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  <compounddef id="group__model__details" kind="group">
    <compoundname>model_details</compoundname>
    <title>Fine-tuning of the Implemented Models</title>
    <innerfile refid="model_8h">model.h</innerfile>
    <innerclass refid="structvrna__md__s" prot="public">vrna_md_s</innerclass>
    <sectiondef kind="typedef">
      <memberdef kind="typedef" id="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" prot="public" static="no">
        <type>struct <ref refid="structvrna__md__s" kindref="compound">vrna_md_s</ref></type>
        <definition>typedef struct vrna_md_s vrna_md_t</definition>
        <argsstring></argsstring>
        <name>vrna_md_t</name>
        <briefdescription>
<para>Typename for the model details data structure <ref refid="structvrna__md__s" kindref="compound">vrna_md_s</ref>. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="32" column="24" bodyfile="ViennaRNA/model.h" bodystart="32" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="var">
      <memberdef kind="variable" id="group__model__details_1gaf3cbac6ff5d706d6e414677841ddf94c" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double cv_fact</definition>
        <argsstring></argsstring>
        <name>cv_fact</name>
        <briefdescription>
<para>This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000016"><xreftitle>Deprecated</xreftitle><xrefdescription><para>See <ref refid="structvrna__md__s_1a62ebefb9d0643e5c4c8a2ec84a105ce6" kindref="member">vrna_md_t.cv_fact</ref>, and <ref refid="group__mfe__global_1ga5577af664e5b9056b44fa5df29e9befb" kindref="member">vrna_mfe()</ref> to avoid using global variables</para>
</xrefdescription></xrefsect></para>
<para>Default is 1. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/alifold.h" line="132" column="18" declfile="ViennaRNA/alifold.h" declline="132" declcolumn="18"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga502948a122a2af5b914355b1f3ea2f61" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double nc_fact</definition>
        <argsstring></argsstring>
        <name>nc_fact</name>
        <briefdescription>
<para>This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000017"><xreftitle>Deprecated</xreftitle><xrefdescription><para>See <ref refid="structvrna__md__s_1abcf568e6124bfcb2f847ff4eb0dfded6" kindref="member">vrna_md_t.nc_fact</ref>, and <ref refid="group__mfe__global_1ga5577af664e5b9056b44fa5df29e9befb" kindref="member">vrna_mfe()</ref> to avoid using global variables</para>
</xrefdescription></xrefsect></para>
<para>Default is 1. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/alifold.h" line="144" column="18" declfile="ViennaRNA/alifold.h" declline="144" declcolumn="18"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gab4b11c8d9c758430960896bc3fe82ead" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double temperature</definition>
        <argsstring></argsstring>
        <name>temperature</name>
        <briefdescription>
<para>Rescale energy parameters to a temperature in degC. </para>
        </briefdescription>
        <detaileddescription>
<para>Default is 37C. You have to call the update_..._params() functions after changing this parameter.</para>
<para><xrefsect id="deprecated_1_deprecated000089"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use <ref refid="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" kindref="member">vrna_md_defaults_temperature()</ref>, and <ref refid="group__model__details_1ga96b24a74437f9ba46c4e06343155bf46" kindref="member">vrna_md_defaults_temperature_get()</ref> to change, and read the global default temperature settings</para>
</xrefdescription></xrefsect></para>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" kindref="member">vrna_md_defaults_temperature()</ref>, <ref refid="group__model__details_1ga96b24a74437f9ba46c4e06343155bf46" kindref="member">vrna_md_defaults_temperature_get()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1078" column="16" declfile="ViennaRNA/model.h" declline="1078" declcolumn="16"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gad3b22044065acc6dee0af68931b52cfd" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double pf_scale</definition>
        <argsstring></argsstring>
        <name>pf_scale</name>
        <briefdescription>
<para>A scaling factor used by <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> to avoid overflows. </para>
        </briefdescription>
        <detaileddescription>
<para>Should be set to approximately <formula id="20">$exp{((-F/kT)/length)}$</formula>, where <formula id="21">$F$</formula> is an estimate for the ensemble free energy, for example the minimum free energy. You must call <ref refid="group__part__func__global__deprecated_1ga384e927890f9c034ff09fa66da102d28" kindref="member">update_pf_params()</ref> after changing this parameter.<linebreak/>
If pf_scale is -1 (the default) , an estimate will be provided automatically when computing partition functions, e.g. <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> The automatic estimate is usually insufficient for sequences more than a few hundred bases long. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1093" column="16" declfile="ViennaRNA/model.h" declline="1093" declcolumn="16"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int dangles</definition>
        <argsstring></argsstring>
        <name>dangles</name>
        <briefdescription>
<para>Switch the energy model for dangling end contributions (0, 1, 2, 3). </para>
        </briefdescription>
        <detaileddescription>
<para>If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref> these checks are neglected. If <ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref> is set to 2, all folding routines will follow this convention. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-axial stacking.<linebreak/>
If dangles = 3 co-axial stacking is explicitly included for adjacent helices in multiloops. The option affects only mfe folding and energy evaluation (<ref refid="group__mfe__global__deprecated_1gaadafcb0f140795ae62e5ca027e335a9b" kindref="member">fold()</ref> and <ref refid="group__eval__deprecated_1gaf93986cb3cb29770ec9cca69c9fab8cf" kindref="member">energy_of_structure()</ref>), as well as suboptimal folding (<ref refid="group__subopt__wuchty_1ga9913b3a58b8d315be3f4f7f4dbe3c481" kindref="member">subopt()</ref>) via re-evaluation of energies. Co-axial stacking with one intervening mismatch is not considered so far.</para>
<para>Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2 </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1117" column="13" declfile="ViennaRNA/model.h" declline="1117" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga4f6265bdf0ead7ff4628a360adbfd77e" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int tetra_loop</definition>
        <argsstring></argsstring>
        <name>tetra_loop</name>
        <briefdescription>
<para>Include special stabilizing energies for some tri-, tetra- and hexa-loops;. </para>
        </briefdescription>
        <detaileddescription>
<para>default is 1. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1125" column="13" declfile="ViennaRNA/model.h" declline="1125" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga097eccaabd6ae8b4fef83cccff85bb5d" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int noLonelyPairs</definition>
        <argsstring></argsstring>
        <name>noLonelyPairs</name>
        <briefdescription>
<para>Global switch to avoid/allow helices of length 1. </para>
        </briefdescription>
        <detaileddescription>
<para>Disallow all pairs which can only occur as lonely pairs (i.e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1135" column="13" declfile="ViennaRNA/model.h" declline="1135" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gabf380d09e4f1ab94fc6af57cf0ad5d32" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int noGU</definition>
        <argsstring></argsstring>
        <name>noGU</name>
        <briefdescription>
<para>Global switch to forbid/allow GU base pairs at all. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1141" column="13" declfile="ViennaRNA/model.h" declline="1141" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gaa8d1c7b92489179e1eafa562b7bdd259" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int no_closingGU</definition>
        <argsstring></argsstring>
        <name>no_closingGU</name>
        <briefdescription>
<para>GU allowed only inside stacks if set to 1. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1147" column="13" declfile="ViennaRNA/model.h" declline="1147" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int circ</definition>
        <argsstring></argsstring>
        <name>circ</name>
        <briefdescription>
<para>backward compatibility variable.. this does not effect anything </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1153" column="13" declfile="ViennaRNA/model.h" declline="1153" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga25f2bdcdf56e813d288845484a13d704" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int gquad</definition>
        <argsstring></argsstring>
        <name>gquad</name>
        <briefdescription>
<para>Allow G-quadruplex formation. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1159" column="13" declfile="ViennaRNA/model.h" declline="1159" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga6c5655c8b272e3e6cab74dd0f540294f" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int uniq_ML</definition>
        <argsstring></argsstring>
        <name>uniq_ML</name>
        <briefdescription>
<para>do ML decomposition uniquely (for subopt) </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1165" column="13" declfile="ViennaRNA/model.h" declline="1165" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int energy_set</definition>
        <argsstring></argsstring>
        <name>energy_set</name>
        <briefdescription>
<para>0 = BP; 1=any with GC; 2=any with AU-parameter </para>
        </briefdescription>
        <detaileddescription>
<para>If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A pairs B, C pairs D, etc. using either GC (1) or AU parameters (2); default is 0, you probably don&apos;t want to change it. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1175" column="13" declfile="ViennaRNA/model.h" declline="1175" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gad512b5dd4dbec60faccfe137bb474489" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int do_backtrack</definition>
        <argsstring></argsstring>
        <name>do_backtrack</name>
        <briefdescription>
<para>do backtracking, i.e. compute secondary structures or base pair probabilities </para>
        </briefdescription>
        <detaileddescription>
<para>If 0, do not calculate pair probabilities in <ref refid="group__part__func__global__deprecated_1gadc3db3d98742427e7001a7fd36ef28c2" kindref="member">pf_fold()</ref>; this is about twice as fast. Default is 1. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1184" column="13" declfile="ViennaRNA/model.h" declline="1184" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga83bdb43472a259c71e69fa9f70f420c3" prot="public" static="no" extern="yes" mutable="no">
        <type>char</type>
        <definition>char backtrack_type</definition>
        <argsstring></argsstring>
        <name>backtrack_type</name>
        <briefdescription>
<para>A backtrack array marker for <ref refid="group__inverse__fold_1ga7af026de55d4babad879f2c92559cbbc" kindref="member">inverse_fold()</ref>. </para>
        </briefdescription>
        <detaileddescription>
<para>If set to &apos;C&apos;: force (1,N) to be paired, &apos;M&apos; fold as if the sequence were inside a multiloop. Otherwise (&apos;F&apos;) the usual mfe structure is computed. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1194" column="14" declfile="ViennaRNA/model.h" declline="1194" declcolumn="14"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" prot="public" static="no" extern="yes" mutable="no">
        <type>char *</type>
        <definition>char* nonstandards</definition>
        <argsstring></argsstring>
        <name>nonstandards</name>
        <briefdescription>
<para>contains allowed non standard base pairs </para>
        </briefdescription>
        <detaileddescription>
<para>Lists additional base pairs that will be allowed to form in addition to GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking energy of 0. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1204" column="14" declfile="ViennaRNA/model.h" declline="1204" declcolumn="14"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga18df869af0d70101106458fc3f027806" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int max_bp_span</definition>
        <argsstring></argsstring>
        <name>max_bp_span</name>
        <briefdescription>
<para>Maximum allowed base pair span. </para>
        </briefdescription>
        <detaileddescription>
<para>A value of -1 indicates no restriction for distant base pairs. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1212" column="13" declfile="ViennaRNA/model.h" declline="1212" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gac408868ba00671cbc7d1d535105af045" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int oldAliEn</definition>
        <argsstring></argsstring>
        <name>oldAliEn</name>
        <briefdescription>
<para>use old alifold energies (with gaps) </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1218" column="13" declfile="ViennaRNA/model.h" declline="1218" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga0656afca1d2853f9ee6591172f5638de" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int ribo</definition>
        <argsstring></argsstring>
        <name>ribo</name>
        <briefdescription>
<para>use ribosum matrices </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1224" column="13" declfile="ViennaRNA/model.h" declline="1224" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gaf3cbac6ff5d706d6e414677841ddf94c" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double cv_fact</definition>
        <argsstring></argsstring>
        <name>cv_fact</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1227" column="16" declfile="ViennaRNA/model.h" declline="1227" declcolumn="16"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga502948a122a2af5b914355b1f3ea2f61" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double nc_fact</definition>
        <argsstring></argsstring>
        <name>nc_fact</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1230" column="16" declfile="ViennaRNA/model.h" declline="1230" declcolumn="16"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga80c3c5fd35e7479704cc91d2d0367743" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int logML</definition>
        <argsstring></argsstring>
        <name>logML</name>
        <briefdescription>
<para>if nonzero use logarithmic ML energy in energy_of_struct </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1234" column="13" declfile="ViennaRNA/model.h" declline="1234" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1ga59bc4fe917f2ad11376d083260e289da" prot="public" static="no" extern="yes" mutable="no">
        <type>double</type>
        <definition>double salt</definition>
        <argsstring></argsstring>
        <name>salt</name>
        <briefdescription>
<para>salt concentration </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1238" column="16" declfile="ViennaRNA/model.h" declline="1238" declcolumn="16"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gafd2b9a6a1d42a6bf2b8be99a4b44dc7e" prot="public" static="no" extern="yes" mutable="no">
        <type>int</type>
        <definition>int saltDPXInit</definition>
        <argsstring></argsstring>
        <name>saltDPXInit</name>
        <briefdescription>
<para>Salt correction for duplex initialization. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1242" column="13" declfile="ViennaRNA/model.h" declline="1242" declcolumn="13"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gabb3f00c97700606dd80705404911318a" prot="public" static="no" extern="yes" mutable="no">
        <type>float</type>
        <definition>float helical_rise</definition>
        <argsstring></argsstring>
        <name>helical_rise</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1245" column="15" declfile="ViennaRNA/model.h" declline="1245" declcolumn="15"/>
      </memberdef>
      <memberdef kind="variable" id="group__model__details_1gac1bcc01a720eba0abe6caa1bf97a8f7d" prot="public" static="no" extern="yes" mutable="no">
        <type>float</type>
        <definition>float backbone_length</definition>
        <argsstring></argsstring>
        <name>backbone_length</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1248" column="15" declfile="ViennaRNA/model.h" declline="1248" declcolumn="15"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__model__details_1ga8ac6ff84936282436f822644bf841f66" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_set_default</definition>
        <argsstring>(vrna_md_t *md)</argsstring>
        <name>vrna_md_set_default</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <briefdescription>
<para>Apply default model details to a provided <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> data structure. </para>
        </briefdescription>
        <detaileddescription>
<para>Use this function to initialize a <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> data structure with its default values</para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>md</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the data structure that is about to be initialized </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="343" column="1" declfile="ViennaRNA/model.h" declline="343" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga36ae40b8c3b82362f5798ad5b047b814" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_update</definition>
        <argsstring>(vrna_md_t *md)</argsstring>
        <name>vrna_md_update</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <briefdescription>
<para>Update the model details data structure. </para>
        </briefdescription>
        <detaileddescription>
<para>This function should be called after changing the <ref refid="structvrna__md__s_1a5eee4e3b468eb690d1407e0178dafb3f" kindref="member">vrna_md_t.energy_set</ref> attribute since it re-initializes base pairing related arrays within the <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> data structure. In particular, <ref refid="structvrna__md__s_1ab4da594c638707e212f64aadb54a7454" kindref="member">vrna_md_t.pair</ref>, <ref refid="structvrna__md__s_1a66136cf9abc8ff790ec0d33245d68fd5" kindref="member">vrna_md_t.alias</ref>, and <ref refid="structvrna__md__s_1ad082d0fea31e002b90cdfe5e6382f8b0" kindref="member">vrna_md_t.rtype</ref> are set to the values that correspond to the specified <ref refid="structvrna__md__s_1a5eee4e3b468eb690d1407e0178dafb3f" kindref="member">vrna_md_t.energy_set</ref> option</para>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="structvrna__md__s_1a5eee4e3b468eb690d1407e0178dafb3f" kindref="member">vrna_md_t.energy_set</ref>, <ref refid="structvrna__md__s_1ab4da594c638707e212f64aadb54a7454" kindref="member">vrna_md_t.pair</ref>, <ref refid="structvrna__md__s_1ad082d0fea31e002b90cdfe5e6382f8b0" kindref="member">vrna_md_t.rtype</ref>, <ref refid="structvrna__md__s_1a66136cf9abc8ff790ec0d33245d68fd5" kindref="member">vrna_md_t.alias</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="359" column="1" declfile="ViennaRNA/model.h" declline="359" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaa7c753fefc98866d5dc0dae3e6bd4486" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
        <definition>vrna_md_t * vrna_md_copy</definition>
        <argsstring>(vrna_md_t *md_to, const vrna_md_t *md_from)</argsstring>
        <name>vrna_md_copy</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md_to</declname>
        </param>
        <param>
          <type>const <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md_from</declname>
        </param>
        <briefdescription>
<para>Copy/Clone a <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> model. </para>
        </briefdescription>
        <detaileddescription>
<para>Use this function to clone a given model either inplace (target container <computeroutput>md_to</computeroutput> given) or create a copy by cloning the source model and returning it (<computeroutput>md_to</computeroutput> == NULL).</para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>md_to</parametername>
</parameternamelist>
<parameterdescription>
<para>The model to be overwritten (if non-NULL and <computeroutput>md_to</computeroutput> != <computeroutput>md_from</computeroutput>) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>md_from</parametername>
</parameternamelist>
<parameterdescription>
<para>The model to copy (if non-NULL) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>A pointer to the copy model (or NULL if <computeroutput>md_from</computeroutput> == NULL) </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="373" column="1" declfile="ViennaRNA/model.h" declline="373" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga2207e3b40295825655c629421fe8f349" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * vrna_md_option_string</definition>
        <argsstring>(vrna_md_t *md)</argsstring>
        <name>vrna_md_option_string</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <briefdescription>
<para>Get a corresponding commandline parameter string of the options in a <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="note"><para>This function is not threadsafe! </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="383" column="1" declfile="ViennaRNA/model.h" declline="383" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga87398a419421bf5d90f246382e6ed70c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_set_nonstandards</definition>
        <argsstring>(vrna_md_t *md, const char *ns_bases)</argsstring>
        <name>vrna_md_set_nonstandards</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <param>
          <type>const char *</type>
          <declname>ns_bases</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="387" column="1" declfile="ViennaRNA/model.h" declline="387" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga70834424cf804d149937de89f80ceb45" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_reset</definition>
        <argsstring>(vrna_md_t *md_p)</argsstring>
        <name>vrna_md_defaults_reset</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md_p</declname>
        </param>
        <briefdescription>
<para>Reset the global default model details to a specific set of parameters, or their initial values. </para>
        </briefdescription>
        <detaileddescription>
<para>This function resets the global default model details to their initial values, i.e. as specified by the ViennaRNA Package release, upon passing NULL as argument. Alternatively it resets them according to a set of provided parameters.</para>
<para><simplesect kind="note"><para>The global default parameters affect all function calls of RNAlib where model details are not explicitly provided. Hence, any change of them is not considered threadsafe</para>
</simplesect>
<simplesect kind="warning"><para>This function first resets the global default settings to factory defaults, and only then applies user provided settings (if any). User settings that do not meet specifications are skipped.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>md_p</parametername>
</parameternamelist>
<parameterdescription>
<para>A set of model details to use as global default (if NULL is passed, factory defaults are restored) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="411" column="1" declfile="ViennaRNA/model.h" declline="411" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_temperature</definition>
        <argsstring>(double T)</argsstring>
        <name>vrna_md_defaults_temperature</name>
        <param>
          <type>double</type>
          <declname>T</declname>
        </param>
        <briefdescription>
<para>Set default temperature for energy evaluation of loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gaf47f9850b3b4763479f7a7e7a15648a2" kindref="member">VRNA_MODEL_DEFAULT_TEMPERATURE</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>T</parametername>
</parameternamelist>
<parameterdescription>
<para>Temperature in centigrade </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="422" column="1" declfile="ViennaRNA/model.h" declline="422" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga96b24a74437f9ba46c4e06343155bf46" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_temperature_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_temperature_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default temperature for energy evaluation of loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" kindref="member">vrna_md_defaults_temperature()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gaf47f9850b3b4763479f7a7e7a15648a2" kindref="member">VRNA_MODEL_DEFAULT_TEMPERATURE</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for temperature in centigrade </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="433" column="1" declfile="ViennaRNA/model.h" declline="433" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gae984567db36c3f9b8731ecc917abf3a2" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_betaScale</definition>
        <argsstring>(double b)</argsstring>
        <name>vrna_md_defaults_betaScale</name>
        <param>
          <type>double</type>
          <declname>b</declname>
        </param>
        <briefdescription>
<para>Set default scaling factor of thermodynamic temperature in Boltzmann factors. </para>
        </briefdescription>
        <detaileddescription>
<para>Bolzmann factors are then computed as <formula id="19">$ exp(-E / (b \cdot kT))$</formula>.</para>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga383d3ac8d08c3b6221754b50871c1200" kindref="member">VRNA_MODEL_DEFAULT_BETA_SCALE</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>b</parametername>
</parameternamelist>
<parameterdescription>
<para>The scaling factor, default is 1.0 </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="446" column="1" declfile="ViennaRNA/model.h" declline="446" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gabb8780f5410c52f970d75b044059bd09" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_betaScale_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_betaScale_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default scaling factor of thermodynamic temperature in Boltzmann factors. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gae984567db36c3f9b8731ecc917abf3a2" kindref="member">vrna_md_defaults_betaScale()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga383d3ac8d08c3b6221754b50871c1200" kindref="member">VRNA_MODEL_DEFAULT_BETA_SCALE</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default thermodynamic temperature scaling factor </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="457" column="1" declfile="ViennaRNA/model.h" declline="457" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga8524ad32519fd3a8a2055fd3a2723cad" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_pf_smooth</definition>
        <argsstring>(int s)</argsstring>
        <name>vrna_md_defaults_pf_smooth</name>
        <param>
          <type>int</type>
          <declname>s</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="461" column="1" declfile="ViennaRNA/model.h" declline="461" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gae3fdc588bf45c8432c532066d6167c51" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_pf_smooth_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_pf_smooth_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="465" column="1" declfile="ViennaRNA/model.h" declline="465" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gac76a5374def8e5e4e644ff6e4cc72dee" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_dangles</definition>
        <argsstring>(int d)</argsstring>
        <name>vrna_md_defaults_dangles</name>
        <param>
          <type>int</type>
          <declname>d</declname>
        </param>
        <briefdescription>
<para>Set default dangle model for structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga2aa7bc2cae774b83a5c468f824c27a42" kindref="member">VRNA_MODEL_DEFAULT_DANGLES</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>d</parametername>
</parameternamelist>
<parameterdescription>
<para>The dangle model </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="476" column="1" declfile="ViennaRNA/model.h" declline="476" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga67ca06f95ae133778c79a4493c9817b8" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_dangles_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_dangles_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default dangle model for structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gac76a5374def8e5e4e644ff6e4cc72dee" kindref="member">vrna_md_defaults_dangles()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga2aa7bc2cae774b83a5c468f824c27a42" kindref="member">VRNA_MODEL_DEFAULT_DANGLES</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for the dangle model </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="487" column="1" declfile="ViennaRNA/model.h" declline="487" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gafff6449a02744add0308e653230c15fc" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_special_hp</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_special_hp</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gabd1ab224e1048defd45c165ed7d1c108" kindref="member">VRNA_MODEL_DEFAULT_SPECIAL_HP</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="498" column="1" declfile="ViennaRNA/model.h" declline="498" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga1d68a6efdaa1253cc63fd9cd06452559" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_special_hp_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_special_hp_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gafff6449a02744add0308e653230c15fc" kindref="member">vrna_md_defaults_special_hp()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gabd1ab224e1048defd45c165ed7d1c108" kindref="member">VRNA_MODEL_DEFAULT_SPECIAL_HP</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for the treatment of special hairpin loops </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="509" column="1" declfile="ViennaRNA/model.h" declline="509" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga2f88ffc393ac9d7987849c965fd29ea8" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_noLP</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_noLP</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for prediction of canonical secondary structures. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gab72462726dd60ed0d43339bbf7ee08ad" kindref="member">VRNA_MODEL_DEFAULT_NO_LP</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="520" column="1" declfile="ViennaRNA/model.h" declline="520" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga934344888fbacaed538bbbfe910f2aa6" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_noLP_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_noLP_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for prediction of canonical secondary structures. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga2f88ffc393ac9d7987849c965fd29ea8" kindref="member">vrna_md_defaults_noLP()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gab72462726dd60ed0d43339bbf7ee08ad" kindref="member">VRNA_MODEL_DEFAULT_NO_LP</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for predicting canonical secondary structures </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="531" column="1" declfile="ViennaRNA/model.h" declline="531" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga98218f85c7a957a1d1ddf4627fdf5a39" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_noGU</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_noGU</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for treatment of G-U wobble pairs. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga34702f7d14d38b877ba8e475281e97e2" kindref="member">VRNA_MODEL_DEFAULT_NO_GU</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="542" column="1" declfile="ViennaRNA/model.h" declline="542" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga5faa7d4e536d7fe36ec25428c0cf2563" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_noGU_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_noGU_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for treatment of G-U wobble pairs. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga98218f85c7a957a1d1ddf4627fdf5a39" kindref="member">vrna_md_defaults_noGU()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga34702f7d14d38b877ba8e475281e97e2" kindref="member">VRNA_MODEL_DEFAULT_NO_GU</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for treatment of G-U wobble pairs </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="553" column="1" declfile="ViennaRNA/model.h" declline="553" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gade5b9951d71ca2fb357a4e6c0c18ccd1" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_noGUclosure</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_noGUclosure</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for G-U pairs as closing pair for loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga5308de46faaca4b9fd16045864901ee7" kindref="member">VRNA_MODEL_DEFAULT_NO_GU_CLOSURE</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="564" column="1" declfile="ViennaRNA/model.h" declline="564" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga4f7fdad083243a5348d63320ddaa70f3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_noGUclosure_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_noGUclosure_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for G-U pairs as closing pair for loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gade5b9951d71ca2fb357a4e6c0c18ccd1" kindref="member">vrna_md_defaults_noGUclosure()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga5308de46faaca4b9fd16045864901ee7" kindref="member">VRNA_MODEL_DEFAULT_NO_GU_CLOSURE</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for treatment of G-U pairs closing a loop </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="575" column="1" declfile="ViennaRNA/model.h" declline="575" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga3de50a73455d88c3957386933b8e1f90" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_logML</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_logML</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior recomputing free energies of multi-branch loops using a logarithmic model. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga938f68463e84fe060aa6502f428a517d" kindref="member">VRNA_MODEL_DEFAULT_LOG_ML</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="586" column="1" declfile="ViennaRNA/model.h" declline="586" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga93f04e070d529c5d0bb87c9681f6ad29" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_logML_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_logML_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior recomputing free energies of multi-branch loops using a logarithmic model. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga3de50a73455d88c3957386933b8e1f90" kindref="member">vrna_md_defaults_logML()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga938f68463e84fe060aa6502f428a517d" kindref="member">VRNA_MODEL_DEFAULT_LOG_ML</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for logarithmic model in multi-branch loop free energy evaluation </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="597" column="1" declfile="ViennaRNA/model.h" declline="597" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga4e1deb3e91a8a99e5c6dd905a5eb0186" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_circ</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_circ</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior whether input sequences are circularized. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga22059033db7bcd875c51fec32425490a" kindref="member">VRNA_MODEL_DEFAULT_CIRC</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="608" column="1" declfile="ViennaRNA/model.h" declline="608" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gad3a7e58de344ad93a08925f58f94f6fb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_circ_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_circ_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior whether input sequences are circularized. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga4e1deb3e91a8a99e5c6dd905a5eb0186" kindref="member">vrna_md_defaults_circ()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga22059033db7bcd875c51fec32425490a" kindref="member">VRNA_MODEL_DEFAULT_CIRC</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for treating input sequences as circular </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="619" column="1" declfile="ViennaRNA/model.h" declline="619" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gae36c04033105fc519e040063341e6f4b" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_circ_penalty</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_circ_penalty</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for fully unpaired circular RNA penalty. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para>vrna_E_exterior_loop(), <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, #VRNA_MODEL_DEFAULT_CIRC_PENALTY</para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="630" column="1" declfile="ViennaRNA/model.h" declline="630" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gadd7f2da829239856a5a14f6c43d26921" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_circ_penalty_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_circ_penalty_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for fully unpaired circular RNA penalty. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gae36c04033105fc519e040063341e6f4b" kindref="member">vrna_md_defaults_circ_penalty()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga22059033db7bcd875c51fec32425490a" kindref="member">VRNA_MODEL_DEFAULT_CIRC</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for adding an entropic penalty for unpaired circular RNA ring </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="641" column="1" declfile="ViennaRNA/model.h" declline="641" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga0685ca2aeb39af76f2421fc308163dce" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_gquad</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_gquad</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for treatment of G-Quadruplexes. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga793ed812e86f43799b14b2deee917f23" kindref="member">VRNA_MODEL_DEFAULT_GQUAD</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="652" column="1" declfile="ViennaRNA/model.h" declline="652" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gae645b8612f879eb38b45244fa9eddb9e" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_gquad_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_gquad_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for treatment of G-Quadruplexes. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga0685ca2aeb39af76f2421fc308163dce" kindref="member">vrna_md_defaults_gquad()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga793ed812e86f43799b14b2deee917f23" kindref="member">VRNA_MODEL_DEFAULT_GQUAD</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for treatment of G-Quadruplexes </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="663" column="1" declfile="ViennaRNA/model.h" declline="663" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga59b944f61c5d2babec2d4c48c820de67" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_uniq_ML</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_uniq_ML</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for creating additional matrix for unique multi-branch loop prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="note"><para>Activating this option usually results in higher memory consumption!</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga63f6006a02ba2d89148441f406c309e7" kindref="member">VRNA_MODEL_DEFAULT_UNIQ_ML</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="676" column="1" declfile="ViennaRNA/model.h" declline="676" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gab48e70fd024bf838404bcbcca0c874a0" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_uniq_ML_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_uniq_ML_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for creating additional matrix for unique multi-branch loop prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga59b944f61c5d2babec2d4c48c820de67" kindref="member">vrna_md_defaults_uniq_ML()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga63f6006a02ba2d89148441f406c309e7" kindref="member">VRNA_MODEL_DEFAULT_UNIQ_ML</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for creating additional matrices for unique multi-branch loop prediction </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="687" column="1" declfile="ViennaRNA/model.h" declline="687" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga8dd29c55787a4576277e1907e92d810c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_energy_set</definition>
        <argsstring>(int e)</argsstring>
        <name>vrna_md_defaults_energy_set</name>
        <param>
          <type>int</type>
          <declname>e</declname>
        </param>
        <briefdescription>
<para>Set default energy set. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga6fcf6b2d0f89256cdbd166486c9b6e1e" kindref="member">VRNA_MODEL_DEFAULT_ENERGY_SET</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>e</parametername>
</parameternamelist>
<parameterdescription>
<para>Energy set (0, 1, 2, 3) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="698" column="1" declfile="ViennaRNA/model.h" declline="698" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga017ed6afb1cba2b7f242412cab618b53" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_energy_set_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_energy_set_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default energy set. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga8dd29c55787a4576277e1907e92d810c" kindref="member">vrna_md_defaults_energy_set()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga6fcf6b2d0f89256cdbd166486c9b6e1e" kindref="member">VRNA_MODEL_DEFAULT_ENERGY_SET</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for the energy set </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="709" column="1" declfile="ViennaRNA/model.h" declline="709" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga978c468b2fe96a70d5191e3dd17d5599" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_backtrack</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_backtrack</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for whether to backtrack secondary structures. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga3fda8006ab84baf817bd8e5ccbc6bb35" kindref="member">VRNA_MODEL_DEFAULT_BACKTRACK</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="720" column="1" declfile="ViennaRNA/model.h" declline="720" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga90da1156e6883ddd68527c2830706648" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_backtrack_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_backtrack_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for whether to backtrack secondary structures. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga978c468b2fe96a70d5191e3dd17d5599" kindref="member">vrna_md_defaults_backtrack()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga3fda8006ab84baf817bd8e5ccbc6bb35" kindref="member">VRNA_MODEL_DEFAULT_BACKTRACK</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for backtracking structures </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="731" column="1" declfile="ViennaRNA/model.h" declline="731" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga68305274de96b56b7799575e222560d8" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_backtrack_type</definition>
        <argsstring>(char t)</argsstring>
        <name>vrna_md_defaults_backtrack_type</name>
        <param>
          <type>char</type>
          <declname>t</declname>
        </param>
        <briefdescription>
<para>Set default backtrack type, i.e. which DP matrix is used. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gad0e81fcaca53c4a826c68e0796de2afb" kindref="member">VRNA_MODEL_DEFAULT_BACKTRACK_TYPE</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>t</parametername>
</parameternamelist>
<parameterdescription>
<para>The type (&apos;F&apos;, &apos;C&apos;, or &apos;M&apos;) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="742" column="1" declfile="ViennaRNA/model.h" declline="742" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga1425b4ebd0e034dead66d79becd64143" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char</type>
        <definition>char vrna_md_defaults_backtrack_type_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_backtrack_type_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default backtrack type, i.e. which DP matrix is used. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga68305274de96b56b7799575e222560d8" kindref="member">vrna_md_defaults_backtrack_type()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gad0e81fcaca53c4a826c68e0796de2afb" kindref="member">VRNA_MODEL_DEFAULT_BACKTRACK_TYPE</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings that specify which DP matrix is used for backtracking </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="753" column="1" declfile="ViennaRNA/model.h" declline="753" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaf1b5db10f1f476767f9a95f8a78e3132" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_compute_bpp</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_compute_bpp</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set the default behavior for whether to compute base pair probabilities after partition function computation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga1d6cd5051940b126c248147c011bac6c" kindref="member">VRNA_MODEL_DEFAULT_COMPUTE_BPP</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="764" column="1" declfile="ViennaRNA/model.h" declline="764" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaa3a537e61fbe0518673bf9f73fd820f3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_compute_bpp_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_compute_bpp_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get the default behavior for whether to compute base pair probabilities after partition function computation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gaf1b5db10f1f476767f9a95f8a78e3132" kindref="member">vrna_md_defaults_compute_bpp()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga1d6cd5051940b126c248147c011bac6c" kindref="member">VRNA_MODEL_DEFAULT_COMPUTE_BPP</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings that specify whether base pair probabilities are computed together with partition function </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="775" column="1" declfile="ViennaRNA/model.h" declline="775" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga4c4bc962f09b4480cb8499f1cf8ae4ec" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_max_bp_span</definition>
        <argsstring>(int span)</argsstring>
        <name>vrna_md_defaults_max_bp_span</name>
        <param>
          <type>int</type>
          <declname>span</declname>
        </param>
        <briefdescription>
<para>Set default maximal base pair span. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga7cb6f4ae8fdebff6746a4410814f2977" kindref="member">VRNA_MODEL_DEFAULT_MAX_BP_SPAN</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>span</parametername>
</parameternamelist>
<parameterdescription>
<para>Maximal base pair span </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="786" column="1" declfile="ViennaRNA/model.h" declline="786" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaa60f989e062fecd4d4bac89c1883da85" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_max_bp_span_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_max_bp_span_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default maximal base pair span. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga4c4bc962f09b4480cb8499f1cf8ae4ec" kindref="member">vrna_md_defaults_max_bp_span()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga7cb6f4ae8fdebff6746a4410814f2977" kindref="member">VRNA_MODEL_DEFAULT_MAX_BP_SPAN</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for maximum base pair span </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="797" column="1" declfile="ViennaRNA/model.h" declline="797" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gac152f1e78c1058a10261022c8dfda0f7" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_min_loop_size</definition>
        <argsstring>(int size)</argsstring>
        <name>vrna_md_defaults_min_loop_size</name>
        <param>
          <type>int</type>
          <declname>size</declname>
        </param>
        <briefdescription>
<para>Set default minimal loop size. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="constants_8h_1ae646250fd59311356c7e5722a81c3a96" kindref="member">TURN</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>size</parametername>
</parameternamelist>
<parameterdescription>
<para>Minimal size, i.e. number of unpaired nucleotides for a hairpin loop </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="808" column="1" declfile="ViennaRNA/model.h" declline="808" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga5cc691174a75c652807dc361b617632a" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_min_loop_size_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_min_loop_size_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default minimal loop size. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gac152f1e78c1058a10261022c8dfda0f7" kindref="member">vrna_md_defaults_min_loop_size()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="constants_8h_1ae646250fd59311356c7e5722a81c3a96" kindref="member">TURN</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for minimal size of hairpin loops </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="819" column="1" declfile="ViennaRNA/model.h" declline="819" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga7b802ce0e8c3181bf5cb580de6d5b26a" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_window_size</definition>
        <argsstring>(int size)</argsstring>
        <name>vrna_md_defaults_window_size</name>
        <param>
          <type>int</type>
          <declname>size</declname>
        </param>
        <briefdescription>
<para>Set default window size for sliding window structure prediction approaches. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga8de04a9cb57e811e313b0f9f207f6bdb" kindref="member">VRNA_MODEL_DEFAULT_WINDOW_SIZE</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>size</parametername>
</parameternamelist>
<parameterdescription>
<para>The size of the sliding window </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="830" column="1" declfile="ViennaRNA/model.h" declline="830" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga670146a9aa3ba77f4d422d60b7c30ac9" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_window_size_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_window_size_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default window size for sliding window structure prediction approaches. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga7b802ce0e8c3181bf5cb580de6d5b26a" kindref="member">vrna_md_defaults_window_size()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga8de04a9cb57e811e313b0f9f207f6bdb" kindref="member">VRNA_MODEL_DEFAULT_WINDOW_SIZE</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for the size of the sliding window </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="841" column="1" declfile="ViennaRNA/model.h" declline="841" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga41521d5b9fb7e0f31e7ea73f5792afab" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_oldAliEn</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_oldAliEn</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for whether to use old energy model for comparative structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="note"><para>This option is outdated. Activating the old energy model usually results in worse consensus structure predictions.</para>
</simplesect>
<simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga2a5bbfc1edf33077e39466d2d9807115" kindref="member">VRNA_MODEL_DEFAULT_ALI_OLD_EN</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="855" column="1" declfile="ViennaRNA/model.h" declline="855" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga2374492b5019df88022fe4c05f0f3630" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_oldAliEn_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_oldAliEn_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for whether to use old energy model for comparative structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga41521d5b9fb7e0f31e7ea73f5792afab" kindref="member">vrna_md_defaults_oldAliEn()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga2a5bbfc1edf33077e39466d2d9807115" kindref="member">VRNA_MODEL_DEFAULT_ALI_OLD_EN</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for using old energy model for comparative structure prediction </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="866" column="1" declfile="ViennaRNA/model.h" declline="866" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga937c45e1d06fd6168730a9b08d130be3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_ribo</definition>
        <argsstring>(int flag)</argsstring>
        <name>vrna_md_defaults_ribo</name>
        <param>
          <type>int</type>
          <declname>flag</declname>
        </param>
        <briefdescription>
<para>Set default behavior for whether to use Ribosum Scoring in comparative structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga64b3ab65a9ca42d4ad1d05e193083147" kindref="member">VRNA_MODEL_DEFAULT_ALI_RIBO</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>flag</parametername>
</parameternamelist>
<parameterdescription>
<para>On/Off switch (0 = OFF, else = ON) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="877" column="1" declfile="ViennaRNA/model.h" declline="877" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga169027f0c0561ea7d87b655e4b336bfc" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_ribo_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_ribo_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get default behavior for whether to use Ribosum Scoring in comparative structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga937c45e1d06fd6168730a9b08d130be3" kindref="member">vrna_md_defaults_ribo()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga64b3ab65a9ca42d4ad1d05e193083147" kindref="member">VRNA_MODEL_DEFAULT_ALI_RIBO</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for using Ribosum scoring in comparative structure prediction </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="888" column="1" declfile="ViennaRNA/model.h" declline="888" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gad3a3f40baafd91a6ce80a91a68e20053" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_cv_fact</definition>
        <argsstring>(double factor)</argsstring>
        <name>vrna_md_defaults_cv_fact</name>
        <param>
          <type>double</type>
          <declname>factor</declname>
        </param>
        <briefdescription>
<para>Set the default co-variance scaling factor used in comparative structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gaaaf3d73d6abc18d3889676952bfedb96" kindref="member">VRNA_MODEL_DEFAULT_ALI_CV_FACT</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>factor</parametername>
</parameternamelist>
<parameterdescription>
<para>The co-variance factor </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="899" column="1" declfile="ViennaRNA/model.h" declline="899" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gae59c68393807217b0a2497adb64d3ee3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_cv_fact_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_cv_fact_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get the default co-variance scaling factor used in comparative structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gad3a3f40baafd91a6ce80a91a68e20053" kindref="member">vrna_md_defaults_cv_fact()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1gaaaf3d73d6abc18d3889676952bfedb96" kindref="member">VRNA_MODEL_DEFAULT_ALI_CV_FACT</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings for the co-variance factor </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="910" column="1" declfile="ViennaRNA/model.h" declline="910" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gac35e596c850dce3ad55c49119fd7d471" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_nc_fact</definition>
        <argsstring>(double factor)</argsstring>
        <name>vrna_md_defaults_nc_fact</name>
        <param>
          <type>double</type>
          <declname>factor</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga8f774daaafec28160c1ca5d09f2cbdba" kindref="member">VRNA_MODEL_DEFAULT_ALI_NC_FACT</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>factor</parametername>
</parameternamelist>
<parameterdescription>
<para></para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="921" column="1" declfile="ViennaRNA/model.h" declline="921" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga7ac759eaa7159bf5f022745f5da59508" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_nc_fact_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_nc_fact_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1gac35e596c850dce3ad55c49119fd7d471" kindref="member">vrna_md_defaults_nc_fact()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>, <ref refid="group__model__details_1ga8f774daaafec28160c1ca5d09f2cbdba" kindref="member">VRNA_MODEL_DEFAULT_ALI_NC_FACT</ref></para>
</simplesect>
<simplesect kind="return"><para></para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="932" column="1" declfile="ViennaRNA/model.h" declline="932" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga3f73d3029d3d0025d4cc311510cd95a3" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_sfact</definition>
        <argsstring>(double factor)</argsstring>
        <name>vrna_md_defaults_sfact</name>
        <param>
          <type>double</type>
          <declname>factor</declname>
        </param>
        <briefdescription>
<para>Set the default scaling factor used to avoid under-/overflows in partition function computation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>factor</parametername>
</parameternamelist>
<parameterdescription>
<para>The scaling factor (default: 1.07) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="943" column="1" declfile="ViennaRNA/model.h" declline="943" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gab2df6aab954b63fd3592d18e90285dae" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_sfact_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_sfact_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get the default scaling factor used to avoid under-/overflows in partition function computation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__model__details_1ga3f73d3029d3d0025d4cc311510cd95a3" kindref="member">vrna_md_defaults_sfact()</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref>, <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref></para>
</simplesect>
<simplesect kind="return"><para>The global default settings of the scaling factor </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="954" column="1" declfile="ViennaRNA/model.h" declline="954" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gabfb475999a35e9af42b21326a9edca12" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_salt</definition>
        <argsstring>(double salt)</argsstring>
        <name>vrna_md_defaults_salt</name>
        <param>
          <type>double</type>
          <declname>salt</declname>
        </param>
        <briefdescription>
<para>Set the default salt concentration. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>salt</parametername>
</parameternamelist>
<parameterdescription>
<para>The sodium concentration in M (default: 1.021) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="963" column="1" declfile="ViennaRNA/model.h" declline="963" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga28eb9dd2f11828da7cc25b93884c965f" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_salt_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_salt_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get the default salt concentration. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="return"><para>The default salt concentration </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="971" column="1" declfile="ViennaRNA/model.h" declline="971" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga807b1615aea57f61cc0a269065beface" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_saltMLLower</definition>
        <argsstring>(int lower)</argsstring>
        <name>vrna_md_defaults_saltMLLower</name>
        <param>
          <type>int</type>
          <declname>lower</declname>
        </param>
        <briefdescription>
<para>Set the default multiloop size lower bound for loop salt correciton linear fitting. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>lower</parametername>
</parameternamelist>
<parameterdescription>
<para>Size lower bound (number of backbone in loop) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="980" column="1" declfile="ViennaRNA/model.h" declline="980" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga0813eb58f9382ae92642016960a4a781" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_saltMLLower_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_saltMLLower_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get the default multiloop size lower bound for loop salt correciton linear fitting. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="return"><para>The default lower bound </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="988" column="1" declfile="ViennaRNA/model.h" declline="988" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaf4d0ae6115687f13d4ccabcd3b45ad7c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_saltMLUpper</definition>
        <argsstring>(int upper)</argsstring>
        <name>vrna_md_defaults_saltMLUpper</name>
        <param>
          <type>int</type>
          <declname>upper</declname>
        </param>
        <briefdescription>
<para>Set the default multiloop size upper bound for loop salt correciton linear fitting. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>upper</parametername>
</parameternamelist>
<parameterdescription>
<para>Size Upper bound (number of backbone in loop) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="997" column="1" declfile="ViennaRNA/model.h" declline="997" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga28bc6652930e82ca1b105e419f6f4595" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_saltMLUpper_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_saltMLUpper_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get the default multiloop size upper bound for loop salt correciton linear fitting. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="return"><para>The default upper bound </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1005" column="1" declfile="ViennaRNA/model.h" declline="1005" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaaa7cca6b6a021221d56a7ee3b2b9b10c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_saltDPXInit</definition>
        <argsstring>(int value)</argsstring>
        <name>vrna_md_defaults_saltDPXInit</name>
        <param>
          <type>int</type>
          <declname>value</declname>
        </param>
        <briefdescription>
<para>Set user-provided salt correciton for duplex initialization If value is 99999 the default value from fitting is used. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>value</parametername>
</parameternamelist>
<parameterdescription>
<para>The value of salt correction for duplex initialization (in dcal/mol) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1015" column="1" declfile="ViennaRNA/model.h" declline="1015" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga02e0db8bf2345c12c28913af1a92186c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_md_defaults_saltDPXInit_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_saltDPXInit_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Get user-provided salt correciton for duplex initialization If value is 99999 the default value from fitting is used. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="return"><para>The user-provided salt correction for duplex initialization </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1025" column="1" declfile="ViennaRNA/model.h" declline="1025" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gab33bd5d2d3170e2e36ab3d7c81f4b35f" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_saltDPXInitFact</definition>
        <argsstring>(float value)</argsstring>
        <name>vrna_md_defaults_saltDPXInitFact</name>
        <param>
          <type>float</type>
          <declname>value</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1029" column="1" declfile="ViennaRNA/model.h" declline="1029" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga8a11417e5b8683e973effa4d874b0d68" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_md_defaults_saltDPXInitFact_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_saltDPXInitFact_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1033" column="1" declfile="ViennaRNA/model.h" declline="1033" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gafdbc3fc166c2d72df0ed2609a7ec6069" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_helical_rise</definition>
        <argsstring>(float value)</argsstring>
        <name>vrna_md_defaults_helical_rise</name>
        <param>
          <type>float</type>
          <declname>value</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1037" column="1" declfile="ViennaRNA/model.h" declline="1037" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gab9bb1dfeeb4aea4644b34d332cb5ec53" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_md_defaults_helical_rise_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_helical_rise_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1041" column="1" declfile="ViennaRNA/model.h" declline="1041" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gad7cc34b70d275f5c7211dd2aa62f6c3c" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_backbone_length</definition>
        <argsstring>(float value)</argsstring>
        <name>vrna_md_defaults_backbone_length</name>
        <param>
          <type>float</type>
          <declname>value</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1045" column="1" declfile="ViennaRNA/model.h" declline="1045" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gacdafdf6d361ee6a9abb46622986c9016" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>float</type>
        <definition>float vrna_md_defaults_backbone_length_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_backbone_length_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1049" column="1" declfile="ViennaRNA/model.h" declline="1049" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaa9e920d3277fdbd25a240db9a7c435cc" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_md_defaults_circ_alpha0</definition>
        <argsstring>(double a0)</argsstring>
        <name>vrna_md_defaults_circ_alpha0</name>
        <param>
          <type>double</type>
          <declname>a0</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1053" column="1" declfile="ViennaRNA/model.h" declline="1053" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1ga53ce984830640c940f101e0cb2077ba0" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_md_defaults_circ_alpha0_get</definition>
        <argsstring>(void)</argsstring>
        <name>vrna_md_defaults_circ_alpha0_get</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1057" column="1" declfile="ViennaRNA/model.h" declline="1057" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gabad896c3650d420f3f3ddefc69e2bceb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void set_model_details</definition>
        <argsstring>(vrna_md_t *md)</argsstring>
        <name>set_model_details</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <briefdescription>
<para>Set default model details. </para>
        </briefdescription>
        <detaileddescription>
<para>Use this function if you wish to initialize a <ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> data structure with its default values, i.e. the global model settings as provided by the deprecated global variables.</para>
<para><xrefsect id="deprecated_1_deprecated000090"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This function will vanish as soon as backward compatibility of RNAlib is dropped (expected in version 3). Use <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> instead!</para>
</xrefdescription></xrefsect></para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>md</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the data structure that is about to be initialized </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1266" column="1" declfile="ViennaRNA/model.h" declline="1266" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__model__details_1gaff4caf2154e6f189a7c09008cefa67a8" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>char *</type>
        <definition>char * option_string</definition>
        <argsstring>(void)</argsstring>
        <name>option_string</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="1270" column="1" declfile="ViennaRNA/model.h" declline="1270" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="define">
      <memberdef kind="define" id="group__model__details_1gad554b4852cd5fec35025db8edbbba3cd" prot="public" static="no">
        <name>NBASES</name>
        <initializer>8</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="28" column="9" bodyfile="ViennaRNA/model.h" bodystart="28" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1gaf47f9850b3b4763479f7a7e7a15648a2" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_TEMPERATURE</name>
        <initializer>37.0</initializer>
        <briefdescription>
<para><htmlonly> Default temperature for structure prediction and free energy evaluation in &amp;#176C </htmlonly> <latexonly> Default temperature for structure prediction and free energy evaluation in $^\circ C$ </latexonly> </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a5f7e5c2b65bada5188443470e576aa4b" kindref="member">vrna_md_t.temperature</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="41" column="9" bodyfile="ViennaRNA/model.h" bodystart="41" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1ga5505389cba74a18bbc116d2bb20256fa" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_PF_SCALE</name>
        <initializer>-1</initializer>
        <briefdescription>
<para>Default scaling factor for partition function computations. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__exp__param__s_1a53c12f0d74f94ce371e0471a8ab5a377" kindref="member">vrna_exp_param_t.pf_scale</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="48" column="9" bodyfile="ViennaRNA/model.h" bodystart="48" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1ga383d3ac8d08c3b6221754b50871c1200" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_BETA_SCALE</name>
        <initializer>1.</initializer>
        <briefdescription>
<para>Default scaling factor for absolute thermodynamic temperature in Boltzmann factors. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__exp__param__s_1a77145830b7bb01b36c3217b363310ef0" kindref="member">vrna_exp_param_t.alpha</ref>, <ref refid="structvrna__md__s_1a19524bf1d8d7ab590ed36edbbcaaba2c" kindref="member">vrna_md_t.betaScale</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="55" column="9" bodyfile="ViennaRNA/model.h" bodystart="55" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1ga2aa7bc2cae774b83a5c468f824c27a42" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_DANGLES</name>
        <initializer>2</initializer>
        <briefdescription>
<para>Default dangling end model. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1adcda4ff2ea77748ae0e8700288282efc" kindref="member">vrna_md_t.dangles</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="62" column="9" bodyfile="ViennaRNA/model.h" bodystart="62" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1gabd1ab224e1048defd45c165ed7d1c108" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_SPECIAL_HP</name>
        <initializer>1</initializer>
        <briefdescription>
<para>Default model behavior for lookup of special tri-, tetra-, and hexa-loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1add64a96d23e77ef1d0ddf8dfc5228143" kindref="member">vrna_md_t.special_hp</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="69" column="9" bodyfile="ViennaRNA/model.h" bodystart="69" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1gab72462726dd60ed0d43339bbf7ee08ad" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_NO_LP</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior for so-called &apos;lonely pairs&apos;. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a753200bf21cee0ea2df64afe43999f5d" kindref="member">vrna_md_t.noLP</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="76" column="9" bodyfile="ViennaRNA/model.h" bodystart="76" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="group__model__details_1ga34702f7d14d38b877ba8e475281e97e2" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_NO_GU</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior for G-U base pairs. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1ad64a5eaf9c4550e7525b36a725fec4b2" kindref="member">vrna_md_t.noGU</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
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</para>
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        <location file="ViennaRNA/model.h" line="83" column="9" bodyfile="ViennaRNA/model.h" bodystart="83" bodyend="-1"/>
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        <name>VRNA_MODEL_DEFAULT_NO_GU_CLOSURE</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior for G-U base pairs closing a loop. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a7e883db1f33f8f3baa5c9b140350c78e" kindref="member">vrna_md_t.noGUclosure</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
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        <location file="ViennaRNA/model.h" line="90" column="9" bodyfile="ViennaRNA/model.h" bodystart="90" bodyend="-1"/>
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        <name>VRNA_MODEL_DEFAULT_CIRC</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior to treat a molecule as a circular RNA (DNA). </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a92762e1008503d4623ff5c01e358a464" kindref="member">vrna_md_t.circ</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
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        <location file="ViennaRNA/model.h" line="96" column="9" bodyfile="ViennaRNA/model.h" bodystart="96" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga793ed812e86f43799b14b2deee917f23" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_GQUAD</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior regarding the treatment of G-Quadruplexes. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1af88a511a2b1f526b4c6213de6cb8fd6e" kindref="member">vrna_md_t.gquad</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="103" column="9" bodyfile="ViennaRNA/model.h" bodystart="103" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga63f6006a02ba2d89148441f406c309e7" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_UNIQ_ML</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default behavior of the model regarding unique multi-branch loop decomposition. </para>
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        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1ade065b814a4e2e72ead93ab502613ed2" kindref="member">vrna_md_t.uniq_ML</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
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</para>
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        <location file="ViennaRNA/model.h" line="110" column="9" bodyfile="ViennaRNA/model.h" bodystart="110" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga6fcf6b2d0f89256cdbd166486c9b6e1e" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_ENERGY_SET</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior on which energy set to use. </para>
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        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a5eee4e3b468eb690d1407e0178dafb3f" kindref="member">vrna_md_t.energy_set</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="117" column="9" bodyfile="ViennaRNA/model.h" bodystart="117" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga3fda8006ab84baf817bd8e5ccbc6bb35" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_BACKTRACK</name>
        <initializer>1</initializer>
        <briefdescription>
<para>Default model behavior with regards to backtracking of structures. </para>
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        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a31f4471608cbdd03887f63c281823adb" kindref="member">vrna_md_t.backtrack</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="123" column="9" bodyfile="ViennaRNA/model.h" bodystart="123" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1gad0e81fcaca53c4a826c68e0796de2afb" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_BACKTRACK_TYPE</name>
        <initializer>&apos;F&apos;</initializer>
        <briefdescription>
<para>Default model behavior on what type of backtracking to perform. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1abb265da25121d22ed11c8435861f0e53" kindref="member">vrna_md_t.backtrack_type</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="130" column="9" bodyfile="ViennaRNA/model.h" bodystart="130" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga1d6cd5051940b126c248147c011bac6c" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_COMPUTE_BPP</name>
        <initializer>1</initializer>
        <briefdescription>
<para>Default model behavior with regards to computing base pair probabilities. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1aa0c3e03d9064363e27adcc92b8d0380f" kindref="member">vrna_md_t.compute_bpp</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        <location file="ViennaRNA/model.h" line="137" column="9" bodyfile="ViennaRNA/model.h" bodystart="137" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga7cb6f4ae8fdebff6746a4410814f2977" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_MAX_BP_SPAN</name>
        <initializer>-1</initializer>
        <briefdescription>
<para>Default model behavior for the allowed maximum base pair span. </para>
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        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a659e5fcc6e8c9f1a68e7de6548eef3b0" kindref="member">vrna_md_t.max_bp_span</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="144" column="9" bodyfile="ViennaRNA/model.h" bodystart="144" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga8de04a9cb57e811e313b0f9f207f6bdb" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_WINDOW_SIZE</name>
        <initializer>-1</initializer>
        <briefdescription>
<para>Default model behavior for the sliding window approach. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" kindref="member">vrna_md_t.window_size</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="151" column="9" bodyfile="ViennaRNA/model.h" bodystart="151" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga938f68463e84fe060aa6502f428a517d" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_LOG_ML</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior on how to evaluate the energy contribution of multi-branch loops. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1ae259f89a94acae0c7f1412603e7f57b5" kindref="member">vrna_md_t.logML</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        <location file="ViennaRNA/model.h" line="158" column="9" bodyfile="ViennaRNA/model.h" bodystart="158" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga2a5bbfc1edf33077e39466d2d9807115" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_ALI_OLD_EN</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior for consensus structure energy evaluation. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1ab53aec4503130877973c6111ae6f0f76" kindref="member">vrna_md_t.oldAliEn</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="164" column="9" bodyfile="ViennaRNA/model.h" bodystart="164" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga64b3ab65a9ca42d4ad1d05e193083147" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_ALI_RIBO</name>
        <initializer>0</initializer>
        <briefdescription>
<para>Default model behavior for consensus structure co-variance contribution assessment. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a3df2ae4bd9c133ef8ab92a53b1d035ec" kindref="member">vrna_md_t.ribo</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
</simplesect>
</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="171" column="9" bodyfile="ViennaRNA/model.h" bodystart="171" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1gaaaf3d73d6abc18d3889676952bfedb96" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_ALI_CV_FACT</name>
        <initializer>1.</initializer>
        <briefdescription>
<para>Default model behavior for weighting the co-variance score in consensus structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1a62ebefb9d0643e5c4c8a2ec84a105ce6" kindref="member">vrna_md_t.cv_fact</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
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</para>
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        </inbodydescription>
        <location file="ViennaRNA/model.h" line="178" column="9" bodyfile="ViennaRNA/model.h" bodystart="178" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga8f774daaafec28160c1ca5d09f2cbdba" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_ALI_NC_FACT</name>
        <initializer>1.</initializer>
        <briefdescription>
<para>Default model behavior for weighting the nucleotide conservation? in consensus structure prediction. </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="structvrna__md__s_1abcf568e6124bfcb2f847ff4eb0dfded6" kindref="member">vrna_md_t.nc_fact</ref>, <ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset()</ref>, <ref refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kindref="member">vrna_md_set_default()</ref> </para>
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        <location file="ViennaRNA/model.h" line="184" column="9" bodyfile="ViennaRNA/model.h" bodystart="184" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1gaef182321c4991e5f434fa236961dd9ad" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_PF_SMOOTH</name>
        <initializer>1</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="187" column="9" bodyfile="ViennaRNA/model.h" bodystart="187" bodyend="-1"/>
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        <name>VRNA_MODEL_DEFAULT_SALT</name>
        <initializer>1.021</initializer>
        <briefdescription>
<para>Default model salt concentration (M). </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="192" column="9" bodyfile="ViennaRNA/model.h" bodystart="192" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1gaec326f45e31be223d4ff2ae33e1a6ee5" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_SALT_MLLOWER</name>
        <initializer>6</initializer>
        <briefdescription>
<para>Default model lower bound of multiloop size for salt correction fiting. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="198" column="9" bodyfile="ViennaRNA/model.h" bodystart="198" bodyend="-1"/>
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        <name>VRNA_MODEL_DEFAULT_SALT_MLUPPER</name>
        <initializer>24</initializer>
        <briefdescription>
<para>Default model upper bound of multiloop size for salt correction fiting. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="204" column="9" bodyfile="ViennaRNA/model.h" bodystart="204" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga9fde1c2000066236e3130dda3ca71a21" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_SALT_DPXINIT</name>
        <initializer>99999</initializer>
        <briefdescription>
<para>Default model value to turn off user-provided salt correction for duplex initializtion. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="210" column="9" bodyfile="ViennaRNA/model.h" bodystart="210" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1gaa927ba890b7810660282172c01eeedd9" prot="public" static="no">
        <name>VRNA_MODEL_SALT_DPXINIT_FACT_RNA</name>
        <initializer>-45.324</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="212" column="9" bodyfile="ViennaRNA/model.h" bodystart="212" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga1531d9f6bc79ca4240635d83e27e9a00" prot="public" static="no">
        <name>VRNA_MODEL_SALT_DPXINIT_FACT_DNA</name>
        <initializer>-58.389</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="213" column="9" bodyfile="ViennaRNA/model.h" bodystart="213" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga3061e5911a3916aee83c40f6c761b872" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_SALT_DPXINIT_FACT</name>
        <initializer>VRNA_MODEL_SALT_DPXINIT_FACT_RNA</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="216" column="9" bodyfile="ViennaRNA/model.h" bodystart="216" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga8b91d97432e8b88c9807d575867f20c0" prot="public" static="no">
        <name>VRNA_MODEL_HELICAL_RISE_RNA</name>
        <initializer>2.8</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="220" column="9" bodyfile="ViennaRNA/model.h" bodystart="220" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga5ea2891b4fd45cc4e4384e56b3d5a7e8" prot="public" static="no">
        <name>VRNA_MODEL_HELICAL_RISE_DNA</name>
        <initializer>3.4</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="221" column="9" bodyfile="ViennaRNA/model.h" bodystart="221" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga6ac110e53604675da1cbed67336e9177" prot="public" static="no">
        <name>VRNA_MODEL_DEFAULT_HELICAL_RISE</name>
        <initializer>VRNA_MODEL_HELICAL_RISE_RNA</initializer>
        <briefdescription>
<para>Default helical rise. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="225" column="9" bodyfile="ViennaRNA/model.h" bodystart="225" bodyend="-1"/>
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      <memberdef kind="define" id="group__model__details_1ga2f9e4a6870666e3acb9709349b96aac0" prot="public" static="no">
        <name>VRNA_MODEL_BACKBONE_LENGTH_RNA</name>
        <initializer>6.0</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="227" column="9" bodyfile="ViennaRNA/model.h" bodystart="227" bodyend="-1"/>
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        <initializer>6.76</initializer>
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        <initializer>VRNA_MODEL_BACKBONE_LENGTH_RNA</initializer>
        <briefdescription>
<para>Default backbone length. </para>
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        </detaileddescription>
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        <initializer>1</initializer>
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        <detaileddescription>
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        </inbodydescription>
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        <initializer>4.385</initializer>
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        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="237" column="9" bodyfile="ViennaRNA/model.h" bodystart="237" bodyend="-1"/>
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        <briefdescription>
<para>Maximal length of alphabet. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
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        <initializer><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>               /* restore compatibility of struct rename */</initializer>
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