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  <compounddef id="group__kl__neighborhood__pf" kind="group">
    <compoundname>kl_neighborhood_pf</compoundname>
    <title>Computing Partition Functions of a Distance Based Partitioning</title>
    <innerclass refid="structvrna__sol__TwoD__pf__t" prot="public">vrna_sol_TwoD_pf_t</innerclass>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__kl__neighborhood__pf_1gac3bf71cefa4414f695e51f5da7269ebb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="structvrna__sol__TwoD__pf__t" kindref="compound">vrna_sol_TwoD_pf_t</ref> *</type>
        <definition>vrna_sol_TwoD_pf_t * vrna_pf_TwoD</definition>
        <argsstring>(vrna_fold_compound_t *fc, int maxDistance1, int maxDistance2)</argsstring>
        <name>vrna_pf_TwoD</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</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 <ref refid="group__kl__neighborhood__mfe_1ga264ac71e75add31dfb1fc72a0b2de709" kindref="member">vrna_mfe_TwoD()</ref> 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 value 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><simplesect kind="see"><para>vrna_fold_compound_TwoD(), <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref>, <ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound</ref> <ref refid="structvrna__sol__TwoD__pf__t" kindref="compound">vrna_sol_TwoD_pf_t</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</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 corresponding distance classes </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/2Dpfold.h" line="74" column="1" declfile="ViennaRNA/2Dpfold.h" declline="74" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
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