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    <sectiondef kind="define">
      <member refid="group__perturbation_1ga81e10993d1ae728e4e02022b33155a12" kind="define"><name>VRNA_OBJECTIVE_FUNCTION_QUADRATIC</name></member>
      <member refid="group__perturbation_1gac070dfb9cafaeb14d5652bd9adf0f6b1" kind="define"><name>VRNA_OBJECTIVE_FUNCTION_ABSOLUTE</name></member>
      <member refid="group__perturbation_1gae5126200d80dbb282f46083fffc606bf" kind="define"><name>VRNA_MINIMIZER_DEFAULT</name></member>
      <member refid="group__perturbation_1gab1d89db58e8c497795a5005f5dbc8c4a" kind="define"><name>VRNA_MINIMIZER_CONJUGATE_FR</name></member>
      <member refid="group__perturbation_1ga5aaeafe1b0aa77a5cda18943ff94b02f" kind="define"><name>VRNA_MINIMIZER_CONJUGATE_PR</name></member>
      <member refid="group__perturbation_1ga9be8a702cddf58235571ace11cc41b22" kind="define"><name>VRNA_MINIMIZER_VECTOR_BFGS</name></member>
      <member refid="group__perturbation_1ga7b0a65c6c92fa1d8012383ba9d3dcb4f" kind="define"><name>VRNA_MINIMIZER_VECTOR_BFGS2</name></member>
      <member refid="group__perturbation_1ga9ecd2144c2ebed7533233da3986521b0" kind="define"><name>VRNA_MINIMIZER_STEEPEST_DESCENT</name></member>
    </sectiondef>
    <sectiondef kind="typedef">
      <member refid="group__perturbation_1gaa715397c7afd2d2955c315512a3d571a" kind="typedef"><name>progress_callback</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__perturbation_1ga64d7137ab57964928e7cd1be96d2e1ea" kind="function"><name>vrna_sc_minimize_pertubation</name></member>
    </sectiondef>
    <briefdescription>
<para>Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight></codeline>
<codeline lineno="20" refid="group__perturbation_1ga81e10993d1ae728e4e02022b33155a12" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OBJECTIVE_FUNCTION_QUADRATIC<sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="29" refid="group__perturbation_1gac070dfb9cafaeb14d5652bd9adf0f6b1" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_OBJECTIVE_FUNCTION_ABSOLUTE<sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight></codeline>
<codeline lineno="36" refid="group__perturbation_1gae5126200d80dbb282f46083fffc606bf" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MINIMIZER_DEFAULT<sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight></codeline>
<codeline lineno="45" refid="group__perturbation_1gab1d89db58e8c497795a5005f5dbc8c4a" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MINIMIZER_CONJUGATE_FR<sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="46"><highlight class="normal"></highlight></codeline>
<codeline lineno="54" refid="group__perturbation_1ga5aaeafe1b0aa77a5cda18943ff94b02f" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MINIMIZER_CONJUGATE_PR<sp/>2</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="55"><highlight class="normal"></highlight></codeline>
<codeline lineno="63" refid="group__perturbation_1ga9be8a702cddf58235571ace11cc41b22" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MINIMIZER_VECTOR_BFGS<sp/>3</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="64"><highlight class="normal"></highlight></codeline>
<codeline lineno="72" refid="group__perturbation_1ga7b0a65c6c92fa1d8012383ba9d3dcb4f" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MINIMIZER_VECTOR_BFGS2<sp/>4</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="73"><highlight class="normal"></highlight></codeline>
<codeline lineno="81" refid="group__perturbation_1ga9ecd2144c2ebed7533233da3986521b0" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MINIMIZER_STEEPEST_DESCENT<sp/>5</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="82"><highlight class="normal"></highlight></codeline>
<codeline lineno="92" refid="group__perturbation_1gaa715397c7afd2d2955c315512a3d571a" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/>void<sp/>(*<ref refid="group__perturbation_1gaa715397c7afd2d2955c315512a3d571a" kindref="member">progress_callback</ref>)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/>iteration,</highlight></codeline>
<codeline lineno="93"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>score,</highlight></codeline>
<codeline lineno="94"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>*epsilon);</highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight></codeline>
<codeline lineno="137" refid="group__perturbation_1ga64d7137ab57964928e7cd1be96d2e1ea" refkind="member"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><ref refid="group__perturbation_1ga64d7137ab57964928e7cd1be96d2e1ea" kindref="member">vrna_sc_minimize_pertubation</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="138"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*q_prob_unpaired,</highlight></codeline>
<codeline lineno="139"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>objective_function,</highlight></codeline>
<codeline lineno="140"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sigma_squared,</highlight></codeline>
<codeline lineno="141"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>tau_squared,</highlight></codeline>
<codeline lineno="142"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>algorithm,</highlight></codeline>
<codeline lineno="143"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>sample_size,</highlight></codeline>
<codeline lineno="144"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*epsilon,</highlight></codeline>
<codeline lineno="145"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>initialStepSize,</highlight></codeline>
<codeline lineno="146"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>minStepSize,</highlight></codeline>
<codeline lineno="147"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>minImprovement,</highlight></codeline>
<codeline lineno="148"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>minimizerTolerance,</highlight></codeline>
<codeline lineno="149"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__perturbation_1gaa715397c7afd2d2955c315512a3d571a" kindref="member">progress_callback</ref><sp/><sp/><sp/><sp/><sp/>callback);</highlight></codeline>
<codeline lineno="150"><highlight class="normal"></highlight></codeline>
<codeline lineno="151"><highlight class="normal"></highlight></codeline>
<codeline lineno="152"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/perturbation_fold.h"/>
  </compounddef>
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