<?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="structvrna__sc__s" kind="struct" language="C++" prot="public">
    <compoundname>vrna_sc_s</compoundname>
    <includes refid="soft_8h" local="no">ViennaRNA/constraints/soft.h</includes>
    <sectiondef kind="user-defined">
      <header>Common data fields</header>
      <memberdef kind="variable" id="structvrna__sc__s_1a97c2625bd6d1bbdaf8ac440f551d2281" prot="public" static="no" mutable="no">
        <type>const <ref refid="group__soft__constraints_1gab926b4d8c342aa5fb2f8f007200635a8" kindref="member">vrna_sc_type_e</ref></type>
        <definition>const vrna_sc_type_e vrna_sc_s::type</definition>
        <argsstring></argsstring>
        <name>type</name>
        <qualifiedname>vrna_sc_s::type</qualifiedname>
        <briefdescription>
<para>Type of the soft constraints data structure. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="238" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="238" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1ab47470efd4ee0211ca78641f57009def" prot="public" static="no" mutable="no">
        <type>unsigned int</type>
        <definition>unsigned int vrna_sc_s::n</definition>
        <argsstring></argsstring>
        <name>n</name>
        <qualifiedname>vrna_sc_s::n</qualifiedname>
        <briefdescription>
<para>Length of the sequence this soft constraints data structure belongs to. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="239" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="239" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a0b46b319b627a4de54deabf2358368a9" prot="public" static="no" mutable="no">
        <type>unsigned char</type>
        <definition>unsigned char vrna_sc_s::state</definition>
        <argsstring></argsstring>
        <name>state</name>
        <qualifiedname>vrna_sc_s::state</qualifiedname>
        <briefdescription>
<para>Current state of the soft constraints data structure. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="241" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="241" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a57e4dbb924ab11f304e3762a3a9b07a1" prot="public" static="no" mutable="no">
        <type>int **</type>
        <definition>int** vrna_sc_s::energy_up</definition>
        <argsstring></argsstring>
        <name>energy_up</name>
        <qualifiedname>vrna_sc_s::energy_up</qualifiedname>
        <briefdescription>
<para>Energy contribution for stretches of unpaired nucleotides. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="243" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="243" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1ad3b4972d3b6c23865587e4ac56a37375" prot="public" static="no" mutable="no">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> **</type>
        <definition>FLT_OR_DBL** vrna_sc_s::exp_energy_up</definition>
        <argsstring></argsstring>
        <name>exp_energy_up</name>
        <qualifiedname>vrna_sc_s::exp_energy_up</qualifiedname>
        <briefdescription>
<para>Boltzmann Factors of the energy contributions for unpaired sequence stretches. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="244" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="244" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a16c564d3170b7357620860de1e5faed6" prot="public" static="no" mutable="no">
        <type>int *</type>
        <definition>int* vrna_sc_s::up_storage</definition>
        <argsstring></argsstring>
        <name>up_storage</name>
        <qualifiedname>vrna_sc_s::up_storage</qualifiedname>
        <briefdescription>
<para>Storage container for energy contributions per unpaired nucleotide. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="246" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="246" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a8e261e29462f6bdba3259e5eb61e48e8" prot="public" static="no" mutable="no">
        <type><ref refid="structvrna__sc__bp__storage__t" kindref="compound">vrna_sc_bp_storage_t</ref> **</type>
        <definition>vrna_sc_bp_storage_t** vrna_sc_s::bp_storage</definition>
        <argsstring></argsstring>
        <name>bp_storage</name>
        <qualifiedname>vrna_sc_s::bp_storage</qualifiedname>
        <briefdescription>
<para>Storage container for energy contributions per base pair. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="247" column="25" bodyfile="ViennaRNA/constraints/soft.h" bodystart="247" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1ac20dded6068e81acd0f1139092f66a22" prot="public" static="no" mutable="no">
        <type>int *</type>
        <definition>int* vrna_sc_s::energy_stack</definition>
        <argsstring></argsstring>
        <name>energy_stack</name>
        <qualifiedname>vrna_sc_s::energy_stack</qualifiedname>
        <briefdescription>
<para>Pseudo Energy contribution per base pair involved in a stack. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="249" column="17" bodyfile="ViennaRNA/constraints/soft.h" bodystart="249" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a4a0058fe3d5ba3416f0aaab677610115" prot="public" static="no" mutable="no">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> *</type>
        <definition>FLT_OR_DBL* vrna_sc_s::exp_energy_stack</definition>
        <argsstring></argsstring>
        <name>exp_energy_stack</name>
        <qualifiedname>vrna_sc_s::exp_energy_stack</qualifiedname>
        <briefdescription>
<para>Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="250" column="17" bodyfile="ViennaRNA/constraints/soft.h" bodystart="250" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Global structure prediction data fields</header>
      <memberdef kind="variable" id="structvrna__sc__s_1ad139b8e06632e00cbcf3909815d0d03d" prot="public" static="no" mutable="no">
        <type>int *</type>
        <definition>int* vrna_sc_s::energy_bp</definition>
        <argsstring></argsstring>
        <name>energy_bp</name>
        <qualifiedname>vrna_sc_s::energy_bp</qualifiedname>
        <briefdescription>
<para>Energy contribution for base pairs. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="264" column="7" bodyfile="ViennaRNA/constraints/soft.h" bodystart="264" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a62c22be478cd630541c91f73e6cb0d75" prot="public" static="no" mutable="no">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> *</type>
        <definition>FLT_OR_DBL* vrna_sc_s::exp_energy_bp</definition>
        <argsstring></argsstring>
        <name>exp_energy_bp</name>
        <qualifiedname>vrna_sc_s::exp_energy_bp</qualifiedname>
        <briefdescription>
<para>Boltzmann Factors of the energy contribution for base pairs. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="265" column="14" bodyfile="ViennaRNA/constraints/soft.h" bodystart="265" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Local structure prediction data fields</header>
      <memberdef kind="variable" id="structvrna__sc__s_1ad939d2511afe7b3db9b802fdeff2bac4" prot="public" static="no" mutable="no">
        <type>int **</type>
        <definition>int** vrna_sc_s::energy_bp_local</definition>
        <argsstring></argsstring>
        <name>energy_bp_local</name>
        <qualifiedname>vrna_sc_s::energy_bp_local</qualifiedname>
        <briefdescription>
<para>Energy contribution for base pairs (sliding window approach). </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="279" column="15" bodyfile="ViennaRNA/constraints/soft.h" bodystart="279" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a6d882019efc1e09d385ef751765b3a80" prot="public" static="no" mutable="no">
        <type><ref refid="group__data__structures_1ga31125aeace516926bf7f251f759b6126" kindref="member">FLT_OR_DBL</ref> **</type>
        <definition>FLT_OR_DBL** vrna_sc_s::exp_energy_bp_local</definition>
        <argsstring></argsstring>
        <name>exp_energy_bp_local</name>
        <qualifiedname>vrna_sc_s::exp_energy_bp_local</qualifiedname>
        <briefdescription>
<para>Boltzmann Factors of the energy contribution for base pairs (sliding window approach). </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="280" column="15" bodyfile="ViennaRNA/constraints/soft.h" bodystart="280" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>User-defined data fields</header>
      <memberdef kind="variable" id="structvrna__sc__s_1a16a4e6c60a18917e0f1f94c1f2670c0a" prot="public" static="no" mutable="no">
        <type><ref refid="group__soft__constraints__generic_1gae2f7ded586b09b12ddaa627eee355a32" kindref="member">vrna_sc_f</ref></type>
        <definition>vrna_sc_f vrna_sc_s::f</definition>
        <argsstring></argsstring>
        <name>f</name>
        <qualifiedname>vrna_sc_s::f</qualifiedname>
        <briefdescription>
<para>A function pointer used for pseudo energy contribution in MFE calculations. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__soft__constraints__generic_1ga4fdbb3b492d2343d827715a7a7a0f689" kindref="member">vrna_sc_add_f()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="296" column="17" bodyfile="ViennaRNA/constraints/soft.h" bodystart="296" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1af1967d443ba9d6aa285fa5d5f9059d92" prot="public" static="no" mutable="no">
        <type><ref refid="group__soft__constraints__generic_1gaaa010a245ab273cd5c265929ff0b8bbd" kindref="member">vrna_sc_bt_f</ref></type>
        <definition>vrna_sc_bt_f vrna_sc_s::bt</definition>
        <argsstring></argsstring>
        <name>bt</name>
        <qualifiedname>vrna_sc_s::bt</qualifiedname>
        <briefdescription>
<para>A function pointer used to obtain backtraced base pairs in loop regions that were altered by soft constrained pseudo energy contributions. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__soft__constraints__generic_1gab0a2cbb121e1589f38144341ba4852bd" kindref="member">vrna_sc_add_bt()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="301" column="17" bodyfile="ViennaRNA/constraints/soft.h" bodystart="301" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a1ff207e74ee11948936a2443bff9813b" prot="public" static="no" mutable="no">
        <type><ref refid="group__soft__constraints__generic_1ga562554815b6717091125bf9782532740" kindref="member">vrna_sc_exp_f</ref></type>
        <definition>vrna_sc_exp_f vrna_sc_s::exp_f</definition>
        <argsstring></argsstring>
        <name>exp_f</name>
        <qualifiedname>vrna_sc_s::exp_f</qualifiedname>
        <briefdescription>
<para>A function pointer used for pseudo energy contribution boltzmann factors in PF calculations. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__soft__constraints__generic_1ga42ae58b56fb10e75a6ee3e131a6ae30e" kindref="member">vrna_sc_add_exp_f()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="307" column="17" bodyfile="ViennaRNA/constraints/soft.h" bodystart="307" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a7574680143df97b9029146c2150bf06d" prot="public" static="no" mutable="no">
        <type>void *</type>
        <definition>void* vrna_sc_s::data</definition>
        <argsstring></argsstring>
        <name>data</name>
        <qualifiedname>vrna_sc_s::data</qualifiedname>
        <briefdescription>
<para>A pointer to the data object provided for for pseudo energy contribution functions of the generic soft constraints feature. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="313" column="23" bodyfile="ViennaRNA/constraints/soft.h" bodystart="313" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1a7e8e14209f773fab99d4e25493ee07d0" prot="public" static="no" mutable="no">
        <type><ref refid="group__fold__compound_1gab78664b2ef71ae6d147d6e74bf2862d3" kindref="member">vrna_auxdata_prepare_f</ref></type>
        <definition>vrna_auxdata_prepare_f vrna_sc_s::prepare_data</definition>
        <argsstring></argsstring>
        <name>prepare_data</name>
        <qualifiedname>vrna_sc_s::prepare_data</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="318" column="27" bodyfile="ViennaRNA/constraints/soft.h" bodystart="318" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__sc__s_1ade4aac85657ebb03c5cba6514df2cca0" prot="public" static="no" mutable="no">
        <type><ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f</ref></type>
        <definition>vrna_auxdata_free_f vrna_sc_s::free_data</definition>
        <argsstring></argsstring>
        <name>free_data</name>
        <qualifiedname>vrna_sc_s::free_data</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="319" column="27" bodyfile="ViennaRNA/constraints/soft.h" bodystart="319" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="public-attrib">
      <memberdef kind="variable" id="structvrna__sc__s_1a5d6dd9d7a0346494ede2476f473e8f5b" prot="public" static="no" mutable="no">
        <type>union <ref refid="structvrna__sc__s" kindref="compound">vrna_sc_s</ref></type>
        <definition>union vrna_sc_s vrna_sc_s</definition>
        <argsstring></argsstring>
        <name></name>
        <qualifiedname>vrna_sc_s</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/soft.h" line="288" column="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>The soft constraints data structure. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <collaborationgraph>
      <node id="6">
        <label>vrna_alignment_s</label>
        <link refid="structvrna__alignment__s"/>
        <childnode refid="5" relation="usage">
          <edgelabel>sequences</edgelabel>
        </childnode>
      </node>
      <node id="3">
        <label>vrna_basepair_t</label>
        <link refid="structvrna__basepair__t"/>
      </node>
      <node id="12">
        <label>vrna_exp_param_s</label>
        <link refid="structvrna__exp__param__s"/>
        <childnode refid="11" relation="usage">
          <edgelabel>model_details</edgelabel>
        </childnode>
      </node>
      <node id="4">
        <label>vrna_fc_s</label>
        <link refid="structvrna__fc__s"/>
        <childnode refid="5" relation="usage">
          <edgelabel>nucleotides</edgelabel>
        </childnode>
        <childnode refid="6" relation="usage">
          <edgelabel>alignment</edgelabel>
        </childnode>
        <childnode refid="7" relation="usage">
          <edgelabel>hc</edgelabel>
        </childnode>
        <childnode refid="8" relation="usage">
          <edgelabel>matrices</edgelabel>
        </childnode>
        <childnode refid="9" relation="usage">
          <edgelabel>exp_matrices</edgelabel>
        </childnode>
        <childnode refid="10" relation="usage">
          <edgelabel>params</edgelabel>
        </childnode>
        <childnode refid="12" relation="usage">
          <edgelabel>exp_params</edgelabel>
        </childnode>
        <childnode refid="4" relation="usage">
          <edgelabel>stat_cb</edgelabel>
        </childnode>
        <childnode refid="13" relation="usage">
          <edgelabel>domains_struc</edgelabel>
        </childnode>
        <childnode refid="14" relation="usage">
          <edgelabel>domains_up</edgelabel>
        </childnode>
        <childnode refid="1" relation="usage">
          <edgelabel>sc</edgelabel>
          <edgelabel>scs</edgelabel>
        </childnode>
      </node>
      <node id="7">
        <label>vrna_hc_s</label>
        <link refid="structvrna__hc__s"/>
        <childnode refid="7" relation="usage">
          <edgelabel>eval_ext</edgelabel>
          <edgelabel>eval_hp</edgelabel>
          <edgelabel>eval_int</edgelabel>
          <edgelabel>eval_mb</edgelabel>
        </childnode>
      </node>
      <node id="11">
        <label>vrna_md_s</label>
        <link refid="structvrna__md__s"/>
      </node>
      <node id="8">
        <label>vrna_mx_mfe_s</label>
        <link refid="structvrna__mx__mfe__s"/>
      </node>
      <node id="9">
        <label>vrna_mx_pf_s</label>
        <link refid="structvrna__mx__pf__s"/>
      </node>
      <node id="10">
        <label>vrna_param_s</label>
        <link refid="structvrna__param__s"/>
        <childnode refid="11" relation="usage">
          <edgelabel>model_details</edgelabel>
        </childnode>
      </node>
      <node id="2">
        <label>vrna_sc_bp_storage_t</label>
        <link refid="structvrna__sc__bp__storage__t"/>
      </node>
      <node id="1">
        <label>vrna_sc_s</label>
        <link refid="structvrna__sc__s"/>
        <childnode refid="2" relation="usage">
          <edgelabel>bp_storage</edgelabel>
        </childnode>
        <childnode refid="3" relation="usage">
          <edgelabel>bt</edgelabel>
        </childnode>
        <childnode refid="4" relation="usage">
          <edgelabel>prepare_data</edgelabel>
        </childnode>
      </node>
      <node id="5">
        <label>vrna_sequence_s</label>
        <link refid="structvrna__sequence__s"/>
      </node>
      <node id="13">
        <label>vrna_structured_domains_s</label>
        <link refid="structvrna__structured__domains__s"/>
      </node>
      <node id="14">
        <label>vrna_unstructured_domain_s</label>
        <link refid="structvrna__unstructured__domain__s"/>
        <childnode refid="4" relation="usage">
          <edgelabel>energy_cb</edgelabel>
          <edgelabel>exp_energy_cb</edgelabel>
          <edgelabel>exp_prod_cb</edgelabel>
          <edgelabel>probs_add</edgelabel>
          <edgelabel>probs_get</edgelabel>
          <edgelabel>prod_cb</edgelabel>
        </childnode>
      </node>
    </collaborationgraph>
    <location file="ViennaRNA/constraints/soft.h" line="233" column="1" bodyfile="ViennaRNA/constraints/soft.h" bodystart="233" bodyend="324"/>
    <listofallmembers>
      <member refid="structvrna__sc__s_1a8e261e29462f6bdba3259e5eb61e48e8" prot="public" virt="non-virtual"><scope>vrna_sc_s</scope><name>bp_storage</name></member>
      <member refid="structvrna__sc__s_1af1967d443ba9d6aa285fa5d5f9059d92" prot="public" virt="non-virtual"><scope>vrna_sc_s</scope><name>bt</name></member>
      <member refid="structvrna__sc__s_1a7574680143df97b9029146c2150bf06d" prot="public" virt="non-virtual"><scope>vrna_sc_s</scope><name>data</name></member>
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</doxygen>
