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  <compounddef id="group__struct__utils__metrics" kind="group">
    <compoundname>struct_utils_metrics</compoundname>
    <title>Distance measures between Secondary Structures</title>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__struct__utils__metrics_1gae08cbd5ff44b7d77a271ceb79c12cfef" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_bp_distance_pt</definition>
        <argsstring>(const short *pt1, const short *pt2)</argsstring>
        <name>vrna_bp_distance_pt</name>
        <param>
          <type>const short *</type>
          <declname>pt1</declname>
        </param>
        <param>
          <type>const short *</type>
          <declname>pt2</declname>
        </param>
        <briefdescription>
<para>Compute the &quot;base pair&quot; distance between two pair tables pt1 and pt2 of secondary structures. </para>
        </briefdescription>
        <detaileddescription>
<para>The pair tables should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set</para>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__metrics_1ga65bdfbac6a16bf30286e8a3f7d15f60a" kindref="member">vrna_bp_distance()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>pt1</parametername>
</parameternamelist>
<parameterdescription>
<para>First structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>pt2</parametername>
</parameternamelist>
<parameterdescription>
<para>Second structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>The base pair distance between pt1 and pt2</para>
</simplesect>
<xrefsect id="wrappers_1_wrappers000179"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as an overloaded method <bold><ref refid="group__struct__utils__deprecated_1ga6ebbcd29a754f0e4f1a66d1fd84184db" kindref="member">bp_distance()</ref></bold>. See, e.g.  <verbatim>embed:rst:inline :py:func:`RNA.bp_distance()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/metrics.h" line="41" column="1" declfile="ViennaRNA/structures/metrics.h" declline="41" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__struct__utils__metrics_1ga65bdfbac6a16bf30286e8a3f7d15f60a" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_bp_distance</definition>
        <argsstring>(const char *str1, const char *str2)</argsstring>
        <name>vrna_bp_distance</name>
        <param>
          <type>const char *</type>
          <declname>str1</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>str2</declname>
        </param>
        <briefdescription>
<para>Compute the &quot;base pair&quot; distance between two secondary structures s1 and s2. </para>
        </briefdescription>
        <detaileddescription>
<para>This is a wrapper around <bold><ref refid="group__struct__utils__metrics_1gae08cbd5ff44b7d77a271ceb79c12cfef" kindref="member">vrna_bp_distance_pt()</ref></bold>. The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set</para>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__metrics_1gae08cbd5ff44b7d77a271ceb79c12cfef" kindref="member">vrna_bp_distance_pt()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>str1</parametername>
</parameternamelist>
<parameterdescription>
<para>First structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>str2</parametername>
</parameternamelist>
<parameterdescription>
<para>Second structure in dot-bracket notation </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>The base pair distance between str1 and str2</para>
</simplesect>
<xrefsect id="wrappers_1_wrappers000180"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is available as an overloaded method <bold><ref refid="group__struct__utils__deprecated_1ga6ebbcd29a754f0e4f1a66d1fd84184db" kindref="member">bp_distance()</ref></bold>. Note that the SWIG wrapper takes two structure in dot-bracket notation and converts them into pair tables using <ref refid="group__struct__utils__pair__table_1ga792503f8b2c6783248e5c8b3d56e9148" kindref="member">vrna_ptable_from_string()</ref>. The resulting pair tables are then internally passed to <ref refid="group__struct__utils__metrics_1gae08cbd5ff44b7d77a271ceb79c12cfef" kindref="member">vrna_bp_distance_pt()</ref>. To control which kind of matching brackets will be used during conversion, the optional argument <computeroutput>options</computeroutput> can be used. See also the description of <ref refid="group__struct__utils__pair__table_1ga792503f8b2c6783248e5c8b3d56e9148" kindref="member">vrna_ptable_from_string()</ref> for available options. (default: <bold>VRNA_BRACKETS_RND</bold>). See, e.g.  <verbatim>embed:rst:inline :py:func:`RNA.bp_distance()` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/metrics.h" line="59" column="1" declfile="ViennaRNA/structures/metrics.h" declline="59" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__struct__utils__metrics_1ga58224cf9335172baa1e725266cc5d90c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_dist_mountain</definition>
        <argsstring>(const char *str1, const char *str2, unsigned int p)</argsstring>
        <name>vrna_dist_mountain</name>
        <param>
          <type>const char *</type>
          <declname>str1</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>str2</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>p</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/metrics.h" line="64" column="1" declfile="ViennaRNA/structures/metrics.h" declline="64" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
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