc6dee0af68931b52cfd" kindref="member">pf_scale</ref>),</highlight></codeline>
<codeline lineno="476" refid="group__energy__parameters_1ga010ff3879cb0a053ce2547948315a10c" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params_comparative()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="477"><highlight class="normal"></highlight></codeline>
<codeline lineno="489"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*<ref refid="group__energy__parameters_1ga5fe3524fd6d2a297099238f117254c13" kindref="member">scale_parameters</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="490" refid="group__energy__parameters_1ga5fe3524fd6d2a297099238f117254c13" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_params()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="491"><highlight class="normal"></highlight></codeline>
<codeline lineno="508"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*<ref refid="group__energy__parameters_1gacdbcef8d5022d9e2eaac347374f5b3a9" kindref="member">get_scaled_parameters</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gab4b11c8d9c758430960896bc3fe82ead" kindref="member">temperature</ref>,</highlight></codeline>
<codeline lineno="509"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>md),</highlight></codeline>
<codeline lineno="510" refid="group__energy__parameters_1gacdbcef8d5022d9e2eaac347374f5b3a9" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Usee<sp/>vrna_params()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="511"><highlight class="normal"></highlight></codeline>
<codeline lineno="512"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*copy_parameters(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_params_copy()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="513"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*set_parameters(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*dest),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_params_copy()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="514"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*scale_pf_parameters(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="515"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*copy_pf_param(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params_copy()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="516"><highlight class="normal">DEPRECATED(<ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*set_pf_param(<ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref><sp/>*dest),</highlight></codeline>
<codeline lineno="517"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_exp_params_copy()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="518"><highlight class="normal"></highlight></codeline>
<codeline lineno="519"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="520"><highlight class="normal"></highlight></codeline>
<codeline lineno="524"><highlight class="normal"></highlight></codeline>
<codeline lineno="525"><highlight class="normal"></highlight></codeline>
<codeline lineno="526"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/params/basic.h"/>
  </compounddef>
</doxygen>
