<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.15.0" xml:lang="en-US">
  <compounddef id="2Dpfold_8h" kind="file" language="C++">
    <compoundname>2Dpfold.h</compoundname>
    <includes refid="fold__compound_8h" local="no">ViennaRNA/fold_compound.h</includes>
    <includes refid="datastructures_2basic_8h" local="no">ViennaRNA/datastructures/basic.h</includes>
    <includes refid="params_2basic_8h" local="no">ViennaRNA/params/basic.h</includes>
    <incdepgraph>
      <node id="1">
        <label>ViennaRNA/2Dpfold.h</label>
        <link refid="2Dpfold_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="4" relation="include">
        </childnode>
      </node>
      <node id="18">
        <label>ViennaRNA/constraints/basic.h</label>
        <link refid="constraints_2basic_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
      </node>
      <node id="17">
        <label>ViennaRNA/constraints/hard.h</label>
        <link refid="hard_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="18" relation="include">
        </childnode>
        <childnode refid="9" relation="include">
        </childnode>
      </node>
      <node id="19">
        <label>ViennaRNA/constraints/soft.h</label>
        <link refid="soft_8h"/>
        <childnode refid="10" relation="include">
        </childnode>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="18" relation="include">
        </childnode>
      </node>
      <node id="11">
        <label>ViennaRNA/datastructures/array.h</label>
        <link refid="array_8h"/>
        <childnode refid="12" relation="include">
        </childnode>
        <childnode refid="13" relation="include">
        </childnode>
      </node>
      <node id="7">
        <label>ViennaRNA/datastructures/basic.h</label>
        <link refid="datastructures_2basic_8h"/>
        <childnode refid="5" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="3" relation="include">
        </childnode>
        <childnode refid="4" relation="include">
        </childnode>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="17" relation="include">
        </childnode>
        <childnode refid="19" relation="include">
        </childnode>
        <childnode refid="20" relation="include">
        </childnode>
        <childnode refid="21" relation="include">
        </childnode>
        <childnode refid="22" relation="include">
        </childnode>
        <childnode refid="23" relation="include">
        </childnode>
        <childnode refid="24" relation="include">
        </childnode>
        <childnode refid="25" relation="include">
        </childnode>
        <childnode refid="26" relation="include">
        </childnode>
        <childnode refid="27" relation="include">
        </childnode>
      </node>
      <node id="8">
        <label>ViennaRNA/datastructures/dp_matrices.h</label>
        <link refid="datastructures_2dp__matrices_8h"/>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="9" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
      </node>
      <node id="9">
        <label>ViennaRNA/datastructures/sparse_mx.h</label>
        <link refid="sparse__mx_8h_source"/>
        <childnode refid="10" relation="include">
        </childnode>
        <childnode refid="11" relation="include">
        </childnode>
      </node>
      <node id="2">
        <label>ViennaRNA/fold_compound.h</label>
        <link refid="fold__compound_8h"/>
        <childnode refid="3" relation="include">
        </childnode>
        <childnode refid="4" relation="include">
        </childnode>
        <childnode refid="28" relation="include">
        </childnode>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="17" relation="include">
        </childnode>
        <childnode refid="19" relation="include">
        </childnode>
        <childnode refid="29" relation="include">
        </childnode>
        <childnode refid="20" relation="include">
        </childnode>
        <childnode refid="21" relation="include">
        </childnode>
        <childnode refid="30" relation="include">
        </childnode>
      </node>
      <node id="29">
        <label>ViennaRNA/grammar/basic.h</label>
        <link refid="grammar_2basic_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="11" relation="include">
        </childnode>
      </node>
      <node id="3">
        <label>ViennaRNA/model.h</label>
        <link refid="model_8h"/>
      </node>
      <node id="4">
        <label>ViennaRNA/params/basic.h</label>
        <link refid="params_2basic_8h"/>
        <childnode refid="5" relation="include">
        </childnode>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="3" relation="include">
        </childnode>
      </node>
      <node id="5">
        <label>ViennaRNA/params/constants.h</label>
        <link refid="constants_8h"/>
        <childnode refid="6" relation="include">
        </childnode>
      </node>
      <node id="28">
        <label>ViennaRNA/sequences/sequence.h</label>
        <link refid="sequences_2sequence_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
      </node>
      <node id="20">
        <label>ViennaRNA/structured_domains.h</label>
        <link refid="structured__domains_8h"/>
      </node>
      <node id="24">
        <label>ViennaRNA/structures/dotbracket.h</label>
        <link refid="dotbracket_8h"/>
        <childnode refid="22" relation="include">
        </childnode>
      </node>
      <node id="27">
        <label>ViennaRNA/structures/helix.h</label>
        <link refid="helix_8h"/>
      </node>
      <node id="26">
        <label>ViennaRNA/structures/metrics.h</label>
        <link refid="metrics_8h"/>
      </node>
      <node id="23">
        <label>ViennaRNA/structures/pairtable.h</label>
        <link refid="pairtable_8h"/>
      </node>
      <node id="22">
        <label>ViennaRNA/structures/problist.h</label>
        <link refid="problist_8h"/>
      </node>
      <node id="25">
        <label>ViennaRNA/structures/utils.h</label>
        <link refid="structures_2utils_8h"/>
      </node>
      <node id="21">
        <label>ViennaRNA/unstructured_domains.h</label>
        <link refid="unstructured__domains_8h"/>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="22" relation="include">
        </childnode>
      </node>
      <node id="13">
        <label>ViennaRNA/utils/log.h</label>
        <link refid="log_8h"/>
        <childnode refid="14" relation="include">
        </childnode>
        <childnode refid="15" relation="include">
        </childnode>
        <childnode refid="16" relation="include">
        </childnode>
      </node>
      <node id="30">
        <label>ViennaRNA/zscore/basic.h</label>
        <link refid="zscore_2basic_8h_source"/>
      </node>
      <node id="6">
        <label>limits.h</label>
      </node>
      <node id="15">
        <label>stdarg.h</label>
      </node>
      <node id="12">
        <label>stddef.h</label>
      </node>
      <node id="14">
        <label>stdio.h</label>
      </node>
      <node id="10">
        <label>stdlib.h</label>
      </node>
      <node id="16">
        <label>time.h</label>
      </node>
    </incdepgraph>
    <innerclass refid="structvrna__sol__TwoD__pf__t" prot="public">vrna_sol_TwoD_pf_t</innerclass>
    <innerclass refid="structTwoDpfold__vars" prot="public">TwoDpfold_vars</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="2Dpfold_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/2Dpfold.h" line="13" column="11" bodyfile="ViennaRNA/2Dpfold.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="2Dpfold_8h_1ab8a8411ac20b57a2f569edd6da7fcbc2" prot="public" static="no">
        <name>TwoDpfold_solution</name>
        <initializer><ref refid="structvrna__sol__TwoD__pf__t" kindref="compound">vrna_sol_TwoD_pf_t</ref>         /* restore compatibility of struct rename */</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="142" column="9" bodyfile="ViennaRNA/2Dpfold.h" bodystart="142" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kind="function"><name>vrna_pf_TwoD</name></member>
      <member refid="group__kl__neighborhood__stochbt_1ga8527c142361ad019ef9b80c50591f215" kind="function"><name>vrna_pbacktrack_TwoD</name></member>
      <member refid="group__kl__neighborhood__stochbt_1gae375170cbf15744a9cf2db33d0a2cb75" kind="function"><name>vrna_pbacktrack5_TwoD</name></member>
      <memberdef kind="function" id="2Dpfold_8h_1a0d0ef6216c2a1f5c83c9b27d26c6efca" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
        <definition>TwoDpfold_vars * get_TwoDpfold_variables</definition>
        <argsstring>(const char *seq, const char *structure1, char *structure2, int circ)</argsstring>
        <name>get_TwoDpfold_variables</name>
        <param>
          <type>const char *</type>
          <declname>seq</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>structure1</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>structure2</declname>
        </param>
        <param>
          <type>int</type>
          <declname>circ</declname>
        </param>
        <briefdescription>
<para>Get a datastructure containing all necessary attributes and global folding switches. </para>
        </briefdescription>
        <detaileddescription>
<para>This function prepares all necessary attributes and matrices etc which are needed for a call of TwoDpfold() . A snapshot of all current global model switches (dangles, temperature and so on) is done and stored in the returned datastructure. Additionally, all matrices that will hold the partition function values are prepared.</para>
<para><xrefsect id="deprecated_1_deprecated000007"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use the new API that relies on <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> and the corresponding functions vrna_fold_compound_TwoD(), <ref refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kindref="member">vrna_pf_TwoD()</ref>, and <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>seq</parametername>
</parameternamelist>
<parameterdescription>
<para>the RNA sequence in uppercase format with letters from the alphabet {AUCG} </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>structure1</parametername>
</parameternamelist>
<parameterdescription>
<para>the first reference structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>structure2</parametername>
</parameternamelist>
<parameterdescription>
<para>the second reference structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>circ</parametername>
</parameternamelist>
<parameterdescription>
<para>a switch indicating if the sequence is linear (0) or circular (1) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>the datastructure containing all necessary partition function attributes </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="276" column="29" declfile="ViennaRNA/2Dpfold.h" declline="276" declcolumn="29"/>
      </memberdef>
      <memberdef kind="function" id="2Dpfold_8h_1afe994291458ee2ac34d3eb825ef62a15" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void destroy_TwoDpfold_variables</definition>
        <argsstring>(TwoDpfold_vars *vars)</argsstring>
        <name>destroy_TwoDpfold_variables</name>
        <param>
          <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
          <declname>vars</declname>
        </param>
        <briefdescription>
<para>Free all memory occupied by a <ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> datastructure. </para>
        </briefdescription>
        <detaileddescription>
<para>This function free&apos;s all memory occupied by a datastructure obtained from from get_TwoDpfold_variabless() or get_TwoDpfold_variables_from_MFE()</para>
<para><xrefsect id="deprecated_1_deprecated000008"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use the new API that relies on <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> and the corresponding functions vrna_fold_compound_TwoD(), <ref refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kindref="member">vrna_pf_TwoD()</ref>, and <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="2Dpfold_8h_1a0d0ef6216c2a1f5c83c9b27d26c6efca" kindref="member">get_TwoDpfold_variables()</ref>, get_TwoDpfold_variables_from_MFE()</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>vars</parametername>
</parameternamelist>
<parameterdescription>
<para>the datastructure to be free&apos;d </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="293" column="18" declfile="ViennaRNA/2Dpfold.h" declline="293" declcolumn="18"/>
      </memberdef>
      <memberdef kind="function" id="2Dpfold_8h_1ace84b32f58d90d7b8779cc31d210d8c8" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>TwoDpfold_solution *</type>
        <definition>TwoDpfold_solution * TwoDpfoldList</definition>
        <argsstring>(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)</argsstring>
        <name>TwoDpfoldList</name>
        <param>
          <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
          <declname>vars</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxDistance1</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxDistance2</declname>
        </param>
        <briefdescription>
<para>Compute the partition function for all distance classes. </para>
        </briefdescription>
        <detaileddescription>
<para>This function computes the partition functions for all distance classes according the two reference structures specified in the datastructure &apos;vars&apos;. Similar to TwoDfold() the arguments maxDistance1 and maxDistance2 specify the maximum distance to both reference structures. A value of &apos;-1&apos; in either of them makes the appropriate distance restrictionless, i.e. all basepair distancies to the reference are taken into account during computation. In case there is a restriction, the returned solution contains an entry where the attribute k=l=-1 contains the partition function for all structures exceeding the restriction. A values of <ref refid="constants_8h_1a12c2040f25d8e3a7b9e1c2024c618cb6" kindref="member">INF</ref> in the attribute &apos;k&apos; of the returned list denotes the end of the list</para>
<para><xrefsect id="deprecated_1_deprecated000009"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use the new API that relies on <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> and the corresponding functions vrna_fold_compound_TwoD(), <ref refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kindref="member">vrna_pf_TwoD()</ref>, and <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="2Dpfold_8h_1a0d0ef6216c2a1f5c83c9b27d26c6efca" kindref="member">get_TwoDpfold_variables()</ref>, <ref refid="2Dpfold_8h_1afe994291458ee2ac34d3eb825ef62a15" kindref="member">destroy_TwoDpfold_variables()</ref>, <ref refid="structvrna__sol__TwoD__pf__t" kindref="compound">vrna_sol_TwoD_pf_t</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>vars</parametername>
</parameternamelist>
<parameterdescription>
<para>the datastructure containing all necessary folding attributes and matrices </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>maxDistance1</parametername>
</parameternamelist>
<parameterdescription>
<para>the maximum basepair distance to reference1 (may be -1) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>maxDistance2</parametername>
</parameternamelist>
<parameterdescription>
<para>the maximum basepair distance to reference2 (may be -1) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>a list of partition funtions for the appropriate distance classes </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="323" column="33" declfile="ViennaRNA/2Dpfold.h" declline="323" declcolumn="33"/>
      </memberdef>
      <memberdef kind="function" id="2Dpfold_8h_1a001da06931aa120569496978bb99479d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * TwoDpfold_pbacktrack</definition>
        <argsstring>(TwoDpfold_vars *vars, int d1, int d2)</argsstring>
        <name>TwoDpfold_pbacktrack</name>
        <param>
          <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
          <declname>vars</declname>
        </param>
        <param>
          <type>int</type>
          <declname>d1</declname>
        </param>
        <param>
          <type>int</type>
          <declname>d2</declname>
        </param>
        <briefdescription>
<para>Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. </para>
        </briefdescription>
        <detaileddescription>
<para>If the argument &apos;d1&apos; is set to &apos;-1&apos;, the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.</para>
<para><simplesect kind="pre"><para>The argument &apos;vars&apos; must contain precalculated partition function matrices, i.e. a call to TwoDpfold() preceding this function is mandatory!</para>
</simplesect>
<xrefsect id="deprecated_1_deprecated000010"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use the new API that relies on <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> and the corresponding functions vrna_fold_compound_TwoD(), <ref refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kindref="member">vrna_pf_TwoD()</ref>, <ref refid="group__kl__neighborhood__stochbt_1ga8527c142361ad019ef9b80c50591f215" kindref="member">vrna_pbacktrack_TwoD()</ref>, and <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para>TwoDpfold()</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername direction="in">vars</parametername>
</parameternamelist>
<parameterdescription>
<para>the datastructure containing all necessary folding attributes and matrices </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">d1</parametername>
</parameternamelist>
<parameterdescription>
<para>the distance to reference1 (may be -1) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">d2</parametername>
</parameternamelist>
<parameterdescription>
<para>the distance to reference2 </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A sampled secondary structure in dot-bracket notation </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="350" column="19" declfile="ViennaRNA/2Dpfold.h" declline="350" declcolumn="19"/>
      </memberdef>
      <memberdef kind="function" id="2Dpfold_8h_1adfb2b7ab8d0cc7d84e0448d52a614838" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * TwoDpfold_pbacktrack5</definition>
        <argsstring>(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)</argsstring>
        <name>TwoDpfold_pbacktrack5</name>
        <param>
          <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
          <declname>vars</declname>
        </param>
        <param>
          <type>int</type>
          <declname>d1</declname>
        </param>
        <param>
          <type>int</type>
          <declname>d2</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>length</declname>
        </param>
        <briefdescription>
<para>Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. </para>
        </briefdescription>
        <detaileddescription>
<para>This function does essentially the same as <ref refid="2Dpfold_8h_1a001da06931aa120569496978bb99479d" kindref="member">TwoDpfold_pbacktrack()</ref> with the only difference that partial structures, i.e. structures beginning from the 5&apos; end with a specified length of the sequence, are backtracked</para>
<para><simplesect kind="note"><para>This function does not work (since it makes no sense) for circular RNA sequences!</para>
</simplesect>
<simplesect kind="pre"><para>The argument &apos;vars&apos; must contain precalculated partition function matrices, i.e. a call to TwoDpfold() preceding this function is mandatory!</para>
</simplesect>
<xrefsect id="deprecated_1_deprecated000011"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use the new API that relies on <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> and the corresponding functions vrna_fold_compound_TwoD(), <ref refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kindref="member">vrna_pf_TwoD()</ref>, <ref refid="group__kl__neighborhood__stochbt_1gae375170cbf15744a9cf2db33d0a2cb75" kindref="member">vrna_pbacktrack5_TwoD()</ref>, and <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="2Dpfold_8h_1a001da06931aa120569496978bb99479d" kindref="member">TwoDpfold_pbacktrack()</ref>, TwoDpfold()</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername direction="in">vars</parametername>
</parameternamelist>
<parameterdescription>
<para>the datastructure containing all necessary folding attributes and matrices </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">d1</parametername>
</parameternamelist>
<parameterdescription>
<para>the distance to reference1 (may be -1) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">d2</parametername>
</parameternamelist>
<parameterdescription>
<para>the distance to reference2 </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername direction="in">length</parametername>
</parameternamelist>
<parameterdescription>
<para>the length of the structure beginning from the 5&apos; end </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A sampled secondary structure in dot-bracket notation </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="381" column="19" declfile="ViennaRNA/2Dpfold.h" declline="381" declcolumn="19"/>
      </memberdef>
      <memberdef kind="function" id="2Dpfold_8h_1a8c3ebc8d1a4b4d9e653ef65d95822a1d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> **</type>
        <definition>FLT_OR_DBL ** TwoDpfold</definition>
        <argsstring>(TwoDpfold_vars *our_variables, int maxDistance1, int maxDistance2)</argsstring>
        <name>TwoDpfold</name>
        <param>
          <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
          <declname>our_variables</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxDistance1</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxDistance2</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="391" column="13" declfile="ViennaRNA/2Dpfold.h" declline="391" declcolumn="13"/>
      </memberdef>
      <memberdef kind="function" id="2Dpfold_8h_1adb16f671cbb14e221bc0f409f9f31d2a" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> **</type>
        <definition>FLT_OR_DBL ** TwoDpfold_circ</definition>
        <argsstring>(TwoDpfold_vars *our_variables, int maxDistance1, int maxDistance2)</argsstring>
        <name>TwoDpfold_circ</name>
        <param>
          <type><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref> *</type>
          <declname>our_variables</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxDistance1</declname>
        </param>
        <param>
          <type>int</type>
          <declname>maxDistance2</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="401" column="13" declfile="ViennaRNA/2Dpfold.h" declline="401" declcolumn="13"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>Partition function implementations for base pair distance classes. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_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="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><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="29"><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="30"><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="31"><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="32"><highlight class="normal"></highlight></codeline>
<codeline lineno="45" refid="structvrna__sol__TwoD__pf__t" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="46" refid="structvrna__sol__TwoD__pf__t_1ad1f23b46dc4ebd373abdeb0382d87b83" 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/><ref refid="structvrna__sol__TwoD__pf__t_1ad1f23b46dc4ebd373abdeb0382d87b83" kindref="member">k</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="47" refid="structvrna__sol__TwoD__pf__t_1a01133c264eff2c988d144e07803d1b8b" 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/><ref refid="structvrna__sol__TwoD__pf__t_1a01133c264eff2c988d144e07803d1b8b" kindref="member">l</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="48" refid="structvrna__sol__TwoD__pf__t_1a17ebbf425b8769ded74b5c7b85e58ee1" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><ref refid="structvrna__sol__TwoD__pf__t_1a17ebbf425b8769ded74b5c7b85e58ee1" kindref="member">q</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="49"><highlight class="normal">}<sp/><ref refid="structvrna__sol__TwoD__pf__t" kindref="compound">vrna_sol_TwoD_pf_t</ref>;</highlight></codeline>
<codeline lineno="50"><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"><ref refid="structvrna__sol__TwoD__pf__t" kindref="compound">vrna_sol_TwoD_pf_t</ref><sp/>*</highlight></codeline>
<codeline lineno="74" refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" refkind="member"><highlight class="normal"><ref refid="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" kindref="member">vrna_pf_TwoD</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="75"><highlight class="normal"><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/><sp/><sp/><sp/><sp/>maxDistance1,</highlight></codeline>
<codeline lineno="76"><highlight class="normal"><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/><sp/><sp/><sp/><sp/>maxDistance2);</highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight></codeline>
<codeline lineno="78"><highlight class="normal"><sp/></highlight><highlight class="comment">/*<sp/>End<sp/>of<sp/>group<sp/>kl_neighborhood_pf<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="80"><highlight class="normal"></highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="103"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="104" refid="group__kl__neighborhood__stochbt_1ga8527c142361ad019ef9b80c50591f215" refkind="member"><highlight class="normal"><ref refid="group__kl__neighborhood__stochbt_1ga8527c142361ad019ef9b80c50591f215" kindref="member">vrna_pbacktrack_TwoD</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="105"><highlight class="normal"><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/><sp/><sp/><sp/><sp/>d1,</highlight></codeline>
<codeline lineno="106"><highlight class="normal"><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/><sp/><sp/><sp/><sp/>d2);</highlight></codeline>
<codeline lineno="107"><highlight class="normal"></highlight></codeline>
<codeline lineno="108"><highlight class="normal"></highlight></codeline>
<codeline lineno="129"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="130" refid="group__kl__neighborhood__stochbt_1gae375170cbf15744a9cf2db33d0a2cb75" refkind="member"><highlight class="normal"><ref refid="group__kl__neighborhood__stochbt_1gae375170cbf15744a9cf2db33d0a2cb75" kindref="member">vrna_pbacktrack5_TwoD</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="131"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d1,</highlight></codeline>
<codeline lineno="132"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d2,</highlight></codeline>
<codeline lineno="133"><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/></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/>length);</highlight></codeline>
<codeline lineno="134"><highlight class="normal"></highlight></codeline>
<codeline lineno="135"><highlight class="normal"><sp/></highlight><highlight class="comment">/*<sp/>End<sp/>of<sp/>group<sp/>kl_neighborhood_stochbt<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="139"><highlight class="normal"></highlight></codeline>
<codeline lineno="140"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="141"><highlight class="normal"></highlight></codeline>
<codeline lineno="142"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>TwoDpfold_solution<sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_sol_TwoD_pf_t<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>restore<sp/>compatibility<sp/>of<sp/>struct<sp/>rename<sp/>*/</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="143"><highlight class="normal"></highlight></codeline>
<codeline lineno="151" refid="structTwoDpfold__vars" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">{</highlight></codeline>
<codeline lineno="152"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>alloc;</highlight></codeline>
<codeline lineno="153" refid="structTwoDpfold__vars_1a67f37b8901b8d0a049c216d4c6241b07" 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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1a67f37b8901b8d0a049c216d4c6241b07" kindref="member">ptype</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="154" refid="structTwoDpfold__vars_1a32c15a1e31856588259556c9020f32c6" 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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1a32c15a1e31856588259556c9020f32c6" kindref="member">sequence</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="155" refid="structTwoDpfold__vars_1a240311ae1e8e121441651d6101e187ac" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*S,<sp/>*<ref refid="structTwoDpfold__vars_1a240311ae1e8e121441651d6101e187ac" kindref="member">S1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="156" refid="structTwoDpfold__vars_1a7292b6cbc1ee5bacf55e842f316c4bef" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structTwoDpfold__vars_1a7292b6cbc1ee5bacf55e842f316c4bef" kindref="member">maxD1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="157" refid="structTwoDpfold__vars_1a8900622d91454d2d037242e290e42834" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structTwoDpfold__vars_1a8900622d91454d2d037242e290e42834" kindref="member">maxD2</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="158"><highlight class="normal"></highlight></codeline>
<codeline lineno="159"><highlight class="normal"><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/>temperature;<sp/><sp/></highlight><highlight class="comment">/*<sp/>temperature<sp/>in<sp/>last<sp/>call<sp/>to<sp/>scale_pf_params<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="160"><highlight class="normal"><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/>init_temp;<sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>temperature<sp/>in<sp/>last<sp/>call<sp/>to<sp/>scale_pf_params<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="161"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*scale;</highlight></codeline>
<codeline lineno="162"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>pf_scale;</highlight></codeline>
<codeline lineno="163"><highlight class="normal"><sp/><sp/><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref><sp/><sp/><sp/><sp/><sp/><sp/>*pf_params;<sp/></highlight><highlight class="comment">/*<sp/>holds<sp/>all<sp/>[unscaled]<sp/>pf<sp/>parameters<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="164"><highlight class="normal"></highlight></codeline>
<codeline lineno="165" refid="structTwoDpfold__vars_1ac2d3e6abf0cb0e1df363904fc938076e" 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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1ac2d3e6abf0cb0e1df363904fc938076e" kindref="member">my_iindx</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="166" refid="structTwoDpfold__vars_1a0699e194a797532c91b284ab10272384" 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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1a0699e194a797532c91b284ab10272384" kindref="member">jindx</ref>;<sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="167"><highlight class="normal"></highlight></codeline>
<codeline lineno="168"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*reference_pt1;</highlight></codeline>
<codeline lineno="169"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*reference_pt2;</highlight></codeline>
<codeline lineno="170"><highlight class="normal"></highlight></codeline>
<codeline lineno="171" refid="structTwoDpfold__vars_1aea15706d27b6b0fc19f5773919f43a8a" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1aea15706d27b6b0fc19f5773919f43a8a" kindref="member">referenceBPs1</ref>;<sp/></highlight></codeline>
<codeline lineno="172" refid="structTwoDpfold__vars_1a1221396d712bf76b7f35297f2ab35a9f" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1a1221396d712bf76b7f35297f2ab35a9f" kindref="member">referenceBPs2</ref>;<sp/></highlight></codeline>
<codeline lineno="173" refid="structTwoDpfold__vars_1accef8eaa05fa57ca33aa22cbc7b7aaff" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1accef8eaa05fa57ca33aa22cbc7b7aaff" kindref="member">bpdist</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="174"><highlight class="normal"></highlight></codeline>
<codeline lineno="175" refid="structTwoDpfold__vars_1a7c9e9af6224d4696118e05835441863d" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1a7c9e9af6224d4696118e05835441863d" kindref="member">mm1</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="176" refid="structTwoDpfold__vars_1affb913470783f9edb12a0bfc22466269" refkind="member"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structTwoDpfold__vars_1affb913470783f9edb12a0bfc22466269" kindref="member">mm2</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="177"><highlight class="normal"></highlight></codeline>
<codeline lineno="178"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>circ;</highlight></codeline>
<codeline lineno="179"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>dangles;</highlight></codeline>
<codeline lineno="180"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>seq_length;</highlight></codeline>
<codeline lineno="181"><highlight class="normal"></highlight></codeline>
<codeline lineno="182"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Q;</highlight></codeline>
<codeline lineno="183"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Q_B;</highlight></codeline>
<codeline lineno="184"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Q_M;</highlight></codeline>
<codeline lineno="185"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Q_M1;</highlight></codeline>
<codeline lineno="186"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>***Q_M2;</highlight></codeline>
<codeline lineno="187"><highlight class="normal"></highlight></codeline>
<codeline lineno="188"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**Q_c;</highlight></codeline>
<codeline lineno="189"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**Q_cH;</highlight></codeline>
<codeline lineno="190"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**Q_cI;</highlight></codeline>
<codeline lineno="191"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**Q_cM;</highlight></codeline>
<codeline lineno="192"><highlight class="normal"></highlight></codeline>
<codeline lineno="193"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_min_values;</highlight></codeline>
<codeline lineno="194"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_max_values;</highlight></codeline>
<codeline lineno="195"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_min_values;</highlight></codeline>
<codeline lineno="196"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_max_values;</highlight></codeline>
<codeline lineno="197"><highlight class="normal"></highlight></codeline>
<codeline lineno="198"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_min_values_b;</highlight></codeline>
<codeline lineno="199"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_max_values_b;</highlight></codeline>
<codeline lineno="200"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_min_values_b;</highlight></codeline>
<codeline lineno="201"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_max_values_b;</highlight></codeline>
<codeline lineno="202"><highlight class="normal"></highlight></codeline>
<codeline lineno="203"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_min_values_m;</highlight></codeline>
<codeline lineno="204"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_max_values_m;</highlight></codeline>
<codeline lineno="205"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_min_values_m;</highlight></codeline>
<codeline lineno="206"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_max_values_m;</highlight></codeline>
<codeline lineno="207"><highlight class="normal"></highlight></codeline>
<codeline lineno="208"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_min_values_m1;</highlight></codeline>
<codeline lineno="209"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_max_values_m1;</highlight></codeline>
<codeline lineno="210"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_min_values_m1;</highlight></codeline>
<codeline lineno="211"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_max_values_m1;</highlight></codeline>
<codeline lineno="212"><highlight class="normal"></highlight></codeline>
<codeline lineno="213"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_min_values_m2;</highlight></codeline>
<codeline lineno="214"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**l_max_values_m2;</highlight></codeline>
<codeline lineno="215"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_min_values_m2;</highlight></codeline>
<codeline lineno="216"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*k_max_values_m2;</highlight></codeline>
<codeline lineno="217"><highlight class="normal"></highlight></codeline>
<codeline lineno="218"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_min_values_qc;</highlight></codeline>
<codeline lineno="219"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_max_values_qc;</highlight></codeline>
<codeline lineno="220"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_min_values_qc;</highlight></codeline>
<codeline lineno="221"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_max_values_qc;</highlight></codeline>
<codeline lineno="222"><highlight class="normal"></highlight></codeline>
<codeline lineno="223"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_min_values_qcH;</highlight></codeline>
<codeline lineno="224"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_max_values_qcH;</highlight></codeline>
<codeline lineno="225"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_min_values_qcH;</highlight></codeline>
<codeline lineno="226"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_max_values_qcH;</highlight></codeline>
<codeline lineno="227"><highlight class="normal"></highlight></codeline>
<codeline lineno="228"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_min_values_qcI;</highlight></codeline>
<codeline lineno="229"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_max_values_qcI;</highlight></codeline>
<codeline lineno="230"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_min_values_qcI;</highlight></codeline>
<codeline lineno="231"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_max_values_qcI;</highlight></codeline>
<codeline lineno="232"><highlight class="normal"></highlight></codeline>
<codeline lineno="233"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_min_values_qcM;</highlight></codeline>
<codeline lineno="234"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*l_max_values_qcM;</highlight></codeline>
<codeline lineno="235"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_min_values_qcM;</highlight></codeline>
<codeline lineno="236"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k_max_values_qcM;</highlight></codeline>
<codeline lineno="237"><highlight class="normal"></highlight></codeline>
<codeline lineno="238"><highlight class="normal"><sp/><sp/></highlight><highlight class="comment">/*<sp/>auxilary<sp/>arrays<sp/>for<sp/>remaining<sp/>set<sp/>of<sp/>coarse<sp/>graining<sp/>(k,l)<sp/>&gt;<sp/>(k_max,<sp/>l_max)<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="239"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*Q_rem;</highlight></codeline>
<codeline lineno="240"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*Q_B_rem;</highlight></codeline>
<codeline lineno="241"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*Q_M_rem;</highlight></codeline>
<codeline lineno="242"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*Q_M1_rem;</highlight></codeline>
<codeline lineno="243"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*Q_M2_rem;</highlight></codeline>
<codeline lineno="244"><highlight class="normal"></highlight></codeline>
<codeline lineno="245"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Q_c_rem;</highlight></codeline>
<codeline lineno="246"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Q_cH_rem;</highlight></codeline>
<codeline lineno="247"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Q_cI_rem;</highlight></codeline>
<codeline lineno="248"><highlight class="normal"><sp/><sp/><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>Q_cM_rem;</highlight></codeline>
<codeline lineno="249"><highlight class="normal"></highlight></codeline>
<codeline lineno="250"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*compatibility;</highlight></codeline>
<codeline lineno="251"><highlight class="normal">}<sp/><ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref>;</highlight></codeline>
<codeline lineno="252"><highlight class="normal"></highlight></codeline>
<codeline lineno="271"><highlight class="normal">DEPRECATED(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/>*</highlight></codeline>
<codeline lineno="272"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="2Dpfold_8h_1a0d0ef6216c2a1f5c83c9b27d26c6efca" kindref="member">get_TwoDpfold_variables</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*seq,</highlight></codeline>
<codeline lineno="273"><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/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*structure1,</highlight></codeline>
<codeline lineno="274"><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/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*structure2,</highlight></codeline>
<codeline lineno="275"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" kindref="member">circ</ref>),</highlight></codeline>
<codeline lineno="276" refid="2Dpfold_8h_1a0d0ef6216c2a1f5c83c9b27d26c6efca" refkind="member"><highlight class="normal"><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_fold_compound_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="277"><highlight class="normal"></highlight></codeline>
<codeline lineno="291"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="292"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="2Dpfold_8h_1afe994291458ee2ac34d3eb825ef62a15" kindref="member">destroy_TwoDpfold_variables</ref>(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/>*vars),</highlight></codeline>
<codeline lineno="293" refid="2Dpfold_8h_1afe994291458ee2ac34d3eb825ef62a15" 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_fold_compound_free()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="294"><highlight class="normal"></highlight></codeline>
<codeline lineno="319"><highlight class="normal">DEPRECATED(TwoDpfold_solution<sp/>*</highlight></codeline>
<codeline lineno="320"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="2Dpfold_8h_1ace84b32f58d90d7b8779cc31d210d8c8" kindref="member">TwoDpfoldList</ref>(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/>*vars,</highlight></codeline>
<codeline lineno="321"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxDistance1,</highlight></codeline>
<codeline lineno="322"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxDistance2),</highlight></codeline>
<codeline lineno="323" refid="2Dpfold_8h_1ace84b32f58d90d7b8779cc31d210d8c8" refkind="member"><highlight class="normal"><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_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="324"><highlight class="normal"></highlight></codeline>
<codeline lineno="346"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="347"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="2Dpfold_8h_1a001da06931aa120569496978bb99479d" kindref="member">TwoDpfold_pbacktrack</ref>(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/><sp/>*vars,</highlight></codeline>
<codeline lineno="348"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d1,</highlight></codeline>
<codeline lineno="349"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d2),</highlight></codeline>
<codeline lineno="350" refid="2Dpfold_8h_1a001da06931aa120569496978bb99479d" refkind="member"><highlight class="normal"><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_pbacktrack_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="351"><highlight class="normal"></highlight></codeline>
<codeline lineno="376"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="377"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="2Dpfold_8h_1adfb2b7ab8d0cc7d84e0448d52a614838" kindref="member">TwoDpfold_pbacktrack5</ref>(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/>*vars,</highlight></codeline>
<codeline lineno="378"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d1,</highlight></codeline>
<codeline lineno="379"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d2,</highlight></codeline>
<codeline lineno="380"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/>length),</highlight></codeline>
<codeline lineno="381" refid="2Dpfold_8h_1adfb2b7ab8d0cc7d84e0448d52a614838" refkind="member"><highlight class="normal"><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_pbacktrack5_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="382"><highlight class="normal"></highlight></codeline>
<codeline lineno="388"><highlight class="normal">DEPRECATED(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**TwoDpfold(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/><sp/>*our_variables,</highlight></codeline>
<codeline lineno="389"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxDistance1,</highlight></codeline>
<codeline lineno="390"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxDistance2),</highlight></codeline>
<codeline lineno="391"><highlight class="normal"><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_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="392"><highlight class="normal"></highlight></codeline>
<codeline lineno="398"><highlight class="normal">DEPRECATED(<ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref><sp/>**TwoDpfold_circ(<ref refid="structTwoDpfold__vars" kindref="compound">TwoDpfold_vars</ref><sp/>*our_variables,</highlight></codeline>
<codeline lineno="399"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxDistance1,</highlight></codeline>
<codeline lineno="400"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>maxDistance2),</highlight></codeline>
<codeline lineno="401"><highlight class="normal"><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_TwoD()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="402"><highlight class="normal"></highlight></codeline>
<codeline lineno="403"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="404"><highlight class="normal"></highlight></codeline>
<codeline lineno="405"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/2Dpfold.h"/>
  </compounddef>
</doxygen>
