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  <compounddef id="group__subopt__stochbt__deprecated" kind="group">
    <compoundname>subopt_stochbt_deprecated</compoundname>
    <title>Deprecated Interface for Stochastic Backtracking</title>
    <sectiondef kind="var">
      <memberdef kind="variable" id="group__subopt__stochbt__deprecated_1gacd79b1a570e6ad9be24cb11fe8cae30a" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int st_back</definition>
        <argsstring></argsstring>
        <name>st_back</name>
        <briefdescription>
<para>Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. </para>
        </briefdescription>
        <detaileddescription>
<para>Set this variable to 1 prior to a call of <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions</para>
<para><xrefsect id="deprecated_1_deprecated000183"><xreftitle>Deprecated</xreftitle><xrefdescription><para>set the <emphasis>uniq_ML</emphasis> flag in <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> before passing it to <ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound()</ref>.</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="group__subopt__stochbt__deprecated_1gaae9de453e396420d6269534d571d6d18" kindref="member">pbacktrack()</ref>, <ref refid="group__subopt__stochbt__deprecated_1ga4b6d04c882ae87b6cee9a516e06c4155" kindref="member">pbacktrack_circ</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="347" column="12" declfile="ViennaRNA/partfunc/global.h" declline="347" declcolumn="12"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__subopt__stochbt__deprecated_1gaae9de453e396420d6269534d571d6d18" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * pbacktrack</definition>
        <argsstring>(char *sequence)</argsstring>
        <name>pbacktrack</name>
        <param>
          <type>char *</type>
          <declname>sequence</declname>
        </param>
        <briefdescription>
<para>Sample a secondary structure from the Boltzmann ensemble according its probability. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="pre"><para><ref refid="group__subopt__stochbt__deprecated_1gacd79b1a570e6ad9be24cb11fe8cae30a" kindref="member">st_back</ref> has to be set to 1 before calling <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> or <ref refid="group__part__func__global__deprecated_1gac4f95bee734b2563a3d6e9932117ebdf" kindref="member">pf_fold_par()</ref><linebreak/>
 <ref refid="group__part__func__global__deprecated_1gac4f95bee734b2563a3d6e9932117ebdf" kindref="member">pf_fold_par()</ref> or <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> have to be called first to fill the partition function matrices</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>sequence</parametername>
</parameternamelist>
<parameterdescription>
<para>The RNA sequence </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/partfunc/global.h" line="496" column="7" declfile="ViennaRNA/partfunc/global.h" declline="496" declcolumn="7"/>
      </memberdef>
      <memberdef kind="function" id="group__subopt__stochbt__deprecated_1ga31aa6bffb2b5c66486f50091a7061320" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * pbacktrack5</definition>
        <argsstring>(char *sequence, int length)</argsstring>
        <name>pbacktrack5</name>
        <param>
          <type>char *</type>
          <declname>sequence</declname>
        </param>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <briefdescription>
<para>Sample a sub-structure from the Boltzmann ensemble according its probability. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/partfunc/global.h" line="504" column="7" declfile="ViennaRNA/partfunc/global.h" declline="504" declcolumn="7"/>
      </memberdef>
      <memberdef kind="function" id="group__subopt__stochbt__deprecated_1ga4b6d04c882ae87b6cee9a516e06c4155" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * pbacktrack_circ</definition>
        <argsstring>(char *sequence)</argsstring>
        <name>pbacktrack_circ</name>
        <param>
          <type>char *</type>
          <declname>sequence</declname>
        </param>
        <briefdescription>
<para>Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. </para>
        </briefdescription>
        <detaileddescription>
<para>This function does the same as <ref refid="group__subopt__stochbt__deprecated_1gaae9de453e396420d6269534d571d6d18" kindref="member">pbacktrack()</ref> but assumes the RNA molecule to be circular</para>
<para><simplesect kind="pre"><para><ref refid="group__subopt__stochbt__deprecated_1gacd79b1a570e6ad9be24cb11fe8cae30a" kindref="member">st_back</ref> has to be set to 1 before calling <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> or <ref refid="group__part__func__global__deprecated_1gac4f95bee734b2563a3d6e9932117ebdf" kindref="member">pf_fold_par()</ref><linebreak/>
 <ref refid="group__part__func__global__deprecated_1gac4f95bee734b2563a3d6e9932117ebdf" kindref="member">pf_fold_par()</ref> or <ref refid="group__part__func__global__deprecated_1ga819ce5fca8984004ac81c4a3b04cb735" kindref="member">pf_circ_fold()</ref> have to be called first to fill the partition function matrices</para>
</simplesect>
<xrefsect id="deprecated_1_deprecated000186"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use <ref refid="group__subopt__stochbt_1ga594844ac73c4e66e00d6791b31540634" kindref="member">vrna_pbacktrack()</ref> instead.</para>
</xrefdescription></xrefsect></para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>sequence</parametername>
</parameternamelist>
<parameterdescription>
<para>The RNA sequence </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/partfunc/global.h" line="521" column="7" declfile="ViennaRNA/partfunc/global.h" declline="521" declcolumn="7"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
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