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      <memberdef kind="variable" id="fold__vars_8h_1a0afc287c2464866d94858c39175154af" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int fold_constrained</definition>
        <argsstring></argsstring>
        <name>fold_constrained</name>
        <briefdescription>
<para>Global switch to activate/deactivate folding with structure constraints. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="22" column="15" declfile="ViennaRNA/fold_vars.h" declline="22" declcolumn="15"/>
      </memberdef>
      <memberdef kind="variable" id="fold__vars_8h_1af2763d55a74663a5e60652b8880baa5b" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int csv</definition>
        <argsstring></argsstring>
        <name>csv</name>
        <briefdescription>
<para>generate comma seperated output </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="27" column="13" declfile="ViennaRNA/fold_vars.h" declline="27" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="fold__vars_8h_1a5dbaa0cca2c8c82048a0f0e38e164944" prot="public" static="no" extern="yes" mutable="no">
        <type>char *</type>
        <definition>char* RibosumFile</definition>
        <argsstring></argsstring>
        <name>RibosumFile</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>warning this variable will vanish in the future ribosums will be compiled in instead </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="33" column="13" declfile="ViennaRNA/fold_vars.h" declline="33" declcolumn="13"/>
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      <memberdef kind="variable" id="fold__vars_8h_1af349001ad3b4d008d0051d935b1b6261" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int james_rule</definition>
        <argsstring></argsstring>
        <name>james_rule</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>internal loops of size 2 get energy 0.8Kcal and no mismatches, default 1 </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="39" column="13" declfile="ViennaRNA/fold_vars.h" declline="39" declcolumn="13"/>
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      <memberdef kind="variable" id="fold__vars_8h_1a80c3c5fd35e7479704cc91d2d0367743" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int logML</definition>
        <argsstring></argsstring>
        <name>logML</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para>use logarithmic multiloop energy function </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="44" column="13" declfile="ViennaRNA/fold_vars.h" declline="44" declcolumn="13"/>
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        <type>int</type>
        <definition>int cut_point</definition>
        <argsstring></argsstring>
        <name>cut_point</name>
        <briefdescription>
<para>Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence. </para>
        </briefdescription>
        <detaileddescription>
<para>To evaluate the energy of a duplex structure (a structure formed by two strands), concatenate the to sequences and set it to the first base of the second strand in the concatenated sequence. The default value of -1 stands for single molecule folding. The cut_point variable is also used by <ref refid="group__plotting__utils_1gabdc8f6548ba4a3bc3cd868ccbcfdb86a" kindref="member">vrna_file_PS_rnaplot()</ref> and <ref refid="group__plotting__utils__deprecated_1ga689a97a7e3b8a2df14728b8204d9d57b" kindref="member">PS_dot_plot()</ref> to mark the chain break in postscript plots. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="57" column="13" declfile="ViennaRNA/fold_vars.h" declline="57" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="fold__vars_8h_1a0244a629b5ab4f58b77590c3dfd130dc" prot="public" static="no" extern="yes" mutable="no">
        <type><ref refid="group__data__structures_1ga6114174c02666861dc12e1f8db32a17e" kindref="member">bondT</ref> *</type>
        <definition>bondT* base_pair</definition>
        <argsstring></argsstring>
        <name>base_pair</name>
        <briefdescription>
<para>Contains a list of base pairs after a call to <ref refid="group__mfe__global__deprecated_1gaadafcb0f140795ae62e5ca027e335a9b" kindref="member">fold()</ref>. </para>
        </briefdescription>
        <detaileddescription>
<para>base_pair[0].i contains the total number of pairs. <xrefsect id="deprecated_1_deprecated000075"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Do not use this variable anymore! </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="65" column="15" declfile="ViennaRNA/fold_vars.h" declline="65" declcolumn="15"/>
      </memberdef>
      <memberdef kind="variable" id="fold__vars_8h_1ac98ec419070aee6831b44e5c700f090f" prot="public" static="no" extern="yes" mutable="no">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> *</type>
        <definition>FLT_OR_DBL* pr</definition>
        <argsstring></argsstring>
        <name>pr</name>
        <briefdescription>
<para>A pointer to the base pair probability matrix. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000076"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Do not use this variable anymore! </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="72" column="19" declfile="ViennaRNA/fold_vars.h" declline="72" declcolumn="19"/>
      </memberdef>
      <memberdef kind="variable" id="fold__vars_8h_1a92089ae3a51b5d75a14ce9cc29cc8317" prot="public" static="no" extern="yes" mutable="no">
        <type>int *</type>
        <definition>int* iindx</definition>
        <argsstring></argsstring>
        <name>iindx</name>
        <briefdescription>
<para>index array to move through pr. </para>
        </briefdescription>
        <detaileddescription>
<para>The probability for base i and j to form a pair is in pr[iindx[i]-j]. <xrefsect id="deprecated_1_deprecated000077"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Do not use this variable anymore! </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_vars.h" line="80" column="14" declfile="ViennaRNA/fold_vars.h" declline="80" declcolumn="14"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>Here all all declarations of the global variables used throughout RNAlib. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_FOLD_VARS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_FOLD_VARS_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="datastructures_2basic_8h" kindref="compound">ViennaRNA/datastructures/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="comment">/*<sp/><sp/>For<sp/>now,<sp/>we<sp/>include<sp/>model.h<sp/>by<sp/>default<sp/>to<sp/>provide<sp/>backwards<sp/>compatibility</highlight></codeline>
<codeline lineno="6"><highlight class="comment"><sp/><sp/><sp/><sp/>However,<sp/>this<sp/>will<sp/>most<sp/>likely<sp/>change,<sp/>since<sp/>fold_vars.h<sp/>is<sp/>scheduled<sp/>to</highlight></codeline>
<codeline lineno="7"><highlight class="comment"><sp/><sp/><sp/><sp/>vanish<sp/>from<sp/>the<sp/>sources<sp/>at<sp/>latest<sp/>in<sp/>ViennaRNA<sp/>Package<sp/>v3</highlight></codeline>
<codeline lineno="8"><highlight class="comment">*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><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="10"><highlight class="normal"></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"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><ref refid="fold__vars_8h_1a0afc287c2464866d94858c39175154af" kindref="member">fold_constrained</ref>;</highlight></codeline>
<codeline lineno="23"><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="fold__vars_8h_1af2763d55a74663a5e60652b8880baa5b" kindref="member">csv</ref>;</highlight></codeline>
<codeline lineno="28"><highlight class="normal"></highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="fold__vars_8h_1a5dbaa0cca2c8c82048a0f0e38e164944" kindref="member">RibosumFile</ref>;<sp/><sp/><sp/></highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="fold__vars_8h_1af349001ad3b4d008d0051d935b1b6261" kindref="member">james_rule</ref>;</highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight></codeline>
<codeline lineno="44"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="fold__vars_8h_1a80c3c5fd35e7479704cc91d2d0367743" kindref="member">logML</ref>;</highlight></codeline>
<codeline lineno="45"><highlight class="normal"></highlight></codeline>
<codeline lineno="57"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><ref refid="fold__vars_8h_1ab9b2c3a37a5516614c06d0ab54b97cda" kindref="member">cut_point</ref>;</highlight></codeline>
<codeline lineno="58"><highlight class="normal"></highlight></codeline>
<codeline lineno="65"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/><ref refid="group__data__structures_1ga6114174c02666861dc12e1f8db32a17e" kindref="member">bondT</ref><sp/><sp/>*<ref refid="fold__vars_8h_1a0244a629b5ab4f58b77590c3dfd130dc" kindref="member">base_pair</ref>;</highlight></codeline>
<codeline lineno="66"><highlight class="normal"></highlight></codeline>
<codeline lineno="72"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><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="73"><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>*<ref refid="fold__vars_8h_1a92089ae3a51b5d75a14ce9cc29cc8317" kindref="member">iindx</ref>;</highlight></codeline>
<codeline lineno="81"><highlight class="normal"></highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight></codeline>
<codeline lineno="83"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="86"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/fold_vars.h"/>
  </compounddef>
</doxygen>
