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    <innerclass refid="structvrna__dimer__pf__s" prot="public">vrna_dimer_pf_s</innerclass>
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      <header>Basic global partition function interface</header>
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    <sectiondef kind="user-defined">
      <header>Simplified global partition function computation using sequence(s) or multiple sequence alignment(s)</header>
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        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
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        <definition>typedef struct vrna_multimer_pf_s vrna_multimer_pf_t</definition>
        <argsstring></argsstring>
        <name>vrna_multimer_pf_t</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
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        <type>void</type>
        <definition>void init_pf_circ_fold</definition>
        <argsstring>(int length)</argsstring>
        <name>init_pf_circ_fold</name>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="692" column="18" declfile="ViennaRNA/partfunc/global.h" declline="692" declcolumn="18"/>
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        <type>char *</type>
        <definition>char * centroid</definition>
        <argsstring>(int length, double *dist)</argsstring>
        <name>centroid</name>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>dist</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000194"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This function is deprecated and should not be used anymore as it is not threadsafe!</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="structures_2centroid_8h_1afbaa555b0060c9043558f8d233d9dcf0" kindref="member">get_centroid_struct_pl()</ref>, <ref refid="structures_2centroid_8h_1a37abcb1821056b6a0be8502b7d1629cf" kindref="member">get_centroid_struct_pr()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="701" column="7" declfile="ViennaRNA/partfunc/global.h" declline="701" declcolumn="7"/>
      </memberdef>
      <memberdef kind="function" id="partfunc_2global_8h_1ac89c333a303e3789b62ae1bc57980884" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * get_centroid_struct_gquad_pr</definition>
        <argsstring>(int length, double *dist)</argsstring>
        <name>get_centroid_struct_gquad_pr</name>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>dist</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000195"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This function is deprecated and should not be used anymore as it is not threadsafe!</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="group__centroid__fold_1gac39e7be7392b2c72bd3a6a14612be5e2" kindref="member">vrna_centroid()</ref>, <ref refid="group__centroid__fold_1gae50c5cd891e5e1a3179735a47887f73a" kindref="member">vrna_centroid_from_probs()</ref>, <ref refid="group__centroid__fold_1ga8e68f31264f2192b0ad02fb2d54f634a" kindref="member">vrna_centroid_from_plist()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="710" column="7" declfile="ViennaRNA/partfunc/global.h" declline="710" declcolumn="7"/>
      </memberdef>
      <memberdef kind="function" id="partfunc_2global_8h_1ae9556ba7ded44fe2321b6f67c3fc02a3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double mean_bp_dist</definition>
        <argsstring>(int length)</argsstring>
        <name>mean_bp_dist</name>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>get the mean pair distance of ensemble</para>
<para><xrefsect id="deprecated_1_deprecated000196"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This function is not threadsafe and should not be used anymore. Use <ref refid="group__part__func__global__deprecated_1ga79cbc375af65f11609feb6b055269e7d" kindref="member">mean_bp_distance()</ref> instead! </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="719" column="20" declfile="ViennaRNA/partfunc/global.h" declline="719" declcolumn="20"/>
      </memberdef>
      <memberdef kind="function" id="partfunc_2global_8h_1a68ba6f3a48e08ca131ab54621ce3a2d7" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double expLoopEnergy</definition>
        <argsstring>(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</argsstring>
        <name>expLoopEnergy</name>
        <param>
          <type>int</type>
          <declname>u1</declname>
        </param>
        <param>
          <type>int</type>
          <declname>u2</declname>
        </param>
        <param>
          <type>int</type>
          <declname>type</declname>
        </param>
        <param>
          <type>int</type>
          <declname>type2</declname>
        </param>
        <param>
          <type>short</type>
          <declname>si1</declname>
        </param>
        <param>
          <type>short</type>
          <declname>sj1</declname>
        </param>
        <param>
          <type>short</type>
          <declname>sp1</declname>
        </param>
        <param>
          <type>short</type>
          <declname>sq1</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000197"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use vrna_exp_E_internal() from <ref refid="loop__energies_8h" kindref="compound">loop_energies.h</ref> instead </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="733" column="20" declfile="ViennaRNA/partfunc/global.h" declline="733" declcolumn="20"/>
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      <memberdef kind="function" id="partfunc_2global_8h_1a7b6ab474cc80accc48010ccfcc59f96b" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double expHairpinEnergy</definition>
        <argsstring>(int u, int type, short si1, short sj1, const char *string)</argsstring>
        <name>expHairpinEnergy</name>
        <param>
          <type>int</type>
          <declname>u</declname>
        </param>
        <param>
          <type>int</type>
          <declname>type</declname>
        </param>
        <param>
          <type>short</type>
          <declname>si1</declname>
        </param>
        <param>
          <type>short</type>
          <declname>sj1</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>string</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000198"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use <ref refid="group__eval__loops__hp_1ga847c34387b29b06448c7c843156bca91" kindref="member">vrna_exp_E_hairpin()</ref> from <ref refid="loop__energies_8h" kindref="compound">loop_energies.h</ref> instead </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="744" column="20" declfile="ViennaRNA/partfunc/global.h" declline="744" declcolumn="20"/>
      </memberdef>
      <memberdef kind="function" id="partfunc_2global_8h_1adfdc1276accdffec098fb372cca28486" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void assign_plist_gquad_from_pr</definition>
        <argsstring>(vrna_ep_t **pl, int length, double cut_off)</argsstring>
        <name>assign_plist_gquad_from_pr</name>
        <param>
          <type><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref> **</type>
          <declname>pl</declname>
        </param>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>double</type>
          <declname>cut_off</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="751" column="18" declfile="ViennaRNA/partfunc/global.h" declline="751" declcolumn="18"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>Partition function implementations. </para>
    </briefdescription>
    <detaileddescription>
<para>, </para>
<para>This file includes (almost) all function declarations within the <bold>RNAlib</bold> that are related to Partion function computations </para>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PARTFUNC_GLOBAL_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PARTFUNC_GLOBAL_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="8" refid="group__pf__cofold_1ga444df1587c9a2ca15b8eb25188f629c3" 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__dimer__pf__s" kindref="compound">vrna_dimer_pf_s</ref><sp/><ref refid="group__pf__cofold_1ga444df1587c9a2ca15b8eb25188f629c3" kindref="member">vrna_dimer_pf_t</ref>;</highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><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__multimer__pf__s" kindref="compound">vrna_multimer_pf_s</ref><sp/>vrna_multimer_pf_t;</highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight></codeline>
<codeline lineno="18" refid="group__pf__cofold_1ga5445d8d96a40e9e79b1fa5a7f1a6b7ea" 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__dimer__pf__s" kindref="compound">vrna_dimer_pf_s</ref><sp/><ref refid="group__pf__cofold_1ga5445d8d96a40e9e79b1fa5a7f1a6b7ea" kindref="member">cofoldF</ref>;</highlight></codeline>
<codeline lineno="19"><highlight class="normal"></highlight></codeline>
<codeline lineno="20"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="23"><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="24"><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="25"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="problist_8h" kindref="compound">ViennaRNA/structures/problist.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="params_2basic_8h" kindref="compound">ViennaRNA/params/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><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="31"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="32"><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="33"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="34"><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="35"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="38"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight></codeline>
<codeline lineno="48"><highlight class="normal"></highlight></codeline>
<codeline lineno="49"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="50"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="51"><highlight class="comment"><sp/>#<sp/>PARTITION<sp/>FUNCTION<sp/>COMPUTATION<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>#</highlight></codeline>
<codeline lineno="52"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="53"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="54"><highlight class="normal"></highlight></codeline>
<codeline lineno="59"><highlight class="normal"></highlight></codeline>
<codeline lineno="63" refid="structvrna__dimer__pf__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__dimer__pf__s" kindref="compound">vrna_dimer_pf_s</ref><sp/>{</highlight></codeline>
<codeline lineno="64"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>free<sp/>energies<sp/>for:<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="65" refid="structvrna__dimer__pf__s_1a82e31d1fb6e95923fab6036f52c370af" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__dimer__pf__s_1a82e31d1fb6e95923fab6036f52c370af" kindref="member">F0AB</ref>;<sp/></highlight></codeline>
<codeline lineno="66" refid="structvrna__dimer__pf__s_1a01a87f59db2b7fbf883b056e6f6c673a" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__dimer__pf__s_1a01a87f59db2b7fbf883b056e6f6c673a" kindref="member">FAB</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="67" refid="structvrna__dimer__pf__s_1a7b01cea5721f61badebc29cf0a9c4266" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__dimer__pf__s_1a7b01cea5721f61badebc29cf0a9c4266" kindref="member">FcAB</ref>;<sp/></highlight></codeline>
<codeline lineno="68" refid="structvrna__dimer__pf__s_1a1aca57247f2c023d08028b1919005b0a" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__dimer__pf__s_1a1aca57247f2c023d08028b1919005b0a" kindref="member">FA</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="69" refid="structvrna__dimer__pf__s_1ab4d307be5400604d3c1d84d58a9981df" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__dimer__pf__s_1ab4d307be5400604d3c1d84d58a9981df" kindref="member">FB</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="70"><highlight class="normal">};</highlight></codeline>
<codeline lineno="71"><highlight class="normal"></highlight></codeline>
<codeline lineno="72" refid="structvrna__multimer__pf__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__multimer__pf__s" kindref="compound">vrna_multimer_pf_s</ref><sp/>{</highlight></codeline>
<codeline lineno="73"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>free<sp/>energies<sp/>for:<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="74" refid="structvrna__multimer__pf__s_1ac9c2a58bc07ae9c0e97d0bfb4b973db3" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__multimer__pf__s_1ac9c2a58bc07ae9c0e97d0bfb4b973db3" kindref="member">F_connected</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="75" refid="structvrna__multimer__pf__s_1a33856f7edf687ad26bafd0c62536c2bc" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>*<ref refid="structvrna__multimer__pf__s_1a33856f7edf687ad26bafd0c62536c2bc" kindref="member">F_monomers</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="76" refid="structvrna__multimer__pf__s_1a1ccd8466abb58ff6cecdc1a1deda0d36" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">size_t</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__multimer__pf__s_1a1ccd8466abb58ff6cecdc1a1deda0d36" kindref="member">num_monomers</ref>;<sp/></highlight></codeline>
<codeline lineno="77"><highlight class="normal">};</highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight></codeline>
<codeline lineno="83"><highlight class="normal"></highlight></codeline>
<codeline lineno="111"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="112" refid="group__part__func__global_1ga82e6e17a04d6784e4d8cdeb8bfef74fb" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1ga82e6e17a04d6784e4d8cdeb8bfef74fb" kindref="member">vrna_pf</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="113"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure);</highlight></codeline>
<codeline lineno="114"><highlight class="normal"></highlight></codeline>
<codeline lineno="115"><highlight class="normal"></highlight></codeline>
<codeline lineno="134"><highlight class="normal"><ref refid="group__pf__cofold_1ga444df1587c9a2ca15b8eb25188f629c3" kindref="member">vrna_dimer_pf_t</ref></highlight></codeline>
<codeline lineno="135" refid="group__part__func__global_1gae796019c176a158f0e9d7741a85c1743" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1gae796019c176a158f0e9d7741a85c1743" kindref="member">vrna_pf_dimer</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="136"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure);</highlight></codeline>
<codeline lineno="137"><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"></highlight></codeline>
<codeline lineno="139"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>*</highlight></codeline>
<codeline lineno="140"><highlight class="normal">vrna_pf_substrands(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="141"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">size_t</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>complex_size);</highlight></codeline>
<codeline lineno="142"><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref></highlight></codeline>
<codeline lineno="144"><highlight class="normal">vrna_pf_add(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/>dG1,</highlight></codeline>
<codeline lineno="145"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/>dG2,</highlight></codeline>
<codeline lineno="146"><highlight class="normal"><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/>kT);</highlight></codeline>
<codeline lineno="147"><highlight class="normal"></highlight></codeline>
<codeline lineno="148"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>basic<sp/>global<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="150"><highlight class="normal"></highlight></codeline>
<codeline lineno="155"><highlight class="normal"></highlight></codeline>
<codeline lineno="177"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="178" refid="group__part__func__global_1gac4a2a74a79e49818bc35412a2b392c7e" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1gac4a2a74a79e49818bc35412a2b392c7e" kindref="member">vrna_pf_fold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="179"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="180"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/>**pl);</highlight></codeline>
<codeline lineno="181"><highlight class="normal"></highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="207"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="208" refid="group__part__func__global_1ga87e5a77b6e50dd54e9d032a9b92973be" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1ga87e5a77b6e50dd54e9d032a9b92973be" kindref="member">vrna_pf_circfold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="209"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="210"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/>**pl);</highlight></codeline>
<codeline lineno="211"><highlight class="normal"></highlight></codeline>
<codeline lineno="212"><highlight class="normal"></highlight></codeline>
<codeline lineno="234"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="235" refid="group__part__func__global_1ga374e31a0f326b2c5da5b84e143a63f38" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1ga374e31a0f326b2c5da5b84e143a63f38" kindref="member">vrna_pf_alifold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>**sequences,</highlight></codeline>
<codeline lineno="236"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="237"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/>**pl);</highlight></codeline>
<codeline lineno="238"><highlight class="normal"></highlight></codeline>
<codeline lineno="239"><highlight class="normal"></highlight></codeline>
<codeline lineno="264"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="265" refid="group__part__func__global_1gab70fe6c9a78b79cc5669881720926e1d" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1gab70fe6c9a78b79cc5669881720926e1d" kindref="member">vrna_pf_circalifold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>**sequences,</highlight></codeline>
<codeline lineno="266"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="267"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/>**pl);</highlight></codeline>
<codeline lineno="268"><highlight class="normal"></highlight></codeline>
<codeline lineno="269"><highlight class="normal"></highlight></codeline>
<codeline lineno="296"><highlight class="normal"><ref refid="group__pf__cofold_1ga444df1587c9a2ca15b8eb25188f629c3" kindref="member">vrna_dimer_pf_t</ref></highlight></codeline>
<codeline lineno="297" refid="group__part__func__global_1gaf2b846f7ac382686f35ff7b9202fdd5c" refkind="member"><highlight class="normal"><ref refid="group__part__func__global_1gaf2b846f7ac382686f35ff7b9202fdd5c" kindref="member">vrna_pf_co_fold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*seq,</highlight></codeline>
<codeline lineno="298"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="299"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/><sp/><sp/>**pl);</highlight></codeline>
<codeline lineno="300"><highlight class="normal"></highlight></codeline>
<codeline lineno="301"><highlight class="normal"></highlight></codeline>
<codeline lineno="302"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>End<sp/>simplified<sp/>global<sp/>interface<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="304"><highlight class="normal"></highlight></codeline>
<codeline lineno="306"><highlight class="normal"></highlight></codeline>
<codeline lineno="307"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="308"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="309"><highlight class="comment"><sp/>#<sp/>OTHER<sp/>PARTITION<sp/>FUNCTION<sp/>RELATED<sp/>DECLARATIONS<sp/>#</highlight></codeline>
<codeline lineno="310"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="311"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="312"><highlight class="normal"></highlight></codeline>
<codeline lineno="323"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="324" refid="group__pf__fold_1gad2b3594f0b50b68029e0f54fdce59313" refkind="member"><highlight class="normal"><ref refid="group__pf__fold_1gad2b3594f0b50b68029e0f54fdce59313" kindref="member">vrna_pf_float_precision</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="325"><highlight class="normal"></highlight></codeline>
<codeline lineno="326"><highlight class="normal"></highlight></codeline>
<codeline lineno="327"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="328"><highlight class="normal"></highlight></codeline>
<codeline lineno="329"><highlight class="normal"></highlight><highlight class="comment">/*</highlight></codeline>
<codeline lineno="330"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="331"><highlight class="comment"><sp/>#<sp/>DEPRECATED<sp/>FUNCTIONS<sp/><sp/><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></codeline>
<codeline lineno="332"><highlight class="comment"><sp/>#################################################</highlight></codeline>
<codeline lineno="333"><highlight class="comment"><sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="334"><highlight class="normal"></highlight></codeline>
<codeline lineno="347"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__subopt__stochbt__deprecated_1gacd79b1a570e6ad9be24cb11fe8cae30a" kindref="member">st_back</ref>;</highlight></codeline>
<codeline lineno="348"><highlight class="normal"></highlight></codeline>
<codeline lineno="392"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="393"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1gac4f95bee734b2563a3d6e9932117ebdf" kindref="member">pf_fold_par</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="394"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure,</highlight></codeline>
<codeline lineno="395"><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/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/>*parameters,</highlight></codeline>
<codeline lineno="396"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>calculate_bppm,</highlight></codeline>
<codeline lineno="397"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>is_constrained,</highlight></codeline>
<codeline lineno="398"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>is_circular),</highlight></codeline>
<codeline lineno="399" refid="group__part__func__global__deprecated_1gac4f95bee734b2563a3d6e9932117ebdf" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>vrna_pf()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="400"><highlight class="normal"></highlight></codeline>
<codeline lineno="444"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="445"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="446"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure),</highlight></codeline>
<codeline lineno="447" refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pf_fold()<sp/>or<sp/>vrna_pf()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="448"><highlight class="normal"></highlight></codeline>
<codeline lineno="480"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="481"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga819ce5fca8984004ac81c4a3b04cb735" kindref="member">pf_circ_fold</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*sequence,</highlight></codeline>
<codeline lineno="482"><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">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure),</highlight></codeline>
<codeline lineno="483" refid="group__part__func__global__deprecated_1ga819ce5fca8984004ac81c4a3b04cb735" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pf_circfold()<sp/>or<sp/>vrna_pf()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="484"><highlight class="normal"></highlight></codeline>
<codeline lineno="496" refid="group__subopt__stochbt__deprecated_1gaae9de453e396420d6269534d571d6d18" refkind="member"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__subopt__stochbt__deprecated_1gaae9de453e396420d6269534d571d6d18" kindref="member">pbacktrack</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pbacktrack()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="497"><highlight class="normal"></highlight></codeline>
<codeline lineno="503"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__subopt__stochbt__deprecated_1ga31aa6bffb2b5c66486f50091a7061320" kindref="member">pbacktrack5</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence,</highlight></codeline>
<codeline lineno="504" refid="group__subopt__stochbt__deprecated_1ga31aa6bffb2b5c66486f50091a7061320" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pbacktrack5()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="505"><highlight class="normal"></highlight></codeline>
<codeline lineno="521" refid="group__subopt__stochbt__deprecated_1ga4b6d04c882ae87b6cee9a516e06c4155" refkind="member"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__subopt__stochbt__deprecated_1ga4b6d04c882ae87b6cee9a516e06c4155" kindref="member">pbacktrack_circ</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*sequence),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_pbacktrack()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="522"><highlight class="normal"></highlight></codeline>
<codeline lineno="542"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="543" refid="group__part__func__global__deprecated_1gae73db3f49a94f0f72e067ecd12681dbd" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1gae73db3f49a94f0f72e067ecd12681dbd" kindref="member">free_pf_arrays</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),<sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="544"><highlight class="normal"></highlight></codeline>
<codeline lineno="556"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="557" refid="group__part__func__global__deprecated_1ga384e927890f9c034ff09fa66da102d28" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga384e927890f9c034ff09fa66da102d28" kindref="member">update_pf_params</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),<sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="558"><highlight class="normal"></highlight></codeline>
<codeline lineno="567"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="568"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1gaafe2d1b21f5418b123b088aa395e827d" kindref="member">update_pf_params_par</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="569"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><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/>*parameters),</highlight></codeline>
<codeline lineno="570" refid="group__part__func__global__deprecated_1gaafe2d1b21f5418b123b088aa395e827d" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="571"><highlight class="normal"></highlight></codeline>
<codeline lineno="589"><highlight class="normal">DEPRECATED(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>*<sp/><ref refid="group__part__func__global__deprecated_1gad2bba2bdfef5a24f69fe10bbb9fc6de9" kindref="member">export_bppm</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="590" refid="group__part__func__global__deprecated_1gad2bba2bdfef5a24f69fe10bbb9fc6de9" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="591"><highlight class="normal"></highlight></codeline>
<codeline lineno="592"><highlight class="normal"></highlight></codeline>
<codeline lineno="611"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="612"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga42faebdfce6f070c5f89adfc8427525c" kindref="member">get_pf_arrays</ref>(</highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>**S_p,</highlight></codeline>
<codeline lineno="613"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/>**S1_p,</highlight></codeline>
<codeline lineno="614"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**ptype_p,</highlight></codeline>
<codeline lineno="615"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**qb_p,</highlight></codeline>
<codeline lineno="616"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**qm_p,</highlight></codeline>
<codeline lineno="617"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**q1k_p,</highlight></codeline>
<codeline lineno="618"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**qln_p),</highlight></codeline>
<codeline lineno="619" refid="group__part__func__global__deprecated_1ga42faebdfce6f070c5f89adfc8427525c" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="620"><highlight class="normal"></highlight></codeline>
<codeline lineno="626"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="627"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga189e2a1ec6cc32c53ea72f7543b0441e" kindref="member">get_subseq_F</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>i,</highlight></codeline>
<codeline lineno="628"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>j),</highlight></codeline>
<codeline lineno="629" refid="group__part__func__global__deprecated_1ga189e2a1ec6cc32c53ea72f7543b0441e" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>with<sp/>vrna_fold_compound_t<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="630"><highlight class="normal"></highlight></codeline>
<codeline lineno="631"><highlight class="normal"></highlight></codeline>
<codeline lineno="644"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="645"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga79cbc375af65f11609feb6b055269e7d" kindref="member">mean_bp_distance</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),</highlight></codeline>
<codeline lineno="646" refid="group__part__func__global__deprecated_1ga79cbc375af65f11609feb6b055269e7d" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mean_bp_distance()<sp/>or<sp/>vrna_mean_bp_distance_pr()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="647"><highlight class="normal"></highlight></codeline>
<codeline lineno="665"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="666"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1gad5ba36cef8d01cf4244cc09b9bf1ce1d" kindref="member">mean_bp_distance_pr</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="667"><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/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>*<ref refid="fold__vars_8h_1ac98ec419070aee6831b44e5c700f090f" kindref="member">pr</ref>),</highlight></codeline>
<codeline lineno="668" refid="group__part__func__global__deprecated_1gad5ba36cef8d01cf4244cc09b9bf1ce1d" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mean_bp_distance()<sp/>or<sp/>vrna_mean_bp_distance_pr()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="669"><highlight class="normal"></highlight></codeline>
<codeline lineno="677" refid="group__part__func__global__deprecated_1ga963dfa795074d53ff23c5b1ab01406f0" refkind="member"><highlight class="normal">DEPRECATED(<ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>*<sp/><ref refid="group__part__func__global__deprecated_1ga963dfa795074d53ff23c5b1ab01406f0" kindref="member">stackProb</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>cutoff),<sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_stack_prob()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="678"><highlight class="normal"></highlight></codeline>
<codeline lineno="679"><highlight class="normal"></highlight></codeline>
<codeline lineno="687"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="688" refid="group__part__func__global__deprecated_1ga15176e23eceeff8c7d14eabcfec8a2af" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__part__func__global__deprecated_1ga15176e23eceeff8c7d14eabcfec8a2af" kindref="member">init_pf_fold</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),<sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="689"><highlight class="normal"></highlight></codeline>
<codeline lineno="690"><highlight class="normal"></highlight></codeline>
<codeline lineno="691"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="692"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>init_pf_circ_fold(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),<sp/></highlight><highlight class="stringliteral">&quot;This<sp/>function<sp/>is<sp/>obsolete&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="693"><highlight class="normal"></highlight></codeline>
<codeline lineno="699"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="partfunc_2global_8h_1ae48516bae820daee8424fbfe56e2ba30" kindref="member">centroid</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length,</highlight></codeline>
<codeline lineno="700"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>*dist),</highlight></codeline>
<codeline lineno="701" refid="partfunc_2global_8h_1ae48516bae820daee8424fbfe56e2ba30" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_centroid()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="702"><highlight class="normal"></highlight></codeline>
<codeline lineno="708"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="partfunc_2global_8h_1ac89c333a303e3789b62ae1bc57980884" kindref="member">get_centroid_struct_gquad_pr</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length,</highlight></codeline>
<codeline lineno="709"><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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>*dist),</highlight></codeline>
<codeline lineno="710" refid="partfunc_2global_8h_1ac89c333a303e3789b62ae1bc57980884" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_centroid()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="711"><highlight class="normal"></highlight></codeline>
<codeline lineno="717"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="718"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="partfunc_2global_8h_1ae9556ba7ded44fe2321b6f67c3fc02a3" kindref="member">mean_bp_dist</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>length),</highlight></codeline>
<codeline lineno="719" refid="partfunc_2global_8h_1ae9556ba7ded44fe2321b6f67c3fc02a3" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_mean_bp_distance()<sp/>or<sp/>vrna_mean_bp_distance_pr()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="720"><highlight class="normal"></highlight></codeline>
<codeline lineno="724"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="725"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="partfunc_2global_8h_1a68ba6f3a48e08ca131ab54621ce3a2d7" kindref="member">expLoopEnergy</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>u1,</highlight></codeline>
<codeline lineno="726"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>u2,</highlight></codeline>
<codeline lineno="727"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="728"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>type2,</highlight></codeline>
<codeline lineno="729"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="730"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="731"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/>sp1,</highlight></codeline>
<codeline lineno="732"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/>sq1),</highlight></codeline>
<codeline lineno="733" refid="partfunc_2global_8h_1a68ba6f3a48e08ca131ab54621ce3a2d7" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="734"><highlight class="normal"></highlight></codeline>
<codeline lineno="738"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="739"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="partfunc_2global_8h_1a7b6ab474cc80accc48010ccfcc59f96b" kindref="member">expHairpinEnergy</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>u,</highlight></codeline>
<codeline lineno="740"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>type,</highlight></codeline>
<codeline lineno="741"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>si1,</highlight></codeline>
<codeline lineno="742"><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/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sj1,</highlight></codeline>
<codeline lineno="743"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/>*</highlight><highlight class="keywordtype">string</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="744" refid="partfunc_2global_8h_1a7b6ab474cc80accc48010ccfcc59f96b" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="745"><highlight class="normal"></highlight></codeline>
<codeline lineno="746"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>this<sp/>doesn&apos;t<sp/>work<sp/>if<sp/>free_pf_arrays()<sp/>is<sp/>called<sp/>before<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="747"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="748"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>assign_plist_gquad_from_pr(<ref refid="group__struct__utils__plist_1gab9ac98ab55ded9fb90043b024b915aca" kindref="member">vrna_ep_t</ref><sp/>**pl,</highlight></codeline>
<codeline lineno="749"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>length,</highlight></codeline>
<codeline lineno="750"><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/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>cut_off),</highlight></codeline>
<codeline lineno="751"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_plist_from_probs()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="752"><highlight class="normal"></highlight></codeline>
<codeline lineno="753"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="754"><highlight class="normal"></highlight></codeline>
<codeline lineno="755"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/partfunc/global.h"/>
  </compounddef>
</doxygen>
