<?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="group__SHAPE__reactivities" kind="group">
    <compoundname>SHAPE_reactivities</compoundname>
    <title>SHAPE Reactivity Data</title>
    <innerfile refid="probing_2SHAPE_8h">SHAPE.h</innerfile>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga67675b3ed48744489a3bcfa4174197cb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_sc_SHAPE_to_pr</definition>
        <argsstring>(const char *shape_conversion, double *values, int length, double default_value)</argsstring>
        <name>vrna_sc_SHAPE_to_pr</name>
        <param>
          <type>const char *</type>
          <declname>shape_conversion</declname>
        </param>
        <param>
          <type>double *</type>
          <declname>values</declname>
        </param>
        <param>
          <type>int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>double</type>
          <declname>default_value</declname>
        </param>
        <briefdescription>
<para>Convert SHAPE reactivity values to probabilities for being unpaired. </para>
        </briefdescription>
        <detaileddescription>
<para>This function parses the informations from a given file and stores the result in the pre-allocated string sequence and the <ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> array values.</para>
<para><simplesect kind="see"><para><ref refid="group__file__formats_1ga646ebf45450a69a7f2533f9ecd283a32" kindref="member">vrna_file_SHAPE_read()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>shape_conversion</parametername>
</parameternamelist>
<parameterdescription>
<para>String defining the method used for the conversion process </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>values</parametername>
</parameternamelist>
<parameterdescription>
<para>Pointer to an array of SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>length</parametername>
</parameternamelist>
<parameterdescription>
<para>Length of the array of SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>default_value</parametername>
</parameternamelist>
<parameterdescription>
<para>Result used for position with invalid/missing reactivity values </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/basic.h" line="329" column="1" declfile="ViennaRNA/probing/basic.h" declline="329" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1gad609895467d59ea53faac4f98b71c099" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_sc_add_SHAPE_deigan</definition>
        <argsstring>(vrna_fold_compound_t *fc, const double *reactivities, double m, double b, unsigned int options)</argsstring>
        <name>vrna_sc_add_SHAPE_deigan</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>double</type>
          <declname>m</declname>
        </param>
        <param>
          <type>double</type>
          <declname>b</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
<para>Add SHAPE reactivity data as soft constraints (Deigan et al. method). </para>
        </briefdescription>
        <detaileddescription>
<para>This approach of SHAPE directed RNA folding uses the simple linear ansatz</para>
<para><formula id="169">\[ \Delta G_{\text{SHAPE}}(i) = m \ln(\text{SHAPE reactivity}(i)+1)+ b \]</formula></para>
<para>to convert SHAPE reactivity values to pseudo energies whenever a nucleotide <formula id="55">$ i $</formula> contributes to a stacked pair. A positive slope <formula id="170">$ m $</formula> penalizes high reactivities in paired regions, while a negative intercept <formula id="88">$ b $</formula> results in a confirmatory <emphasis>bonus</emphasis> free energy for correctly predicted base pairs. Since the energy evaluation of a base pair stack involves two pairs, the pseudo energies are added for all four contributing nucleotides. Consequently, the energy term is applied twice for pairs inside a helix and only once for pairs adjacent to other structures. For all other loop types the energy model remains unchanged even when the experimental data highly disagrees with a certain motif.</para>
<para><simplesect kind="note"><para>For further details, we refer to  <verbatim>embed:rst:inline  :cite:t:`deigan:2009` </verbatim>.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__soft__constraints_1gac81478a33880029ca9975bd89cc26fa9" kindref="member">vrna_sc_remove()</ref>, <ref refid="group__SHAPE__reactivities_1ga5a673837ebe42d790bdf3ccf8982d3dc" kindref="member">vrna_sc_add_SHAPE_zarringhalam()</ref>, <ref refid="group__perturbation_1ga64d7137ab57964928e7cd1be96d2e1ea" kindref="member">vrna_sc_minimize_pertubation()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</parametername>
</parameternamelist>
<parameterdescription>
<para>The <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> the soft constraints are associated with </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>reactivities</parametername>
</parameternamelist>
<parameterdescription>
<para>A vector of normalized SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>m</parametername>
</parameternamelist>
<parameterdescription>
<para>The slope of the conversion function </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>b</parametername>
</parameternamelist>
<parameterdescription>
<para>The intercept of the conversion function </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>options</parametername>
</parameternamelist>
<parameterdescription>
<para>The options flag indicating how/where to store the soft constraints </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>1 on successful extraction of the method, 0 on errors</para>
</simplesect>
<xrefsect id="wrappers_1_wrappers000168"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as method <computeroutput>sc_add_SHAPE_deigan()</computeroutput> to objects of type <computeroutput>fold_compound</computeroutput>. See, e.g.  <verbatim>embed:rst:inline  :py:meth:`RNA.fold_compound.sc_add_SHAPE_deigan()` in the :doc:`/api_python` </verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="67" column="1" declfile="ViennaRNA/probing/SHAPE.h" declline="67" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga2a3fbf037d5e2844792997a92ef36285" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_sc_add_SHAPE_deigan_ali</definition>
        <argsstring>(vrna_fold_compound_t *fc, const char **shape_files, const int *shape_file_association, double m, double b, unsigned int options)</argsstring>
        <name>vrna_sc_add_SHAPE_deigan_ali</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>shape_files</declname>
        </param>
        <param>
          <type>const int *</type>
          <declname>shape_file_association</declname>
        </param>
        <param>
          <type>double</type>
          <declname>m</declname>
        </param>
        <param>
          <type>double</type>
          <declname>b</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
<para>Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method). </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</parametername>
</parameternamelist>
<parameterdescription>
<para>The <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> the soft constraints are associated with </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>shape_files</parametername>
</parameternamelist>
<parameterdescription>
<para>A set of filenames that contain normalized SHAPE reactivity data </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>shape_file_association</parametername>
</parameternamelist>
<parameterdescription>
<para>An array of integers that associate the files with sequences in the alignment </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>m</parametername>
</parameternamelist>
<parameterdescription>
<para>The slope of the conversion function </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>b</parametername>
</parameternamelist>
<parameterdescription>
<para>The intercept of the conversion function </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>options</parametername>
</parameternamelist>
<parameterdescription>
<para>The options flag indicating how/where to store the soft constraints </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>1 on successful extraction of the method, 0 on errors</para>
</simplesect>
<xrefsect id="wrappers_1_wrappers000169"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as method <computeroutput>sc_add_SHAPE_deigan_ali()</computeroutput> to objects of type <computeroutput>fold_compound</computeroutput>. See, e.g.  <verbatim>embed:rst:inline  :py:meth:`RNA.fold_compound.sc_add_SHAPE_deigan_ali()` in the :doc:`/api_python` </verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="86" column="1" declfile="ViennaRNA/probing/SHAPE.h" declline="86" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga5a673837ebe42d790bdf3ccf8982d3dc" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_sc_add_SHAPE_zarringhalam</definition>
        <argsstring>(vrna_fold_compound_t *fc, const double *reactivities, double b, double default_value, const char *shape_conversion, unsigned int options)</argsstring>
        <name>vrna_sc_add_SHAPE_zarringhalam</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>double</type>
          <declname>b</declname>
        </param>
        <param>
          <type>double</type>
          <declname>default_value</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>shape_conversion</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
<para>Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method). </para>
        </briefdescription>
        <detaileddescription>
<para>This method first converts the observed SHAPE reactivity of nucleotide <formula id="55">$ i $</formula> into a probability <formula id="171">$ q_i $</formula> that position <formula id="55">$ i $</formula> is unpaired by means of a non-linear map. Then pseudo-energies of the form</para>
<para><formula id="172">\[ \Delta G_{\text{SHAPE}}(x,i) = \beta\ |x_i - q_i| \]</formula></para>
<para>are computed, where <formula id="173">$ x_i=0 $</formula> if position <formula id="55">$ i $</formula> is unpaired and <formula id="174">$ x_i=1 $</formula> if <formula id="55">$ i $</formula> is paired in a given secondary structure. The parameter <formula id="175">$ \beta $</formula> serves as scaling factor. The magnitude of discrepancy between prediction and experimental observation is represented by <formula id="176">$ |x_i - q_i| $</formula>.</para>
<para><simplesect kind="note"><para>For further details, we refer to  <verbatim>embed:rst:inline  :cite:t:`zarringhalam:2012` </verbatim></para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__soft__constraints_1gac81478a33880029ca9975bd89cc26fa9" kindref="member">vrna_sc_remove()</ref>, <ref refid="group__SHAPE__reactivities_1gad609895467d59ea53faac4f98b71c099" kindref="member">vrna_sc_add_SHAPE_deigan()</ref>, <ref refid="group__perturbation_1ga64d7137ab57964928e7cd1be96d2e1ea" kindref="member">vrna_sc_minimize_pertubation()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</parametername>
</parameternamelist>
<parameterdescription>
<para>The <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> the soft constraints are associated with </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>reactivities</parametername>
</parameternamelist>
<parameterdescription>
<para>A vector of normalized SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>b</parametername>
</parameternamelist>
<parameterdescription>
<para>The scaling factor <formula id="175">$ \beta $</formula> of the conversion function </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>default_value</parametername>
</parameternamelist>
<parameterdescription>
<para>The default value for a nucleotide where reactivity data is missing for </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>shape_conversion</parametername>
</parameternamelist>
<parameterdescription>
<para>A flag that specifies how to convert reactivities to probabilities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>options</parametername>
</parameternamelist>
<parameterdescription>
<para>The options flag indicating how/where to store the soft constraints </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>1 on successful extraction of the method, 0 on errors</para>
</simplesect>
<xrefsect id="wrappers_1_wrappers000170"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para>This function is attached as method <computeroutput>sc_add_SHAPE_zarringhalam()</computeroutput> to objects of type <computeroutput>fold_compound</computeroutput>. See, e.g.  <verbatim>embed:rst:inline  :py:meth:`RNA.fold_compound.sc_add_SHAPE_zarringhalam()` in the :doc:`/api_python` </verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="121" column="1" declfile="ViennaRNA/probing/SHAPE.h" declline="121" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga41b1e8f2f4c82d7bd515ec452b4024cb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_sc_add_SHAPE_eddy_2</definition>
        <argsstring>(vrna_fold_compound_t *fc, const double *reactivities, int unpaired_nb, const double *unpaired_data, int paired_nb, const double *paired_data)</argsstring>
        <name>vrna_sc_add_SHAPE_eddy_2</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>reactivities</declname>
        </param>
        <param>
          <type>int</type>
          <declname>unpaired_nb</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>unpaired_data</declname>
        </param>
        <param>
          <type>int</type>
          <declname>paired_nb</declname>
        </param>
        <param>
          <type>const double *</type>
          <declname>paired_data</declname>
        </param>
        <briefdescription>
<para>Add SHAPE reactivity data as soft constraints (Eddy/RNAprob-2 method). </para>
        </briefdescription>
        <detaileddescription>
<para>This approach of SHAPE directed RNA folding uses the probability framework proposed by Eddy</para>
<para><formula id="177">\[ \Delta G_{\text{SHAPE}}(i) = - RT\ln(\mathbb{P}(\text{SHAPE reactivity}(i)\mid x_i\pi_i))+ \]</formula></para>
<para>to convert SHAPE reactivity values to pseudo energies for given nucleotide <formula id="178">$ x_i $</formula> and pairedness <formula id="179">$ \pi_i $</formula> at position <formula id="55">$ i $</formula>. The reactivity distribution is computed using Gaussian kernel density estimation (KDE) with bandwidth <formula id="114">$ h $</formula> computed using Scott factor</para>
<para><formula id="180">\[ h = n^{-\frac{1}{5}} \]</formula></para>
<para>where <formula id="113">$ n $</formula> is the number of data points.</para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>fc</parametername>
</parameternamelist>
<parameterdescription>
<para>The <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> the soft constraints are associated with </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>reactivities</parametername>
</parameternamelist>
<parameterdescription>
<para>A vector of normalized SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>unpaired_nb</parametername>
</parameternamelist>
<parameterdescription>
<para>Length of the array of unpaired SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>unpaired_data</parametername>
</parameternamelist>
<parameterdescription>
<para>Pointer to an array of unpaired SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>paired_nb</parametername>
</parameternamelist>
<parameterdescription>
<para>Length of the array of paired SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>paired_data</parametername>
</parameternamelist>
<parameterdescription>
<para>Pointer to an array of paired SHAPE reactivities </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>1 on successful extraction of the method, 0 on errors </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="154" column="1" declfile="ViennaRNA/probing/SHAPE.h" declline="154" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga71b84eb0dd69e5c256f4ecf8f78cf314" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_sc_SHAPE_parse_method</definition>
        <argsstring>(const char *method_string, char *method, float *param_1, float *param_2)</argsstring>
        <name>vrna_sc_SHAPE_parse_method</name>
        <param>
          <type>const char *</type>
          <declname>method_string</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>method</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>param_1</declname>
        </param>
        <param>
          <type>float *</type>
          <declname>param_2</declname>
        </param>
        <briefdescription>
<para>Parse a character string and extract the encoded SHAPE reactivity conversion method and possibly the parameters for conversion into pseudo free energies. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>method_string</parametername>
</parameternamelist>
<parameterdescription>
<para>The string that contains the encoded SHAPE reactivity conversion method </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>method</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the memory location where the method character will be stored </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>param_1</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the memory location where the first parameter of the corresponding method will be stored </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>param_2</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the memory location where the second parameter of the corresponding method will be stored </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>1 on successful extraction of the method, 0 on errors </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="182" column="6" declfile="ViennaRNA/probing/SHAPE.h" declline="182" declcolumn="6"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga1b402c8ff2d77abc957faca66da9378d" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_constraints_add_SHAPE_ali</definition>
        <argsstring>(vrna_fold_compound_t *fc, const char *shape_method, const char **shape_files, const int *shape_file_association, int verbose, unsigned int constraint_type)</argsstring>
        <name>vrna_constraints_add_SHAPE_ali</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>shape_method</declname>
        </param>
        <param>
          <type>const char **</type>
          <declname>shape_files</declname>
        </param>
        <param>
          <type>const int *</type>
          <declname>shape_file_association</declname>
        </param>
        <param>
          <type>int</type>
          <declname>verbose</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>constraint_type</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="193" column="7" declfile="ViennaRNA/probing/SHAPE.h" declline="193" declcolumn="7"/>
      </memberdef>
      <memberdef kind="function" id="group__SHAPE__reactivities_1ga2fc1bede8b6ccf153c2a2bbbb0c08646" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_constraints_add_SHAPE</definition>
        <argsstring>(vrna_fold_compound_t *fc, const char *shape_file, const char *shape_method, const char *shape_conversion, int verbose, unsigned int constraint_type)</argsstring>
        <name>vrna_constraints_add_SHAPE</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>shape_file</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>shape_method</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>shape_conversion</declname>
        </param>
        <param>
          <type>int</type>
          <declname>verbose</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>constraint_type</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="204" column="7" declfile="ViennaRNA/probing/SHAPE.h" declline="204" declcolumn="7"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="define">
      <memberdef kind="define" id="group__SHAPE__reactivities_1ga10cd3f02aec34b7e763cae23a56dfa75" prot="public" static="no">
        <name>VRNA_PROBING_DATA_CHECK_SEQUENCE</name>
        <initializer>1U</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/probing/SHAPE.h" line="36" column="9" bodyfile="ViennaRNA/probing/SHAPE.h" bodystart="36" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
</doxygen>
