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  <compounddef id="group__struct__utils__tree" kind="group">
    <compoundname>struct_utils_tree</compoundname>
    <title>Tree Representation of Secondary Structures</title>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * vrna_db_to_tree_string</definition>
        <argsstring>(const char *structure, unsigned int type)</argsstring>
        <name>vrna_db_to_tree_string</name>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>type</declname>
        </param>
        <briefdescription>
<para>Convert a Dot-Bracket structure string into tree string representation. </para>
        </briefdescription>
        <detaileddescription>
<para>This function allows one to convert a secondary structure in dot-bracket notation into one of the various tree representations for secondary structures. The resulting tree is then represented as a string of parenthesis and node symbols, similar to to the Newick format.</para>
<para>Currently we support conversion into the following formats, denoted by the value of parameter <computeroutput>type:</computeroutput> <itemizedlist>
<listitem><para><ref refid="group__struct__utils__tree_1ga3ad5609bc93ef20034c3ab989365c1f0" kindref="member">VRNA_STRUCTURE_TREE_HIT</ref> -   Homeomorphically Irreducible <ref refid="structTree" kindref="compound">Tree</ref> (HIT) representation of a secondary structure.    (See also  <verbatim>embed:rst:inline  :cite:t:`fontana:1993b` </verbatim>)</para>
</listitem><listitem><para><ref refid="group__struct__utils__tree_1ga549e259a963d77e2d5b7e14083fc016e" kindref="member">VRNA_STRUCTURE_TREE_SHAPIRO_SHORT</ref> -   (short) Coarse Grained representation of a secondary structure    (same as  <verbatim>embed:rst:inline  :cite:t:`shapiro:1988` </verbatim>, but with root node <computeroutput>R</computeroutput> and without <computeroutput>S</computeroutput> nodes for the stems)</para>
</listitem><listitem><para><ref refid="group__struct__utils__tree_1ga4acd9991a0250ccd4cd44c4725b31927" kindref="member">VRNA_STRUCTURE_TREE_SHAPIRO</ref> -   (full) Coarse Grained representation of a secondary structure    (See also  <verbatim>embed:rst:inline  :cite:t:`shapiro:1988` </verbatim>)</para>
</listitem><listitem><para><ref refid="group__struct__utils__tree_1ga8666a10982a4f7a26892066ff07b4b48" kindref="member">VRNA_STRUCTURE_TREE_SHAPIRO_EXT</ref> -   (extended) Coarse Grained representation of a secondary structure    (same as  <verbatim>embed:rst:inline  :cite:t:`shapiro:1988` </verbatim>, but external nodes denoted as <computeroutput>E</computeroutput> )</para>
</listitem><listitem><para><ref refid="group__struct__utils__tree_1ga91f2e3a3a502d5445fd7fe5983a5fe92" kindref="member">VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT</ref> -   (weighted) Coarse Grained representation of a secondary structure    (same as <ref refid="group__struct__utils__tree_1ga8666a10982a4f7a26892066ff07b4b48" kindref="member">VRNA_STRUCTURE_TREE_SHAPIRO_EXT</ref> but with additional weights for number of unpaired nucleotides in loop, and number of pairs in stems)</para>
</listitem><listitem><para><ref refid="group__struct__utils__tree_1gab3b65489d1322da65d3a3e53242307ef" kindref="member">VRNA_STRUCTURE_TREE_EXPANDED</ref> -   Expanded <ref refid="structTree" kindref="compound">Tree</ref> representation of a secondary structure.   </para>
</listitem></itemizedlist>
</para>
<para><simplesect kind="see"><para>sec_structure_representations_tree</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>structure</parametername>
</parameternamelist>
<parameterdescription>
<para>The null-terminated dot-bracket structure string </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>type</parametername>
</parameternamelist>
<parameterdescription>
<para>A switch to determine the type of tree string representation </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A tree representation of the input <computeroutput>structure</computeroutput> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="99" column="1" declfile="ViennaRNA/structures/tree.h" declline="99" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__struct__utils__tree_1ga6531febe012d26927a87fae9e7bb4e76" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * vrna_tree_string_unweight</definition>
        <argsstring>(const char *structure)</argsstring>
        <name>vrna_tree_string_unweight</name>
        <param>
          <type>const char *</type>
          <declname>structure</declname>
        </param>
        <briefdescription>
<para>Remove weights from a linear string tree representation of a secondary structure. </para>
        </briefdescription>
        <detaileddescription>
<para>This function strips the weights of a linear string tree representation such as <computeroutput>HIT</computeroutput>, or Coarse Grained <ref refid="structTree" kindref="compound">Tree</ref> sensu  <verbatim>embed:rst:inline  :cite:t:`shapiro:1988` </verbatim></para>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>structure</parametername>
</parameternamelist>
<parameterdescription>
<para>A linear string tree representation of a secondary structure with weights </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A linear string tree representation of a secondary structure without weights </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="115" column="1" declfile="ViennaRNA/structures/tree.h" declline="115" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__struct__utils__tree_1ga33f017d7a065a92a1055a818b0ccbef4" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * vrna_tree_string_to_db</definition>
        <argsstring>(const char *tree)</argsstring>
        <name>vrna_tree_string_to_db</name>
        <param>
          <type>const char *</type>
          <declname>tree</declname>
        </param>
        <briefdescription>
<para>Convert a linear tree string representation of a secondary structure back to Dot-Bracket notation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>This function only accepts <emphasis>Expanded</emphasis> and <emphasis>HIT</emphasis> tree representations!</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref>, <ref refid="group__struct__utils__tree_1gab3b65489d1322da65d3a3e53242307ef" kindref="member">VRNA_STRUCTURE_TREE_EXPANDED</ref>, <ref refid="group__struct__utils__tree_1ga3ad5609bc93ef20034c3ab989365c1f0" kindref="member">VRNA_STRUCTURE_TREE_HIT</ref>, sec_structure_representations_tree</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>tree</parametername>
</parameternamelist>
<parameterdescription>
<para>A linear tree string representation of a secondary structure </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A dot-bracket notation of the secondary structure provided in <computeroutput>tree</computeroutput> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="130" column="1" declfile="ViennaRNA/structures/tree.h" declline="130" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="define">
      <memberdef kind="define" id="group__struct__utils__tree_1ga3ad5609bc93ef20034c3ab989365c1f0" prot="public" static="no">
        <name>VRNA_STRUCTURE_TREE_HIT</name>
        <initializer>1U</initializer>
        <briefdescription>
<para>Homeomorphically Irreducible <ref refid="structTree" kindref="compound">Tree</ref> (HIT) representation of a secondary structure. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="32" column="11" bodyfile="ViennaRNA/structures/tree.h" bodystart="32" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__struct__utils__tree_1ga549e259a963d77e2d5b7e14083fc016e" prot="public" static="no">
        <name>VRNA_STRUCTURE_TREE_SHAPIRO_SHORT</name>
        <initializer>2U</initializer>
        <briefdescription>
<para>(short) Coarse Grained representation of a secondary structure </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="39" column="11" bodyfile="ViennaRNA/structures/tree.h" bodystart="39" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__struct__utils__tree_1ga4acd9991a0250ccd4cd44c4725b31927" prot="public" static="no">
        <name>VRNA_STRUCTURE_TREE_SHAPIRO</name>
        <initializer>3U</initializer>
        <briefdescription>
<para>(full) Coarse Grained representation of a secondary structure </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="46" column="11" bodyfile="ViennaRNA/structures/tree.h" bodystart="46" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__struct__utils__tree_1ga8666a10982a4f7a26892066ff07b4b48" prot="public" static="no">
        <name>VRNA_STRUCTURE_TREE_SHAPIRO_EXT</name>
        <initializer>4U</initializer>
        <briefdescription>
<para>(extended) Coarse Grained representation of a secondary structure </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="53" column="11" bodyfile="ViennaRNA/structures/tree.h" bodystart="53" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__struct__utils__tree_1ga91f2e3a3a502d5445fd7fe5983a5fe92" prot="public" static="no">
        <name>VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT</name>
        <initializer>5U</initializer>
        <briefdescription>
<para>(weighted) Coarse Grained representation of a secondary structure </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="60" column="11" bodyfile="ViennaRNA/structures/tree.h" bodystart="60" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__struct__utils__tree_1gab3b65489d1322da65d3a3e53242307ef" prot="public" static="no">
        <name>VRNA_STRUCTURE_TREE_EXPANDED</name>
        <initializer>6U</initializer>
        <briefdescription>
<para>Expanded <ref refid="structTree" kindref="compound">Tree</ref> representation of a secondary structure. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__struct__utils__tree_1ga6a315cabbaf0868d640dfc9d922f0393" kindref="member">vrna_db_to_tree_string()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/structures/tree.h" line="66" column="11" bodyfile="ViennaRNA/structures/tree.h" bodystart="66" bodyend="-1"/>
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