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  <compounddef id="structvrna__fc__s" kind="struct" language="C++" prot="public">
    <compoundname>vrna_fc_s</compoundname>
    <includes refid="fold__compound_8h" local="no">ViennaRNA/fold_compound.h</includes>
    <sectiondef kind="user-defined">
      <header>Common data fields</header>
      <memberdef kind="variable" id="structvrna__fc__s_1a391bcf8ac5997784aaf780cdd251c464" prot="public" static="no" mutable="no">
        <type>const <ref refid="group__fold__compound_1ga01a4ff86fa71deaaa5d1abbd95a1447d" kindref="member">vrna_fc_type_e</ref></type>
        <definition>const vrna_fc_type_e vrna_fc_s::type</definition>
        <argsstring></argsstring>
        <name>type</name>
        <qualifiedname>vrna_fc_s::type</qualifiedname>
        <briefdescription>
<para>The type of the <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref>. </para>
        </briefdescription>
        <detaileddescription>
<para>Currently possible values are <ref refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447da7e264dd3cf2dc9b6448caabcb7763cd6" kindref="member">VRNA_FC_TYPE_SINGLE</ref>, and <ref refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447dab821ce46ea3cf665be97df22a76f5023" kindref="member">VRNA_FC_TYPE_COMPARATIVE</ref> <simplesect kind="warning"><para>Do not edit this attribute, it will be automagically set by the corresponding get() methods for the <ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref>. The value specified in this attribute dictates the set of other attributes to use within this data structure. </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="176" column="24" bodyfile="ViennaRNA/fold_compound.h" bodystart="176" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a95fbfed770b858e50c766505dc4bf998" prot="public" static="no" mutable="no">
        <type>unsigned int</type>
        <definition>unsigned int vrna_fc_s::length</definition>
        <argsstring></argsstring>
        <name>length</name>
        <qualifiedname>vrna_fc_s::length</qualifiedname>
        <briefdescription>
<para>The length of the sequence (or sequence alignment). </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="183" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="183" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ae1a7bbff0256577e2b22709bac11fdb4" prot="public" static="no" mutable="no">
        <type>int</type>
        <definition>int vrna_fc_s::cutpoint</definition>
        <argsstring></argsstring>
        <name>cutpoint</name>
        <qualifiedname>vrna_fc_s::cutpoint</qualifiedname>
        <briefdescription>
<para>The position of the (cofold) cutpoint within the provided sequence. If there is no cutpoint, this field will be set to -1. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="186" column="6" bodyfile="ViennaRNA/fold_compound.h" bodystart="186" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a23304c5186dfae97bc69dc19d37f70c3" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::strand_number</definition>
        <argsstring></argsstring>
        <name>strand_number</name>
        <qualifiedname>vrna_fc_s::strand_number</qualifiedname>
        <briefdescription>
<para>The strand number a particular nucleotide is associated with. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="191" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="191" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a3bf15e0e44539f9f622fd09227bf3de1" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::strand_order</definition>
        <argsstring></argsstring>
        <name>strand_order</name>
        <qualifiedname>vrna_fc_s::strand_order</qualifiedname>
        <briefdescription>
<para>The strand order, i.e. permutation of current concatenated sequence. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="192" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="192" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1af698d79085056aa9a9075e834b0748ed" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::strand_order_uniq</definition>
        <argsstring></argsstring>
        <name>strand_order_uniq</name>
        <qualifiedname>vrna_fc_s::strand_order_uniq</qualifiedname>
        <briefdescription>
<para>The strand order array where identical sequences have the same ID. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="193" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="193" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a571ee9a932f633c7d9167ae029573935" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::strand_start</definition>
        <argsstring></argsstring>
        <name>strand_start</name>
        <qualifiedname>vrna_fc_s::strand_start</qualifiedname>
        <briefdescription>
<para>The start position of a particular strand within the current concatenated sequence. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="194" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="194" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aaa1b51bc6eb47cc661fea834d7175a54" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::strand_end</definition>
        <argsstring></argsstring>
        <name>strand_end</name>
        <qualifiedname>vrna_fc_s::strand_end</qualifiedname>
        <briefdescription>
<para>The end (last) position of a particular strand within the current concatenated sequence. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="195" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="195" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ad8962b97f5e5e233d9bfb5b16a691d26" prot="public" static="no" mutable="no">
        <type>unsigned int</type>
        <definition>unsigned int vrna_fc_s::strands</definition>
        <argsstring></argsstring>
        <name>strands</name>
        <qualifiedname>vrna_fc_s::strands</qualifiedname>
        <briefdescription>
<para>Number of interacting strands. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="197" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="197" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a855b503aefd052430bf463d8518d2ff5" prot="public" static="no" mutable="no">
        <type><ref refid="group__alphabet__utils_1gaa35bee3061759495467070b47d0e1f22" kindref="member">vrna_seq_t</ref> *</type>
        <definition>vrna_seq_t* vrna_fc_s::nucleotides</definition>
        <argsstring></argsstring>
        <name>nucleotides</name>
        <qualifiedname>vrna_fc_s::nucleotides</qualifiedname>
        <briefdescription>
<para>Set of nucleotide sequences. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="198" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="198" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a0387efd460429ca0847c8009d327c0fb" prot="public" static="no" mutable="no">
        <type>vrna_msa_t *</type>
        <definition>vrna_msa_t* vrna_fc_s::alignment</definition>
        <argsstring></argsstring>
        <name>alignment</name>
        <qualifiedname>vrna_fc_s::alignment</qualifiedname>
        <briefdescription>
<para>Set of alignments. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="199" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="199" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aceaa904dbf50092d403ca99422e8f824" prot="public" static="no" mutable="no">
        <type><ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref> *</type>
        <definition>vrna_hc_t* vrna_fc_s::hc</definition>
        <argsstring></argsstring>
        <name>hc</name>
        <qualifiedname>vrna_fc_s::hc</qualifiedname>
        <briefdescription>
<para>The hard constraints data structure used for structure prediction. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="201" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="201" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aca8be7bdc65bafe2172c6ee777f18568" prot="public" static="no" mutable="no">
        <type><ref refid="group__dp__matrices_1gae5aef35d016475e758f619b7bcb534f9" kindref="member">vrna_mx_mfe_t</ref> *</type>
        <definition>vrna_mx_mfe_t* vrna_fc_s::matrices</definition>
        <argsstring></argsstring>
        <name>matrices</name>
        <qualifiedname>vrna_fc_s::matrices</qualifiedname>
        <briefdescription>
<para>The MFE DP matrices. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="203" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="203" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1afc38ed5a1028a2712d2365274bf49727" prot="public" static="no" mutable="no">
        <type><ref refid="group__dp__matrices_1ga68729ab3fed26bdd1806fa814f172fc1" kindref="member">vrna_mx_pf_t</ref> *</type>
        <definition>vrna_mx_pf_t* vrna_fc_s::exp_matrices</definition>
        <argsstring></argsstring>
        <name>exp_matrices</name>
        <qualifiedname>vrna_fc_s::exp_matrices</qualifiedname>
        <briefdescription>
<para>The PF DP matrices. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="204" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="204" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a19b8720c2c5321c1b97c830bd17566ea" prot="public" static="no" mutable="no">
        <type><ref refid="group__energy__parameters_1ga8a69ca7d787e4fd6079914f5343a1f35" kindref="member">vrna_param_t</ref> *</type>
        <definition>vrna_param_t* vrna_fc_s::params</definition>
        <argsstring></argsstring>
        <name>params</name>
        <qualifiedname>vrna_fc_s::params</qualifiedname>
        <briefdescription>
<para>The precomputed free energy contributions for each type of loop. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="206" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="206" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a7052a5d24f6091b9c5f79edcc9456a12" prot="public" static="no" mutable="no">
        <type><ref refid="group__energy__parameters_1ga01d8b92fe734df8d79a6169482c7d8d8" kindref="member">vrna_exp_param_t</ref> *</type>
        <definition>vrna_exp_param_t* vrna_fc_s::exp_params</definition>
        <argsstring></argsstring>
        <name>exp_params</name>
        <qualifiedname>vrna_fc_s::exp_params</qualifiedname>
        <briefdescription>
<para>The precomputed free energy contributions as Boltzmann factors. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="207" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="207" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1afdead4cf55c882d3497e779573e17e03" prot="public" static="no" mutable="no">
        <type>int *</type>
        <definition>int* vrna_fc_s::iindx</definition>
        <argsstring></argsstring>
        <name>iindx</name>
        <qualifiedname>vrna_fc_s::iindx</qualifiedname>
        <briefdescription>
<para>DP matrix accessor. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="209" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="209" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a5037235dee512efd85ca543780bbca1a" prot="public" static="no" mutable="no">
        <type>int *</type>
        <definition>int* vrna_fc_s::jindx</definition>
        <argsstring></argsstring>
        <name>jindx</name>
        <qualifiedname>vrna_fc_s::jindx</qualifiedname>
        <briefdescription>
<para>DP matrix accessor. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="210" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="210" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>User-defined data fields</header>
      <memberdef kind="variable" id="structvrna__fc__s_1aef282a5d126e0038f3855e59a99ef360" prot="public" static="no" mutable="no">
        <type><ref refid="group__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" kindref="member">vrna_recursion_status_f</ref></type>
        <definition>vrna_recursion_status_f vrna_fc_s::stat_cb</definition>
        <argsstring></argsstring>
        <name>stat_cb</name>
        <qualifiedname>vrna_fc_s::stat_cb</qualifiedname>
        <briefdescription>
<para>Recursion status callback (usually called just before, and after recursive computations in the library. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__fold__compound_1gabc02e2d02dad91e66eca6656c68987c1" kindref="member">vrna_recursion_status_f()</ref>, <ref refid="group__fold__compound_1ga579952cc017127b81e89a186c0d6b9c2" kindref="member">vrna_fold_compound_add_callback()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="218" column="29" bodyfile="ViennaRNA/fold_compound.h" bodystart="218" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a20048e0c369e9f24b55423d600037c68" prot="public" static="no" mutable="no">
        <type>void *</type>
        <definition>void* vrna_fc_s::auxdata</definition>
        <argsstring></argsstring>
        <name>auxdata</name>
        <qualifiedname>vrna_fc_s::auxdata</qualifiedname>
        <briefdescription>
<para>A pointer to auxiliary, user-defined data. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__fold__compound_1gad6c0747712712bda6d94702e0de895a7" kindref="member">vrna_fold_compound_add_auxdata()</ref>, <ref refid="structvrna__fc__s_1a02b2bfc9d563b4748f933308de09791c" kindref="member">vrna_fold_compound_t.free_auxdata</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="223" column="29" bodyfile="ViennaRNA/fold_compound.h" bodystart="223" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a02b2bfc9d563b4748f933308de09791c" 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_fc_s::free_auxdata</definition>
        <argsstring></argsstring>
        <name>free_auxdata</name>
        <qualifiedname>vrna_fc_s::free_auxdata</qualifiedname>
        <briefdescription>
<para>A callback to free auxiliary user data whenever the fold_compound itself is free&apos;d. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__fc__s_1a20048e0c369e9f24b55423d600037c68" kindref="member">vrna_fold_compound_t.auxdata</ref>, <ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="227" column="29" bodyfile="ViennaRNA/fold_compound.h" bodystart="227" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Secondary Structure Decomposition (grammar) related data fields</header>
      <memberdef kind="variable" id="structvrna__fc__s_1ac25a84f2658de0d7a54cd710c16198b1" prot="public" static="no" mutable="no">
        <type>vrna_sd_t *</type>
        <definition>vrna_sd_t* vrna_fc_s::domains_struc</definition>
        <argsstring></argsstring>
        <name>domains_struc</name>
        <qualifiedname>vrna_fc_s::domains_struc</qualifiedname>
        <briefdescription>
<para>Additional structured domains. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="239" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="239" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a4f70b6d32681fc8ca061236f21819ae7" prot="public" static="no" mutable="no">
        <type><ref refid="group__domains__up_1ga0009117b14d29143e8b18ab891f48c2d" kindref="member">vrna_ud_t</ref> *</type>
        <definition>vrna_ud_t* vrna_fc_s::domains_up</definition>
        <argsstring></argsstring>
        <name>domains_up</name>
        <qualifiedname>vrna_fc_s::domains_up</qualifiedname>
        <briefdescription>
<para>Additional unstructured domains. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="242" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="242" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a4dbcba59425e0d4b222adae148e3041a" prot="public" static="no" mutable="no">
        <type><ref refid="group__grammar_1gab771519c88455091fff89211cc8b1f97" kindref="member">vrna_gr_aux_t</ref></type>
        <definition>vrna_gr_aux_t vrna_fc_s::aux_grammar</definition>
        <argsstring></argsstring>
        <name>aux_grammar</name>
        <qualifiedname>vrna_fc_s::aux_grammar</qualifiedname>
        <briefdescription>
<para>Additional decomposition grammar rules. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="245" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="245" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Data fields available for single/hybrid structure prediction</header>
      <memberdef kind="variable" id="structvrna__fc__s_1a87f6abcda89cfb7a486c97e1f5371525" prot="public" static="no" mutable="no">
        <type>char *</type>
        <definition>char* vrna_fc_s::sequence</definition>
        <argsstring></argsstring>
        <name>sequence</name>
        <qualifiedname>vrna_fc_s::sequence</qualifiedname>
        <briefdescription>
<para>The input sequence string. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_SINGLE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="261" column="12" bodyfile="ViennaRNA/fold_compound.h" bodystart="261" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a9934bdb695d35a3544285cbcc19f9763" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::sequence_encoding</definition>
        <argsstring></argsstring>
        <name>sequence_encoding</name>
        <qualifiedname>vrna_fc_s::sequence_encoding</qualifiedname>
        <briefdescription>
<para>Numerical encoding of the input sequence. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para>vrna_sequence_encode() </para>
</simplesect>
<simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_SINGLE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="264" column="13" bodyfile="ViennaRNA/fold_compound.h" bodystart="264" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a7a230013f7a1ccbd0345e9fc56ca4982" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::encoding5</definition>
        <argsstring></argsstring>
        <name>encoding5</name>
        <qualifiedname>vrna_fc_s::encoding5</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="268" column="13" bodyfile="ViennaRNA/fold_compound.h" bodystart="268" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ae38ca011ec0e06fbff139b885d7f476e" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::encoding3</definition>
        <argsstring></argsstring>
        <name>encoding3</name>
        <qualifiedname>vrna_fc_s::encoding3</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="269" column="13" bodyfile="ViennaRNA/fold_compound.h" bodystart="269" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aaf9064092f674882e78665e1646ffdbf" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::sequence_encoding2</definition>
        <argsstring></argsstring>
        <name>sequence_encoding2</name>
        <qualifiedname>vrna_fc_s::sequence_encoding2</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="271" column="13" bodyfile="ViennaRNA/fold_compound.h" bodystart="271" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a3fbea559f1d1976b2d67c215cdeee0b2" prot="public" static="no" mutable="no">
        <type>char *</type>
        <definition>char* vrna_fc_s::ptype</definition>
        <argsstring></argsstring>
        <name>ptype</name>
        <qualifiedname>vrna_fc_s::ptype</qualifiedname>
        <briefdescription>
<para>Pair type array. </para>
        </briefdescription>
        <detaileddescription>
<para>Contains the numerical encoding of the pair type for each pair (i,j) used in MFE, Partition function and Evaluation computations. <simplesect kind="note"><para>This array is always indexed via jindx, in contrast to previously different indexing between mfe and pf variants! </para>
</simplesect>
<simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_SINGLE </verbatim> </para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__utils_1ga93a00c17b7644d1e755943d01664cae0" kindref="member">vrna_idx_col_wise()</ref>, <ref refid="group__alphabet__utils_1ga495e6f5c88129128114fcb437b1fddeb" kindref="member">vrna_ptypes()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="274" column="12" bodyfile="ViennaRNA/fold_compound.h" bodystart="274" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a7fe1235ce3d41287695f1ae1e283e8fc" prot="public" static="no" mutable="no">
        <type>char *</type>
        <definition>char* vrna_fc_s::ptype_pf_compat</definition>
        <argsstring></argsstring>
        <name>ptype_pf_compat</name>
        <qualifiedname>vrna_fc_s::ptype_pf_compat</qualifiedname>
        <briefdescription>
<para>ptype array indexed via iindx </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000073"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This attribute will vanish in the future! It&apos;s meant for backward compatibility only! </para>
</xrefdescription></xrefsect><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_SINGLE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="283" column="12" bodyfile="ViennaRNA/fold_compound.h" bodystart="283" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ac7089e90460ad3990a308808c8044c9f" prot="public" static="no" mutable="no">
        <type><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref> *</type>
        <definition>vrna_sc_t* vrna_fc_s::sc</definition>
        <argsstring></argsstring>
        <name>sc</name>
        <qualifiedname>vrna_fc_s::sc</qualifiedname>
        <briefdescription>
<para>The soft constraints for usage in structure prediction and evaluation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_SINGLE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="288" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="288" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Data fields for consensus structure prediction</header>
      <memberdef kind="variable" id="structvrna__fc__s_1a965dbb42f2e13cace5aa3bbab4396530" prot="public" static="no" mutable="no">
        <type>char **</type>
        <definition>char** vrna_fc_s::sequences</definition>
        <argsstring></argsstring>
        <name>sequences</name>
        <qualifiedname>vrna_fc_s::sequences</qualifiedname>
        <briefdescription>
<para>The aligned sequences. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="note"><para>The end of the alignment is indicated by a NULL pointer in the second dimension </para>
</simplesect>
<simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="306" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="306" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a614702ab74478e786272be44f8cebfe3" prot="public" static="no" mutable="no">
        <type>unsigned int</type>
        <definition>unsigned int vrna_fc_s::n_seq</definition>
        <argsstring></argsstring>
        <name>n_seq</name>
        <qualifiedname>vrna_fc_s::n_seq</qualifiedname>
        <briefdescription>
<para>The number of sequences in the alignment. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="310" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="310" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ac472afde64d8b3c8b84e4809fda7d814" prot="public" static="no" mutable="no">
        <type>char *</type>
        <definition>char* vrna_fc_s::cons_seq</definition>
        <argsstring></argsstring>
        <name>cons_seq</name>
        <qualifiedname>vrna_fc_s::cons_seq</qualifiedname>
        <briefdescription>
<para>The consensus sequence of the aligned sequences. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="313" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="313" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aa3fab7ae38ebfed2028375221d295686" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::S_cons</definition>
        <argsstring></argsstring>
        <name>S_cons</name>
        <qualifiedname>vrna_fc_s::S_cons</qualifiedname>
        <briefdescription>
<para>Numerical encoding of the consensus sequence. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="316" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="316" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aebb37297f92c7bd22aac6343f8f61d61" prot="public" static="no" mutable="no">
        <type>short **</type>
        <definition>short** vrna_fc_s::S</definition>
        <argsstring></argsstring>
        <name>S</name>
        <qualifiedname>vrna_fc_s::S</qualifiedname>
        <briefdescription>
<para>Numerical encoding of the sequences in the alignment. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="319" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="319" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a78d089b475e2230bd536b9a6ed8bb17c" prot="public" static="no" mutable="no">
        <type>short **</type>
        <definition>short** vrna_fc_s::S5</definition>
        <argsstring></argsstring>
        <name>S5</name>
        <qualifiedname>vrna_fc_s::S5</qualifiedname>
        <briefdescription>
<para>S5[s][i] holds next base 5&apos; of i in sequence s. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="322" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="322" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1af6ab2a25b84d2308ee23f6b11b5fd52d" prot="public" static="no" mutable="no">
        <type>short **</type>
        <definition>short** vrna_fc_s::S3</definition>
        <argsstring></argsstring>
        <name>S3</name>
        <qualifiedname>vrna_fc_s::S3</qualifiedname>
        <briefdescription>
<para>Sl[s][i] holds next base 3&apos; of i in sequence s. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="325" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="325" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1abf4a526147da57db63990892987fea29" prot="public" static="no" mutable="no">
        <type>char **</type>
        <definition>char** vrna_fc_s::Ss</definition>
        <argsstring></argsstring>
        <name>Ss</name>
        <qualifiedname>vrna_fc_s::Ss</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="328" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="328" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a1e8ab3e7d0ba41bdd86e12044903881a" prot="public" static="no" mutable="no">
        <type>unsigned int **</type>
        <definition>unsigned int** vrna_fc_s::a2s</definition>
        <argsstring></argsstring>
        <name>a2s</name>
        <qualifiedname>vrna_fc_s::a2s</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="329" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="329" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a14dc7755af6019ddbd0cf94b209e89dd" prot="public" static="no" mutable="no">
        <type>int *</type>
        <definition>int* vrna_fc_s::pscore</definition>
        <argsstring></argsstring>
        <name>pscore</name>
        <qualifiedname>vrna_fc_s::pscore</qualifiedname>
        <briefdescription>
<para>Precomputed array of pair types expressed as pairing scores. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="330" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="330" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ad966c15907e6c2e32b0910c7a3154509" prot="public" static="no" mutable="no">
        <type>int **</type>
        <definition>int** vrna_fc_s::pscore_local</definition>
        <argsstring></argsstring>
        <name>pscore_local</name>
        <qualifiedname>vrna_fc_s::pscore_local</qualifiedname>
        <briefdescription>
<para>Precomputed array of pair types expressed as pairing scores. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="333" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="333" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1abf5e82d14649b6179ae60ed7da6e4fc0" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::pscore_pf_compat</definition>
        <argsstring></argsstring>
        <name>pscore_pf_compat</name>
        <qualifiedname>vrna_fc_s::pscore_pf_compat</qualifiedname>
        <briefdescription>
<para>Precomputed array of pair types expressed as pairing scores indexed via iindx. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000074"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This attribute will vanish in the future! </para>
</xrefdescription></xrefsect><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="336" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="336" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ac2b047fddabc51a76a96511174e47db1" prot="public" static="no" mutable="no">
        <type><ref refid="group__soft__constraints_1ga75401ce219ef8dbcceb672db82d434c6" kindref="member">vrna_sc_t</ref> **</type>
        <definition>vrna_sc_t** vrna_fc_s::scs</definition>
        <argsstring></argsstring>
        <name>scs</name>
        <qualifiedname>vrna_fc_s::scs</qualifiedname>
        <briefdescription>
<para>A set of soft constraints (for each sequence in the alignment). </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="warning"><para>Only available if <verbatim>type==VRNA_FC_TYPE_COMPARATIVE </verbatim> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="340" column="21" bodyfile="ViennaRNA/fold_compound.h" bodystart="340" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1ac539df9233472dd76d070f4a821185a9" prot="public" static="no" mutable="no">
        <type>int</type>
        <definition>int vrna_fc_s::oldAliEn</definition>
        <argsstring></argsstring>
        <name>oldAliEn</name>
        <qualifiedname>vrna_fc_s::oldAliEn</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="343" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="343" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Additional data fields for Distance Class Partitioning</header>
      <description><para>These data fields are typically populated with meaningful data only if used in the context of Distance Class Partitioning </para>
</description>
      <memberdef kind="variable" id="structvrna__fc__s_1a426305721b16023f2f3247f7354d2c46" prot="public" static="no" mutable="no">
        <type>unsigned int</type>
        <definition>unsigned int vrna_fc_s::maxD1</definition>
        <argsstring></argsstring>
        <name>maxD1</name>
        <qualifiedname>vrna_fc_s::maxD1</qualifiedname>
        <briefdescription>
<para>Maximum allowed base pair distance to first reference. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="359" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="359" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a38695774fd396c892f9a70d39978b231" prot="public" static="no" mutable="no">
        <type>unsigned int</type>
        <definition>unsigned int vrna_fc_s::maxD2</definition>
        <argsstring></argsstring>
        <name>maxD2</name>
        <qualifiedname>vrna_fc_s::maxD2</qualifiedname>
        <briefdescription>
<para>Maximum allowed base pair distance to second reference. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="360" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="360" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1aa279ba4bd0ff541d435d3a049687f3ac" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::reference_pt1</definition>
        <argsstring></argsstring>
        <name>reference_pt1</name>
        <qualifiedname>vrna_fc_s::reference_pt1</qualifiedname>
        <briefdescription>
<para>A pairtable of the first reference structure. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="361" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="361" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a926ad253f5f0eed642bc227493d0278d" prot="public" static="no" mutable="no">
        <type>short *</type>
        <definition>short* vrna_fc_s::reference_pt2</definition>
        <argsstring></argsstring>
        <name>reference_pt2</name>
        <qualifiedname>vrna_fc_s::reference_pt2</qualifiedname>
        <briefdescription>
<para>A pairtable of the second reference structure. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="362" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="362" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a62a8d4ab8dadffbf09da917adff6c71e" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::referenceBPs1</definition>
        <argsstring></argsstring>
        <name>referenceBPs1</name>
        <qualifiedname>vrna_fc_s::referenceBPs1</qualifiedname>
        <briefdescription>
<para>Matrix containing number of basepairs of reference structure1 in interval [i,j]. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="364" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="364" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a19187f33433e84683730dedff8544f71" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::referenceBPs2</definition>
        <argsstring></argsstring>
        <name>referenceBPs2</name>
        <qualifiedname>vrna_fc_s::referenceBPs2</qualifiedname>
        <briefdescription>
<para>Matrix containing number of basepairs of reference structure2 in interval [i,j]. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="365" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="365" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a5c53e55583ce096148075bc240fc2bce" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::bpdist</definition>
        <argsstring></argsstring>
        <name>bpdist</name>
        <qualifiedname>vrna_fc_s::bpdist</qualifiedname>
        <briefdescription>
<para>Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j]. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="366" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="366" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a0af5a888bac2ae32107da32776144504" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::mm1</definition>
        <argsstring></argsstring>
        <name>mm1</name>
        <qualifiedname>vrna_fc_s::mm1</qualifiedname>
        <briefdescription>
<para>Maximum matching matrix, reference struct 1 disallowed. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="368" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="368" bodyend="-1"/>
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      <memberdef kind="variable" id="structvrna__fc__s_1a54c0b979274b285a7e093ed54aa3252e" prot="public" static="no" mutable="no">
        <type>unsigned int *</type>
        <definition>unsigned int* vrna_fc_s::mm2</definition>
        <argsstring></argsstring>
        <name>mm2</name>
        <qualifiedname>vrna_fc_s::mm2</qualifiedname>
        <briefdescription>
<para>Maximum matching matrix, reference struct 2 disallowed. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="369" column="17" bodyfile="ViennaRNA/fold_compound.h" bodystart="369" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="user-defined">
      <header>Additional data fields for local folding</header>
      <description><para>These data fields are typically populated with meaningful data only if used in the context of local folding </para>
</description>
      <memberdef kind="variable" id="structvrna__fc__s_1adacbf7cdfb47d3072683ab509de735f6" prot="public" static="no" mutable="no">
        <type>int</type>
        <definition>int vrna_fc_s::window_size</definition>
        <argsstring></argsstring>
        <name>window_size</name>
        <qualifiedname>vrna_fc_s::window_size</qualifiedname>
        <briefdescription>
<para>window size for local folding sliding window approach </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="381" column="9" bodyfile="ViennaRNA/fold_compound.h" bodystart="381" bodyend="-1"/>
      </memberdef>
      <memberdef kind="variable" id="structvrna__fc__s_1a2ecb8ff5e21190936a8a146be7a251ff" prot="public" static="no" mutable="no">
        <type>char **</type>
        <definition>char** vrna_fc_s::ptype_local</definition>
        <argsstring></argsstring>
        <name>ptype_local</name>
        <qualifiedname>vrna_fc_s::ptype_local</qualifiedname>
        <briefdescription>
<para>Pair type array (for local folding). </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="382" column="9" bodyfile="ViennaRNA/fold_compound.h" bodystart="382" bodyend="-1"/>
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      <memberdef kind="variable" id="structvrna__fc__s_1ab9e9e3fd24c960c6e2390be1a070e4c5" prot="public" static="no" mutable="no">
        <type>vrna_zsc_dat_t</type>
        <definition>vrna_zsc_dat_t vrna_fc_s::zscore_data</definition>
        <argsstring></argsstring>
        <name>zscore_data</name>
        <qualifiedname>vrna_fc_s::zscore_data</qualifiedname>
        <briefdescription>
<para>Data structure with settings for z-score computations. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="384" column="19" bodyfile="ViennaRNA/fold_compound.h" bodystart="384" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="public-attrib">
      <memberdef kind="variable" id="structvrna__fc__s_1aad0e944111aa7280683876be90ebba87" prot="public" static="no" mutable="no">
        <type>union <ref refid="structvrna__fc__s" kindref="compound">vrna_fc_s</ref></type>
        <definition>union vrna_fc_s vrna_fc_s</definition>
        <argsstring></argsstring>
        <name></name>
        <qualifiedname>vrna_fc_s</qualifiedname>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/fold_compound.h" line="350" column="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>The most basic data structure required by many functions throughout the RNAlib. </para>
    </briefdescription>
    <detaileddescription>
<para><simplesect kind="note"><para>Please read the documentation of this data structure carefully! Some attributes are only available for specific types this data structure can adopt.</para>
</simplesect>
<simplesect kind="warning"><para>Reading/Writing from/to attributes that are not within the scope of the current type usually result in undefined behavior!</para>
</simplesect>
<simplesect kind="see"><para><ref refid="structvrna__fc__s_1a391bcf8ac5997784aaf780cdd251c464" kindref="member">vrna_fold_compound_t.type</ref>, <ref refid="group__fold__compound_1gab89fe9844031711d42c70d1b9277c0d5" kindref="member">vrna_fold_compound()</ref>, <ref refid="group__fold__compound_1gabbaffe56b1a37f6ed1a31e9e4f5613f1" kindref="member">vrna_fold_compound_comparative()</ref>, <ref refid="group__fold__compound_1ga576a077b418a9c3650e06f8e5d296fc2" kindref="member">vrna_fold_compound_free()</ref>, <ref refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447da7e264dd3cf2dc9b6448caabcb7763cd6" kindref="member">VRNA_FC_TYPE_SINGLE</ref>, <ref refid="group__fold__compound_1gga01a4ff86fa71deaaa5d1abbd95a1447dab821ce46ea3cf665be97df22a76f5023" kindref="member">VRNA_FC_TYPE_COMPARATIVE</ref></para>
</simplesect>
<xrefsect id="wrappers_1_wrappers000099"><xreftitle>SWIG Wrapper Notes</xreftitle><xrefdescription><para><parblock><para></para>
<para>This data structure is wrapped as class <computeroutput>fold_compound</computeroutput> with several related functions attached as methods.</para>
<para>A new <computeroutput>fold_compound</computeroutput> can be obtained by calling one of its constructors:<linebreak/>
<itemizedlist>
<listitem><para><computeroutput>fold_compound(seq)</computeroutput> - Initialize with a single sequence, or two concatenated sequences separated by an ampersand character <computeroutput>&amp;</computeroutput> (for cofolding)</para>
</listitem><listitem><para><computeroutput>fold_compound(aln)</computeroutput> - Initialize with a sequence alignment <emphasis>aln</emphasis> stored as a list of sequences (with gap characters).</para>
</listitem></itemizedlist>
</para>
<para>The resulting object has a list of attached methods which in most cases directly correspond to functions that mainly operate on the corresponding <computeroutput>C</computeroutput> data structure:<linebreak/>
<itemizedlist>
<listitem><para><computeroutput><ref refid="structvrna__fc__s_1a391bcf8ac5997784aaf780cdd251c464" kindref="member">type()</ref></computeroutput> - Get the type of the <emphasis>fold_compound</emphasis> (See <ref refid="group__fold__compound_1ga01a4ff86fa71deaaa5d1abbd95a1447d" kindref="member">vrna_fc_type_e</ref>)</para>
</listitem><listitem><para><computeroutput><ref refid="structvrna__fc__s_1a95fbfed770b858e50c766505dc4bf998" kindref="member">length()</ref></computeroutput> - Get the length of the <ref refid="structvrna__fc__s_1a87f6abcda89cfb7a486c97e1f5371525" kindref="member">sequence(s)</ref> or alignment stored within the <computeroutput>fold_compound</computeroutput>.</para>
</listitem></itemizedlist>
</para>
<para>See, e.g.  <verbatim>embed:rst:inline :py:class:`RNA.fold_compound` in the :doc:`/api_python`</verbatim>. </para>
</parblock></para>
</xrefdescription></xrefsect></para>
    </detaileddescription>
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          <edgelabel>probs_get</edgelabel>
          <edgelabel>prod_cb</edgelabel>
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    </listofallmembers>
  </compounddef>
</doxygen>
