<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<doxygen xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="compound.xsd" version="1.15.0" xml:lang="en-US">
  <compounddef id="model_8h" kind="file" language="C++">
    <compoundname>model.h</compoundname>
    <includedby refid="datastructures_2basic_8h" local="no">ViennaRNA/datastructures/basic.h</includedby>
    <includedby refid="fold__compound_8h" local="no">ViennaRNA/fold_compound.h</includedby>
    <includedby refid="fold__vars_8h" local="no">ViennaRNA/fold_vars.h</includedby>
    <includedby refid="params_2basic_8h" local="no">ViennaRNA/params/basic.h</includedby>
    <includedby refid="salt_8h" local="yes">ViennaRNA/params/salt.h</includedby>
    <includedby refid="plotting_2structures_8h" local="no">ViennaRNA/plotting/structures.h</includedby>
    <includedby refid="plotting_2utils_8h" local="no">ViennaRNA/plotting/utils.h</includedby>
    <includedby refid="sequences_2alignments_8h" local="no">ViennaRNA/sequences/alignments.h</includedby>
    <includedby refid="sequences_2alphabet_8h" local="no">ViennaRNA/sequences/alphabet.h</includedby>
    <invincdepgraph>
      <node id="3">
        <label>ViennaRNA/2Dfold.h</label>
        <link refid="2Dfold_8h"/>
      </node>
      <node id="4">
        <label>ViennaRNA/2Dpfold.h</label>
        <link refid="2Dpfold_8h"/>
      </node>
      <node id="5">
        <label>ViennaRNA/LPfold.h</label>
        <link refid="LPfold_8h"/>
      </node>
      <node id="69">
        <label>ViennaRNA/Lfold.h</label>
        <link refid="Lfold_8h"/>
      </node>
      <node id="85">
        <label>ViennaRNA/MEA.h</label>
        <link refid="MEA_8h"/>
      </node>
      <node id="6">
        <label>ViennaRNA/PKplex.h</label>
        <link refid="PKplex_8h_source"/>
      </node>
      <node id="129">
        <label>ViennaRNA/PS_dot.h</label>
        <link refid="PS__dot_8h"/>
      </node>
      <node id="7">
        <label>ViennaRNA/ali_plex.h</label>
        <link refid="ali__plex_8h_source"/>
      </node>
      <node id="8">
        <label>ViennaRNA/alifold.h</label>
        <link refid="alifold_8h"/>
      </node>
      <node id="106">
        <label>ViennaRNA/aln_util.h</label>
        <link refid="aln__util_8h"/>
      </node>
      <node id="109">
        <label>ViennaRNA/alphabet.h</label>
        <link refid="alphabet_8h"/>
        <childnode refid="110" relation="include">
        </childnode>
      </node>
      <node id="9">
        <label>ViennaRNA/backtrack/exterior.h</label>
        <link refid="backtrack_2exterior_8h"/>
        <childnode refid="10" relation="include">
        </childnode>
      </node>
      <node id="14">
        <label>ViennaRNA/backtrack/global.h</label>
        <link refid="backtrack_2global_8h"/>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="15" relation="include">
        </childnode>
        <childnode refid="16" relation="include">
        </childnode>
      </node>
      <node id="17">
        <label>ViennaRNA/backtrack/gquad.h</label>
        <link refid="backtrack_2gquad_8h_source"/>
        <childnode refid="18" relation="include">
        </childnode>
      </node>
      <node id="19">
        <label>ViennaRNA/backtrack/hairpin.h</label>
        <link refid="backtrack_2hairpin_8h"/>
        <childnode refid="20" relation="include">
        </childnode>
      </node>
      <node id="22">
        <label>ViennaRNA/backtrack/internal.h</label>
        <link refid="backtrack_2internal_8h"/>
        <childnode refid="23" relation="include">
        </childnode>
      </node>
      <node id="25">
        <label>ViennaRNA/backtrack/multibranch.h</label>
        <link refid="backtrack_2multibranch_8h"/>
        <childnode refid="26" relation="include">
        </childnode>
      </node>
      <node id="104">
        <label>ViennaRNA/boltzmann_sampling.h</label>
        <link refid="boltzmann__sampling_8h"/>
      </node>
      <node id="114">
        <label>ViennaRNA/centroid.h</label>
        <link refid="centroid_8h"/>
      </node>
      <node id="28">
        <label>ViennaRNA/cofold.h</label>
        <link refid="cofold_8h"/>
      </node>
      <node id="37">
        <label>ViennaRNA/combinatorics.h</label>
        <link refid="combinatorics_8h"/>
      </node>
      <node id="36">
        <label>ViennaRNA/combinatorics/basic.h</label>
        <link refid="combinatorics_2basic_8h"/>
        <childnode refid="37" relation="include">
        </childnode>
      </node>
      <node id="56">
        <label>ViennaRNA/commands.h</label>
        <link refid="commands_8h"/>
      </node>
      <node id="74">
        <label>ViennaRNA/concentrations.h</label>
        <link refid="concentrations_8h"/>
        <childnode refid="75" relation="include">
        </childnode>
      </node>
      <node id="30">
        <label>ViennaRNA/constraints.h</label>
        <link refid="constraints_8h"/>
      </node>
      <node id="96">
        <label>ViennaRNA/constraints/SHAPE.h</label>
        <link refid="constraints_2SHAPE_8h"/>
        <childnode refid="30" relation="include">
        </childnode>
      </node>
      <node id="38">
        <label>ViennaRNA/constraints/basic.h</label>
        <link refid="constraints_2basic_8h"/>
        <childnode refid="30" relation="include">
        </childnode>
        <childnode refid="39" relation="include">
        </childnode>
        <childnode refid="32" relation="include">
        </childnode>
      </node>
      <node id="39">
        <label>ViennaRNA/constraints/hard.h</label>
        <link refid="hard_8h"/>
        <childnode refid="30" relation="include">
        </childnode>
        <childnode refid="40" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="35" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
      </node>
      <node id="29">
        <label>ViennaRNA/constraints/ligand.h</label>
        <link refid="ligand_8h"/>
        <childnode refid="30" relation="include">
        </childnode>
        <childnode refid="31" relation="include">
        </childnode>
      </node>
      <node id="32">
        <label>ViennaRNA/constraints/soft.h</label>
        <link refid="soft_8h"/>
        <childnode refid="30" relation="include">
        </childnode>
        <childnode refid="33" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="35" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
      </node>
      <node id="97">
        <label>ViennaRNA/constraints_SHAPE.h</label>
        <link refid="constraints__SHAPE_8h"/>
      </node>
      <node id="40">
        <label>ViennaRNA/constraints_hard.h</label>
        <link refid="constraints__hard_8h"/>
      </node>
      <node id="31">
        <label>ViennaRNA/constraints_ligand.h</label>
        <link refid="constraints__ligand_8h"/>
      </node>
      <node id="33">
        <label>ViennaRNA/constraints_soft.h</label>
        <link refid="constraints__soft_8h"/>
      </node>
      <node id="42">
        <label>ViennaRNA/data/transform.h</label>
        <link refid="transform_8h"/>
      </node>
      <node id="119">
        <label>ViennaRNA/data_structures.h</label>
        <link refid="data__structures_8h"/>
      </node>
      <node id="2">
        <label>ViennaRNA/datastructures/basic.h</label>
        <link refid="datastructures_2basic_8h"/>
        <childnode refid="3" relation="include">
        </childnode>
        <childnode refid="4" relation="include">
        </childnode>
        <childnode refid="5" relation="include">
        </childnode>
        <childnode refid="6" relation="include">
        </childnode>
        <childnode refid="7" relation="include">
        </childnode>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="9" relation="include">
        </childnode>
        <childnode refid="14" relation="include">
        </childnode>
        <childnode refid="17" relation="include">
        </childnode>
        <childnode refid="19" relation="include">
        </childnode>
        <childnode refid="22" relation="include">
        </childnode>
        <childnode refid="25" relation="include">
        </childnode>
        <childnode refid="28" relation="include">
        </childnode>
        <childnode refid="29" relation="include">
        </childnode>
        <childnode refid="32" relation="include">
        </childnode>
        <childnode refid="119" relation="include">
        </childnode>
        <childnode refid="43" relation="include">
        </childnode>
        <childnode refid="120" relation="include">
        </childnode>
        <childnode refid="45" relation="include">
        </childnode>
        <childnode refid="46" relation="include">
        </childnode>
        <childnode refid="47" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="48" relation="include">
        </childnode>
        <childnode refid="49" relation="include">
        </childnode>
        <childnode refid="15" relation="include">
        </childnode>
        <childnode refid="121" relation="include">
        </childnode>
        <childnode refid="51" relation="include">
        </childnode>
        <childnode refid="53" relation="include">
        </childnode>
        <childnode refid="54" relation="include">
        </childnode>
        <childnode refid="123" relation="include">
        </childnode>
        <childnode refid="124" relation="include">
        </childnode>
        <childnode refid="64" relation="include">
        </childnode>
        <childnode refid="65" relation="include">
        </childnode>
        <childnode refid="66" relation="include">
        </childnode>
        <childnode refid="67" relation="include">
        </childnode>
        <childnode refid="71" relation="include">
        </childnode>
        <childnode refid="73" relation="include">
        </childnode>
        <childnode refid="75" relation="include">
        </childnode>
        <childnode refid="126" relation="include">
        </childnode>
        <childnode refid="77" relation="include">
        </childnode>
        <childnode refid="78" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
        <childnode refid="89" relation="include">
        </childnode>
        <childnode refid="80" relation="include">
        </childnode>
        <childnode refid="127" relation="include">
        </childnode>
        <childnode refid="128" relation="include">
        </childnode>
        <childnode refid="133" relation="include">
        </childnode>
        <childnode refid="134" relation="include">
        </childnode>
        <childnode refid="81" relation="include">
        </childnode>
        <childnode refid="83" relation="include">
        </childnode>
        <childnode refid="136" relation="include">
        </childnode>
        <childnode refid="137" relation="include">
        </childnode>
        <childnode refid="138" relation="include">
        </childnode>
        <childnode refid="139" relation="include">
        </childnode>
        <childnode refid="113" relation="include">
        </childnode>
        <childnode refid="84" relation="include">
        </childnode>
        <childnode refid="86" relation="include">
        </childnode>
        <childnode refid="118" relation="include">
        </childnode>
        <childnode refid="142" relation="include">
        </childnode>
        <childnode refid="144" relation="include">
        </childnode>
      </node>
      <node id="43">
        <label>ViennaRNA/datastructures/dp_matrices.h</label>
        <link refid="datastructures_2dp__matrices_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="44" relation="include">
        </childnode>
        <childnode refid="35" relation="include">
        </childnode>
      </node>
      <node id="44">
        <label>ViennaRNA/dp_matrices.h</label>
        <link refid="dp__matrices_8h"/>
      </node>
      <node id="120">
        <label>ViennaRNA/duplex.h</label>
        <link refid="duplex_8h"/>
      </node>
      <node id="82">
        <label>ViennaRNA/equilibrium_probs.h</label>
        <link refid="equilibrium__probs_8h"/>
      </node>
      <node id="50">
        <label>ViennaRNA/eval.h</label>
        <link refid="eval_8h"/>
      </node>
      <node id="45">
        <label>ViennaRNA/eval/exterior.h</label>
        <link refid="eval_2exterior_8h"/>
        <childnode refid="10" relation="include">
        </childnode>
      </node>
      <node id="46">
        <label>ViennaRNA/eval/gquad.h</label>
        <link refid="eval_2gquad_8h"/>
        <childnode refid="18" relation="include">
        </childnode>
      </node>
      <node id="47">
        <label>ViennaRNA/eval/hairpin.h</label>
        <link refid="eval_2hairpin_8h_source"/>
        <childnode refid="20" relation="include">
        </childnode>
      </node>
      <node id="34">
        <label>ViennaRNA/eval/internal.h</label>
        <link refid="eval_2internal_8h"/>
        <childnode refid="23" relation="include">
        </childnode>
      </node>
      <node id="48">
        <label>ViennaRNA/eval/multibranch.h</label>
        <link refid="eval_2multibranch_8h"/>
        <childnode refid="26" relation="include">
        </childnode>
      </node>
      <node id="49">
        <label>ViennaRNA/eval/structures.h</label>
        <link refid="eval_2structures_8h"/>
        <childnode refid="50" relation="include">
        </childnode>
        <childnode refid="15" relation="include">
        </childnode>
      </node>
      <node id="11">
        <label>ViennaRNA/exterior_loops.h</label>
        <link refid="exterior__loops_8h"/>
      </node>
      <node id="125">
        <label>ViennaRNA/file_formats.h</label>
        <link refid="file__formats_8h"/>
      </node>
      <node id="58">
        <label>ViennaRNA/findpath.h</label>
        <link refid="findpath_8h"/>
      </node>
      <node id="15">
        <label>ViennaRNA/fold.h</label>
        <link refid="fold_8h"/>
      </node>
      <node id="35">
        <label>ViennaRNA/fold_compound.h</label>
        <link refid="fold__compound_8h"/>
        <childnode refid="3" relation="include">
        </childnode>
        <childnode refid="4" relation="include">
        </childnode>
        <childnode refid="9" relation="include">
        </childnode>
        <childnode refid="14" relation="include">
        </childnode>
        <childnode refid="17" relation="include">
        </childnode>
        <childnode refid="19" relation="include">
        </childnode>
        <childnode refid="22" relation="include">
        </childnode>
        <childnode refid="25" relation="include">
        </childnode>
        <childnode refid="36" relation="include">
        </childnode>
        <childnode refid="38" relation="include">
        </childnode>
        <childnode refid="39" relation="include">
        </childnode>
        <childnode refid="29" relation="include">
        </childnode>
        <childnode refid="32" relation="include">
        </childnode>
        <childnode refid="42" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="43" relation="include">
        </childnode>
        <childnode refid="45" relation="include">
        </childnode>
        <childnode refid="46" relation="include">
        </childnode>
        <childnode refid="47" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="48" relation="include">
        </childnode>
        <childnode refid="49" relation="include">
        </childnode>
        <childnode refid="51" relation="include">
        </childnode>
        <childnode refid="53" relation="include">
        </childnode>
        <childnode refid="54" relation="include">
        </childnode>
        <childnode refid="55" relation="include">
        </childnode>
        <childnode refid="57" relation="include">
        </childnode>
        <childnode refid="59" relation="include">
        </childnode>
        <childnode refid="62" relation="include">
        </childnode>
        <childnode refid="63" relation="include">
        </childnode>
        <childnode refid="64" relation="include">
        </childnode>
        <childnode refid="65" relation="include">
        </childnode>
        <childnode refid="66" relation="include">
        </childnode>
        <childnode refid="67" relation="include">
        </childnode>
        <childnode refid="68" relation="include">
        </childnode>
        <childnode refid="71" relation="include">
        </childnode>
        <childnode refid="72" relation="include">
        </childnode>
        <childnode refid="73" relation="include">
        </childnode>
        <childnode refid="77" relation="include">
        </childnode>
        <childnode refid="78" relation="include">
        </childnode>
        <childnode refid="88" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
        <childnode refid="89" relation="include">
        </childnode>
        <childnode refid="80" relation="include">
        </childnode>
        <childnode refid="91" relation="include">
        </childnode>
        <childnode refid="93" relation="include">
        </childnode>
        <childnode refid="94" relation="include">
        </childnode>
        <childnode refid="81" relation="include">
        </childnode>
        <childnode refid="83" relation="include">
        </childnode>
        <childnode refid="95" relation="include">
        </childnode>
        <childnode refid="98" relation="include">
        </childnode>
        <childnode refid="103" relation="include">
        </childnode>
        <childnode refid="105" relation="include">
        </childnode>
        <childnode refid="108" relation="include">
        </childnode>
        <childnode refid="111" relation="include">
        </childnode>
        <childnode refid="113" relation="include">
        </childnode>
        <childnode refid="115" relation="include">
        </childnode>
        <childnode refid="86" relation="include">
        </childnode>
        <childnode refid="116" relation="include">
        </childnode>
        <childnode refid="118" relation="include">
        </childnode>
      </node>
      <node id="121">
        <label>ViennaRNA/fold_vars.h</label>
        <link refid="fold__vars_8h"/>
        <childnode refid="122" relation="include">
        </childnode>
      </node>
      <node id="18">
        <label>ViennaRNA/gquad.h</label>
        <link refid="gquad_8h"/>
      </node>
      <node id="52">
        <label>ViennaRNA/grammar.h</label>
        <link refid="grammar_8h"/>
      </node>
      <node id="51">
        <label>ViennaRNA/grammar/basic.h</label>
        <link refid="grammar_2basic_8h"/>
        <childnode refid="35" relation="include">
        </childnode>
        <childnode refid="52" relation="include">
        </childnode>
        <childnode refid="53" relation="include">
        </childnode>
        <childnode refid="54" relation="include">
        </childnode>
      </node>
      <node id="53">
        <label>ViennaRNA/grammar/mfe.h</label>
        <link refid="grammar_2mfe_8h"/>
        <childnode refid="52" relation="include">
        </childnode>
      </node>
      <node id="54">
        <label>ViennaRNA/grammar/partfunc.h</label>
        <link refid="partfunc_8h"/>
        <childnode refid="52" relation="include">
        </childnode>
      </node>
      <node id="21">
        <label>ViennaRNA/hairpin_loops.h</label>
        <link refid="hairpin__loops_8h"/>
      </node>
      <node id="123">
        <label>ViennaRNA/heat_capacity.h</label>
        <link refid="heat__capacity_8h"/>
      </node>
      <node id="24">
        <label>ViennaRNA/interior_loops.h</label>
        <link refid="interior__loops_8h"/>
      </node>
      <node id="55">
        <label>ViennaRNA/io/commands.h</label>
        <link refid="io_2commands_8h"/>
        <childnode refid="56" relation="include">
        </childnode>
      </node>
      <node id="124">
        <label>ViennaRNA/io/file_formats.h</label>
        <link refid="io_2file__formats_8h"/>
        <childnode refid="125" relation="include">
        </childnode>
      </node>
      <node id="57">
        <label>ViennaRNA/landscape/findpath.h</label>
        <link refid="landscape_2findpath_8h"/>
        <childnode refid="58" relation="include">
        </childnode>
      </node>
      <node id="59">
        <label>ViennaRNA/landscape/neighbor.h</label>
        <link refid="landscape_2neighbor_8h"/>
        <childnode refid="60" relation="include">
        </childnode>
        <childnode refid="61" relation="include">
        </childnode>
      </node>
      <node id="62">
        <label>ViennaRNA/landscape/paths.h</label>
        <link refid="paths_8h"/>
        <childnode refid="57" relation="include">
        </childnode>
      </node>
      <node id="63">
        <label>ViennaRNA/landscape/walk.h</label>
        <link refid="landscape_2walk_8h"/>
        <childnode refid="61" relation="include">
        </childnode>
      </node>
      <node id="13">
        <label>ViennaRNA/loop_energies.h</label>
        <link refid="loop__energies_8h"/>
      </node>
      <node id="12">
        <label>ViennaRNA/loops/all.h</label>
        <link refid="all_8h"/>
        <childnode refid="13" relation="include">
        </childnode>
      </node>
      <node id="10">
        <label>ViennaRNA/loops/external.h</label>
        <link refid="external_8h"/>
        <childnode refid="11" relation="include">
        </childnode>
        <childnode refid="12" relation="include">
        </childnode>
      </node>
      <node id="20">
        <label>ViennaRNA/loops/hairpin.h</label>
        <link refid="loops_2hairpin_8h"/>
        <childnode refid="21" relation="include">
        </childnode>
        <childnode refid="12" relation="include">
        </childnode>
      </node>
      <node id="23">
        <label>ViennaRNA/loops/internal.h</label>
        <link refid="loops_2internal_8h"/>
        <childnode refid="24" relation="include">
        </childnode>
        <childnode refid="12" relation="include">
        </childnode>
      </node>
      <node id="26">
        <label>ViennaRNA/loops/multibranch.h</label>
        <link refid="loops_2multibranch_8h"/>
        <childnode refid="12" relation="include">
        </childnode>
        <childnode refid="27" relation="include">
        </childnode>
      </node>
      <node id="16">
        <label>ViennaRNA/mfe.h</label>
        <link refid="mfe_8h"/>
      </node>
      <node id="64">
        <label>ViennaRNA/mfe/exterior.h</label>
        <link refid="mfe_2exterior_8h"/>
        <childnode refid="10" relation="include">
        </childnode>
      </node>
      <node id="65">
        <label>ViennaRNA/mfe/global.h</label>
        <link refid="mfe_2global_8h"/>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="28" relation="include">
        </childnode>
        <childnode refid="15" relation="include">
        </childnode>
        <childnode refid="16" relation="include">
        </childnode>
      </node>
      <node id="66">
        <label>ViennaRNA/mfe/gquad.h</label>
        <link refid="mfe_2gquad_8h"/>
        <childnode refid="18" relation="include">
        </childnode>
      </node>
      <node id="67">
        <label>ViennaRNA/mfe/internal.h</label>
        <link refid="mfe_2internal_8h"/>
        <childnode refid="23" relation="include">
        </childnode>
      </node>
      <node id="68">
        <label>ViennaRNA/mfe/local.h</label>
        <link refid="mfe_2local_8h"/>
        <childnode refid="69" relation="include">
        </childnode>
        <childnode refid="70" relation="include">
        </childnode>
      </node>
      <node id="71">
        <label>ViennaRNA/mfe/multibranch.h</label>
        <link refid="mfe_2multibranch_8h"/>
        <childnode refid="26" relation="include">
        </childnode>
      </node>
      <node id="70">
        <label>ViennaRNA/mfe_window.h</label>
        <link refid="mfe__window_8h"/>
      </node>
      <node id="72">
        <label>ViennaRNA/mm.h</label>
        <link refid="mm_8h"/>
      </node>
      <node id="1">
        <label>ViennaRNA/model.h</label>
        <link refid="model_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="35" relation="include">
        </childnode>
        <childnode refid="121" relation="include">
        </childnode>
        <childnode refid="73" relation="include">
        </childnode>
        <childnode refid="143" relation="include">
        </childnode>
        <childnode refid="131" relation="include">
        </childnode>
        <childnode refid="134" relation="include">
        </childnode>
        <childnode refid="105" relation="include">
        </childnode>
        <childnode refid="108" relation="include">
        </childnode>
      </node>
      <node id="27">
        <label>ViennaRNA/multibranch_loops.h</label>
        <link refid="multibranch__loops_8h"/>
      </node>
      <node id="60">
        <label>ViennaRNA/neighbor.h</label>
        <link refid="neighbor_8h"/>
      </node>
      <node id="122">
        <label>ViennaRNA/pair_mat.h</label>
        <link refid="pair__mat_8h_source"/>
      </node>
      <node id="76">
        <label>ViennaRNA/params.h</label>
        <link refid="params_8h"/>
      </node>
      <node id="73">
        <label>ViennaRNA/params/basic.h</label>
        <link refid="params_2basic_8h"/>
        <childnode refid="3" relation="include">
        </childnode>
        <childnode refid="4" relation="include">
        </childnode>
        <childnode refid="5" relation="include">
        </childnode>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="17" relation="include">
        </childnode>
        <childnode refid="25" relation="include">
        </childnode>
        <childnode refid="28" relation="include">
        </childnode>
        <childnode refid="74" relation="include">
        </childnode>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="45" relation="include">
        </childnode>
        <childnode refid="46" relation="include">
        </childnode>
        <childnode refid="47" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="48" relation="include">
        </childnode>
        <childnode refid="49" relation="include">
        </childnode>
        <childnode refid="15" relation="include">
        </childnode>
        <childnode refid="35" relation="include">
        </childnode>
        <childnode refid="64" relation="include">
        </childnode>
        <childnode refid="66" relation="include">
        </childnode>
        <childnode refid="67" relation="include">
        </childnode>
        <childnode refid="71" relation="include">
        </childnode>
        <childnode refid="76" relation="include">
        </childnode>
        <childnode refid="75" relation="include">
        </childnode>
        <childnode refid="77" relation="include">
        </childnode>
        <childnode refid="78" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
        <childnode refid="80" relation="include">
        </childnode>
        <childnode refid="81" relation="include">
        </childnode>
        <childnode refid="83" relation="include">
        </childnode>
        <childnode refid="84" relation="include">
        </childnode>
        <childnode refid="86" relation="include">
        </childnode>
      </node>
      <node id="143">
        <label>ViennaRNA/params/salt.h</label>
        <link refid="salt_8h"/>
        <childnode refid="47" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
      </node>
      <node id="79">
        <label>ViennaRNA/part_func.h</label>
        <link refid="part__func_8h"/>
      </node>
      <node id="75">
        <label>ViennaRNA/part_func_co.h</label>
        <link refid="part__func__co_8h"/>
      </node>
      <node id="126">
        <label>ViennaRNA/part_func_up.h</label>
        <link refid="part__func__up_8h"/>
      </node>
      <node id="90">
        <label>ViennaRNA/part_func_window.h</label>
        <link refid="part__func__window_8h"/>
      </node>
      <node id="77">
        <label>ViennaRNA/partfunc/exterior.h</label>
        <link refid="partfunc_2exterior_8h"/>
        <childnode refid="10" relation="include">
        </childnode>
      </node>
      <node id="78">
        <label>ViennaRNA/partfunc/global.h</label>
        <link refid="partfunc_2global_8h"/>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="79" relation="include">
        </childnode>
        <childnode refid="75" relation="include">
        </childnode>
      </node>
      <node id="88">
        <label>ViennaRNA/partfunc/gquad.h</label>
        <link refid="partfunc_2gquad_8h"/>
        <childnode refid="18" relation="include">
        </childnode>
      </node>
      <node id="41">
        <label>ViennaRNA/partfunc/internal.h</label>
        <link refid="partfunc_2internal_8h"/>
        <childnode refid="23" relation="include">
        </childnode>
      </node>
      <node id="89">
        <label>ViennaRNA/partfunc/local.h</label>
        <link refid="partfunc_2local_8h"/>
        <childnode refid="5" relation="include">
        </childnode>
        <childnode refid="90" relation="include">
        </childnode>
      </node>
      <node id="80">
        <label>ViennaRNA/partfunc/multibranch.h</label>
        <link refid="partfunc_2multibranch_8h"/>
        <childnode refid="26" relation="include">
        </childnode>
      </node>
      <node id="91">
        <label>ViennaRNA/partfunc/multifold.h</label>
        <link refid="multifold_8h_source"/>
        <childnode refid="92" relation="include">
        </childnode>
      </node>
      <node id="93">
        <label>ViennaRNA/perturbation_fold.h</label>
        <link refid="perturbation__fold_8h"/>
      </node>
      <node id="92">
        <label>ViennaRNA/pf_multifold.h</label>
        <link refid="pf__multifold_8h"/>
      </node>
      <node id="94">
        <label>ViennaRNA/pk_plex.h</label>
        <link refid="pk__plex_8h"/>
        <childnode refid="6" relation="include">
        </childnode>
      </node>
      <node id="127">
        <label>ViennaRNA/plex.h</label>
        <link refid="plex_8h_source"/>
      </node>
      <node id="130">
        <label>ViennaRNA/plot_layouts.h</label>
        <link refid="plot__layouts_8h"/>
      </node>
      <node id="132">
        <label>ViennaRNA/plot_structure.h</label>
        <link refid="plot__structure_8h"/>
      </node>
      <node id="135">
        <label>ViennaRNA/plot_utils.h</label>
        <link refid="plot__utils_8h"/>
      </node>
      <node id="128">
        <label>ViennaRNA/plotting/layouts.h</label>
        <link refid="layouts_8h"/>
        <childnode refid="129" relation="include">
        </childnode>
        <childnode refid="130" relation="include">
        </childnode>
        <childnode refid="131" relation="include">
        </childnode>
      </node>
      <node id="133">
        <label>ViennaRNA/plotting/probabilities.h</label>
        <link refid="probabilities_8h"/>
        <childnode refid="129" relation="include">
        </childnode>
      </node>
      <node id="131">
        <label>ViennaRNA/plotting/structures.h</label>
        <link refid="plotting_2structures_8h"/>
        <childnode refid="129" relation="include">
        </childnode>
        <childnode refid="132" relation="include">
        </childnode>
      </node>
      <node id="134">
        <label>ViennaRNA/plotting/utils.h</label>
        <link refid="plotting_2utils_8h"/>
        <childnode refid="135" relation="include">
        </childnode>
      </node>
      <node id="81">
        <label>ViennaRNA/probabilities/basepairs.h</label>
        <link refid="basepairs_8h"/>
        <childnode refid="82" relation="include">
        </childnode>
        <childnode refid="79" relation="include">
        </childnode>
        <childnode refid="75" relation="include">
        </childnode>
      </node>
      <node id="83">
        <label>ViennaRNA/probabilities/structures.h</label>
        <link refid="probabilities_2structures_8h"/>
        <childnode refid="82" relation="include">
        </childnode>
        <childnode refid="75" relation="include">
        </childnode>
      </node>
      <node id="95">
        <label>ViennaRNA/probing/SHAPE.h</label>
        <link refid="probing_2SHAPE_8h"/>
        <childnode refid="96" relation="include">
        </childnode>
        <childnode refid="97" relation="include">
        </childnode>
      </node>
      <node id="98">
        <label>ViennaRNA/probing/basic.h</label>
        <link refid="probing_2basic_8h"/>
        <childnode refid="95" relation="include">
        </childnode>
        <childnode refid="99" relation="include">
        </childnode>
        <childnode refid="100" relation="include">
        </childnode>
        <childnode refid="101" relation="include">
        </childnode>
        <childnode refid="102" relation="include">
        </childnode>
      </node>
      <node id="99">
        <label>ViennaRNA/probing/strategy_deigan.h</label>
        <link refid="strategy__deigan_8h"/>
      </node>
      <node id="100">
        <label>ViennaRNA/probing/strategy_eddy.h</label>
        <link refid="strategy__eddy_8h"/>
      </node>
      <node id="101">
        <label>ViennaRNA/probing/strategy_nlogp.h</label>
        <link refid="strategy__nlogp_8h"/>
      </node>
      <node id="102">
        <label>ViennaRNA/probing/strategy_zarringhalam.h</label>
        <link refid="strategy__zarringhalam_8h"/>
      </node>
      <node id="136">
        <label>ViennaRNA/profiledist.h</label>
        <link refid="profiledist_8h"/>
      </node>
      <node id="103">
        <label>ViennaRNA/sampling/basic.h</label>
        <link refid="sampling_2basic_8h"/>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="104" relation="include">
        </childnode>
        <childnode refid="79" relation="include">
        </childnode>
      </node>
      <node id="112">
        <label>ViennaRNA/sequence.h</label>
        <link refid="sequence_8h"/>
      </node>
      <node id="105">
        <label>ViennaRNA/sequences/alignments.h</label>
        <link refid="sequences_2alignments_8h_source"/>
        <childnode refid="8" relation="include">
        </childnode>
        <childnode refid="106" relation="include">
        </childnode>
        <childnode refid="107" relation="include">
        </childnode>
      </node>
      <node id="108">
        <label>ViennaRNA/sequences/alphabet.h</label>
        <link refid="sequences_2alphabet_8h"/>
        <childnode refid="109" relation="include">
        </childnode>
        <childnode refid="46" relation="include">
        </childnode>
        <childnode refid="66" relation="include">
        </childnode>
      </node>
      <node id="111">
        <label>ViennaRNA/sequences/sequence.h</label>
        <link refid="sequences_2sequence_8h"/>
        <childnode refid="35" relation="include">
        </childnode>
        <childnode refid="112" relation="include">
        </childnode>
      </node>
      <node id="137">
        <label>ViennaRNA/snofold.h</label>
        <link refid="snofold_8h_source"/>
      </node>
      <node id="138">
        <label>ViennaRNA/snoop.h</label>
        <link refid="snoop_8h_source"/>
      </node>
      <node id="145">
        <label>ViennaRNA/string_utils.h</label>
        <link refid="string__utils_8h"/>
      </node>
      <node id="140">
        <label>ViennaRNA/structure_utils.h</label>
        <link refid="structure__utils_8h"/>
      </node>
      <node id="139">
        <label>ViennaRNA/structures/benchmark.h</label>
        <link refid="benchmark_8h"/>
        <childnode refid="140" relation="include">
        </childnode>
        <childnode refid="141" relation="include">
        </childnode>
      </node>
      <node id="113">
        <label>ViennaRNA/structures/centroid.h</label>
        <link refid="structures_2centroid_8h"/>
        <childnode refid="114" relation="include">
        </childnode>
      </node>
      <node id="84">
        <label>ViennaRNA/structures/mea.h</label>
        <link refid="mea_8h_source"/>
        <childnode refid="85" relation="include">
        </childnode>
      </node>
      <node id="87">
        <label>ViennaRNA/subopt.h</label>
        <link refid="subopt_8h"/>
      </node>
      <node id="115">
        <label>ViennaRNA/subopt/gquad.h</label>
        <link refid="subopt_2gquad_8h"/>
      </node>
      <node id="86">
        <label>ViennaRNA/subopt/wuchty.h</label>
        <link refid="wuchty_8h"/>
        <childnode refid="87" relation="include">
        </childnode>
      </node>
      <node id="116">
        <label>ViennaRNA/subopt/zuker.h</label>
        <link refid="zuker_8h_source"/>
        <childnode refid="117" relation="include">
        </childnode>
      </node>
      <node id="117">
        <label>ViennaRNA/subopt_zuker.h</label>
        <link refid="subopt__zuker_8h"/>
      </node>
      <node id="118">
        <label>ViennaRNA/unstructured_domains.h</label>
        <link refid="unstructured__domains_8h"/>
        <childnode refid="2" relation="include">
        </childnode>
        <childnode refid="35" relation="include">
        </childnode>
      </node>
      <node id="110">
        <label>ViennaRNA/utils.h</label>
        <link refid="utils_8h"/>
      </node>
      <node id="107">
        <label>ViennaRNA/utils/alignments.h</label>
        <link refid="utils_2alignments_8h"/>
      </node>
      <node id="142">
        <label>ViennaRNA/utils/basic.h</label>
        <link refid="utils_2basic_8h"/>
        <childnode refid="19" relation="include">
        </childnode>
        <childnode refid="22" relation="include">
        </childnode>
        <childnode refid="25" relation="include">
        </childnode>
        <childnode refid="47" relation="include">
        </childnode>
        <childnode refid="34" relation="include">
        </childnode>
        <childnode refid="48" relation="include">
        </childnode>
        <childnode refid="67" relation="include">
        </childnode>
        <childnode refid="71" relation="include">
        </childnode>
        <childnode refid="122" relation="include">
        </childnode>
        <childnode refid="143" relation="include">
        </childnode>
        <childnode refid="41" relation="include">
        </childnode>
        <childnode refid="80" relation="include">
        </childnode>
        <childnode refid="110" relation="include">
        </childnode>
      </node>
      <node id="144">
        <label>ViennaRNA/utils/strings.h</label>
        <link refid="strings_8h"/>
        <childnode refid="145" relation="include">
        </childnode>
        <childnode refid="110" relation="include">
        </childnode>
      </node>
      <node id="141">
        <label>ViennaRNA/utils/structures.h</label>
        <link refid="utils_2structures_8h"/>
        <childnode refid="110" relation="include">
        </childnode>
      </node>
      <node id="61">
        <label>ViennaRNA/walk.h</label>
        <link refid="walk_8h"/>
      </node>
    </invincdepgraph>
    <innerclass refid="structvrna__md__s" prot="public">vrna_md_s</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="model_8h_1aab347a3c03fbe8e7319551b9fa0cce4a" prot="public" static="no">
        <name>DEPRECATED</name>
        <param><defname>func   </defname></param>
        <param><defname>msg</defname></param>
        <initializer>func</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/model.h" line="13" column="11" bodyfile="ViennaRNA/model.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <member refid="group__model__details_1gad554b4852cd5fec35025db8edbbba3cd" kind="define"><name>NBASES</name></member>
      <member refid="group__model__details_1gaf47f9850b3b4763479f7a7e7a15648a2" kind="define"><name>VRNA_MODEL_DEFAULT_TEMPERATURE</name></member>
      <member refid="group__model__details_1ga5505389cba74a18bbc116d2bb20256fa" kind="define"><name>VRNA_MODEL_DEFAULT_PF_SCALE</name></member>
      <member refid="group__model__details_1ga383d3ac8d08c3b6221754b50871c1200" kind="define"><name>VRNA_MODEL_DEFAULT_BETA_SCALE</name></member>
      <member refid="group__model__details_1ga2aa7bc2cae774b83a5c468f824c27a42" kind="define"><name>VRNA_MODEL_DEFAULT_DANGLES</name></member>
      <member refid="group__model__details_1gabd1ab224e1048defd45c165ed7d1c108" kind="define"><name>VRNA_MODEL_DEFAULT_SPECIAL_HP</name></member>
      <member refid="group__model__details_1gab72462726dd60ed0d43339bbf7ee08ad" kind="define"><name>VRNA_MODEL_DEFAULT_NO_LP</name></member>
      <member refid="group__model__details_1ga34702f7d14d38b877ba8e475281e97e2" kind="define"><name>VRNA_MODEL_DEFAULT_NO_GU</name></member>
      <member refid="group__model__details_1ga5308de46faaca4b9fd16045864901ee7" kind="define"><name>VRNA_MODEL_DEFAULT_NO_GU_CLOSURE</name></member>
      <member refid="group__model__details_1ga22059033db7bcd875c51fec32425490a" kind="define"><name>VRNA_MODEL_DEFAULT_CIRC</name></member>
      <member refid="group__model__details_1ga793ed812e86f43799b14b2deee917f23" kind="define"><name>VRNA_MODEL_DEFAULT_GQUAD</name></member>
      <member refid="group__model__details_1ga63f6006a02ba2d89148441f406c309e7" kind="define"><name>VRNA_MODEL_DEFAULT_UNIQ_ML</name></member>
      <member refid="group__model__details_1ga6fcf6b2d0f89256cdbd166486c9b6e1e" kind="define"><name>VRNA_MODEL_DEFAULT_ENERGY_SET</name></member>
      <member refid="group__model__details_1ga3fda8006ab84baf817bd8e5ccbc6bb35" kind="define"><name>VRNA_MODEL_DEFAULT_BACKTRACK</name></member>
      <member refid="group__model__details_1gad0e81fcaca53c4a826c68e0796de2afb" kind="define"><name>VRNA_MODEL_DEFAULT_BACKTRACK_TYPE</name></member>
      <member refid="group__model__details_1ga1d6cd5051940b126c248147c011bac6c" kind="define"><name>VRNA_MODEL_DEFAULT_COMPUTE_BPP</name></member>
      <member refid="group__model__details_1ga7cb6f4ae8fdebff6746a4410814f2977" kind="define"><name>VRNA_MODEL_DEFAULT_MAX_BP_SPAN</name></member>
      <member refid="group__model__details_1ga8de04a9cb57e811e313b0f9f207f6bdb" kind="define"><name>VRNA_MODEL_DEFAULT_WINDOW_SIZE</name></member>
      <member refid="group__model__details_1ga938f68463e84fe060aa6502f428a517d" kind="define"><name>VRNA_MODEL_DEFAULT_LOG_ML</name></member>
      <member refid="group__model__details_1ga2a5bbfc1edf33077e39466d2d9807115" kind="define"><name>VRNA_MODEL_DEFAULT_ALI_OLD_EN</name></member>
      <member refid="group__model__details_1ga64b3ab65a9ca42d4ad1d05e193083147" kind="define"><name>VRNA_MODEL_DEFAULT_ALI_RIBO</name></member>
      <member refid="group__model__details_1gaaaf3d73d6abc18d3889676952bfedb96" kind="define"><name>VRNA_MODEL_DEFAULT_ALI_CV_FACT</name></member>
      <member refid="group__model__details_1ga8f774daaafec28160c1ca5d09f2cbdba" kind="define"><name>VRNA_MODEL_DEFAULT_ALI_NC_FACT</name></member>
      <member refid="group__model__details_1gaef182321c4991e5f434fa236961dd9ad" kind="define"><name>VRNA_MODEL_DEFAULT_PF_SMOOTH</name></member>
      <member refid="group__model__details_1gaa68703da9ccc5ae6da508bfda36b533f" kind="define"><name>VRNA_MODEL_DEFAULT_SALT</name></member>
      <member refid="group__model__details_1gaec326f45e31be223d4ff2ae33e1a6ee5" kind="define"><name>VRNA_MODEL_DEFAULT_SALT_MLLOWER</name></member>
      <member refid="group__model__details_1ga1d16fa20d2c6099957e975746f5fb610" kind="define"><name>VRNA_MODEL_DEFAULT_SALT_MLUPPER</name></member>
      <member refid="group__model__details_1ga9fde1c2000066236e3130dda3ca71a21" kind="define"><name>VRNA_MODEL_DEFAULT_SALT_DPXINIT</name></member>
      <member refid="group__model__details_1gaa927ba890b7810660282172c01eeedd9" kind="define"><name>VRNA_MODEL_SALT_DPXINIT_FACT_RNA</name></member>
      <member refid="group__model__details_1ga1531d9f6bc79ca4240635d83e27e9a00" kind="define"><name>VRNA_MODEL_SALT_DPXINIT_FACT_DNA</name></member>
      <member refid="group__model__details_1ga3061e5911a3916aee83c40f6c761b872" kind="define"><name>VRNA_MODEL_DEFAULT_SALT_DPXINIT_FACT</name></member>
      <member refid="group__model__details_1ga8b91d97432e8b88c9807d575867f20c0" kind="define"><name>VRNA_MODEL_HELICAL_RISE_RNA</name></member>
      <member refid="group__model__details_1ga5ea2891b4fd45cc4e4384e56b3d5a7e8" kind="define"><name>VRNA_MODEL_HELICAL_RISE_DNA</name></member>
      <member refid="group__model__details_1ga6ac110e53604675da1cbed67336e9177" kind="define"><name>VRNA_MODEL_DEFAULT_HELICAL_RISE</name></member>
      <member refid="group__model__details_1ga2f9e4a6870666e3acb9709349b96aac0" kind="define"><name>VRNA_MODEL_BACKBONE_LENGTH_RNA</name></member>
      <member refid="group__model__details_1ga4feb9245ca60b88c5e3bc1ee1b2af89f" kind="define"><name>VRNA_MODEL_BACKBONE_LENGTH_DNA</name></member>
      <member refid="group__model__details_1ga62e1e462516736e9e4482e2e4a550aab" kind="define"><name>VRNA_MODEL_DEFAULT_BACKBONE_LENGTH</name></member>
      <member refid="group__model__details_1gad3c920c31df1215337ec6a2ee50385bd" kind="define"><name>VRNA_MODEL_DEFAULT_CIRC_PENALTY</name></member>
      <member refid="group__model__details_1gad5aafaa5aedc62cb6e128229e9735f63" kind="define"><name>VRNA_MODEL_DEFAULT_CIRC_ALPHA0</name></member>
      <member refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kind="define"><name>MAXALPHA</name></member>
      <member refid="group__model__details_1ga590b5539f4560d5b02e24db8d3ed1977" kind="define"><name>model_detailsT</name></member>
    </sectiondef>
    <sectiondef kind="typedef">
      <member refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kind="typedef"><name>vrna_md_t</name></member>
    </sectiondef>
    <sectiondef kind="var">
      <member refid="group__model__details_1gab4b11c8d9c758430960896bc3fe82ead" kind="variable"><name>temperature</name></member>
      <member refid="group__model__details_1gad3b22044065acc6dee0af68931b52cfd" kind="variable"><name>pf_scale</name></member>
      <member refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kind="variable"><name>dangles</name></member>
      <member refid="group__model__details_1ga4f6265bdf0ead7ff4628a360adbfd77e" kind="variable"><name>tetra_loop</name></member>
      <member refid="group__model__details_1ga097eccaabd6ae8b4fef83cccff85bb5d" kind="variable"><name>noLonelyPairs</name></member>
      <member refid="group__model__details_1gabf380d09e4f1ab94fc6af57cf0ad5d32" kind="variable"><name>noGU</name></member>
      <member refid="group__model__details_1gaa8d1c7b92489179e1eafa562b7bdd259" kind="variable"><name>no_closingGU</name></member>
      <member refid="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" kind="variable"><name>circ</name></member>
      <member refid="group__model__details_1ga25f2bdcdf56e813d288845484a13d704" kind="variable"><name>gquad</name></member>
      <member refid="group__model__details_1ga6c5655c8b272e3e6cab74dd0f540294f" kind="variable"><name>uniq_ML</name></member>
      <member refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kind="variable"><name>energy_set</name></member>
      <member refid="group__model__details_1gad512b5dd4dbec60faccfe137bb474489" kind="variable"><name>do_backtrack</name></member>
      <member refid="group__model__details_1ga83bdb43472a259c71e69fa9f70f420c3" kind="variable"><name>backtrack_type</name></member>
      <member refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kind="variable"><name>nonstandards</name></member>
      <member refid="group__model__details_1ga18df869af0d70101106458fc3f027806" kind="variable"><name>max_bp_span</name></member>
      <member refid="group__model__details_1gac408868ba00671cbc7d1d535105af045" kind="variable"><name>oldAliEn</name></member>
      <member refid="group__model__details_1ga0656afca1d2853f9ee6591172f5638de" kind="variable"><name>ribo</name></member>
      <member refid="group__model__details_1gaf3cbac6ff5d706d6e414677841ddf94c" kind="variable"><name>cv_fact</name></member>
      <member refid="group__model__details_1ga502948a122a2af5b914355b1f3ea2f61" kind="variable"><name>nc_fact</name></member>
      <member refid="group__model__details_1ga80c3c5fd35e7479704cc91d2d0367743" kind="variable"><name>logML</name></member>
      <member refid="group__model__details_1ga59bc4fe917f2ad11376d083260e289da" kind="variable"><name>salt</name></member>
      <member refid="group__model__details_1gafd2b9a6a1d42a6bf2b8be99a4b44dc7e" kind="variable"><name>saltDPXInit</name></member>
      <member refid="group__model__details_1gabb3f00c97700606dd80705404911318a" kind="variable"><name>helical_rise</name></member>
      <member refid="group__model__details_1gac1bcc01a720eba0abe6caa1bf97a8f7d" kind="variable"><name>backbone_length</name></member>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" kind="function"><name>vrna_md_set_default</name></member>
      <member refid="group__model__details_1ga36ae40b8c3b82362f5798ad5b047b814" kind="function"><name>vrna_md_update</name></member>
      <member refid="group__model__details_1gaa7c753fefc98866d5dc0dae3e6bd4486" kind="function"><name>vrna_md_copy</name></member>
      <member refid="group__model__details_1ga2207e3b40295825655c629421fe8f349" kind="function"><name>vrna_md_option_string</name></member>
      <member refid="group__model__details_1ga87398a419421bf5d90f246382e6ed70c" kind="function"><name>vrna_md_set_nonstandards</name></member>
      <member refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kind="function"><name>vrna_md_defaults_reset</name></member>
      <member refid="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" kind="function"><name>vrna_md_defaults_temperature</name></member>
      <member refid="group__model__details_1ga96b24a74437f9ba46c4e06343155bf46" kind="function"><name>vrna_md_defaults_temperature_get</name></member>
      <member refid="group__model__details_1gae984567db36c3f9b8731ecc917abf3a2" kind="function"><name>vrna_md_defaults_betaScale</name></member>
      <member refid="group__model__details_1gabb8780f5410c52f970d75b044059bd09" kind="function"><name>vrna_md_defaults_betaScale_get</name></member>
      <member refid="group__model__details_1ga8524ad32519fd3a8a2055fd3a2723cad" kind="function"><name>vrna_md_defaults_pf_smooth</name></member>
      <member refid="group__model__details_1gae3fdc588bf45c8432c532066d6167c51" kind="function"><name>vrna_md_defaults_pf_smooth_get</name></member>
      <member refid="group__model__details_1gac76a5374def8e5e4e644ff6e4cc72dee" kind="function"><name>vrna_md_defaults_dangles</name></member>
      <member refid="group__model__details_1ga67ca06f95ae133778c79a4493c9817b8" kind="function"><name>vrna_md_defaults_dangles_get</name></member>
      <member refid="group__model__details_1gafff6449a02744add0308e653230c15fc" kind="function"><name>vrna_md_defaults_special_hp</name></member>
      <member refid="group__model__details_1ga1d68a6efdaa1253cc63fd9cd06452559" kind="function"><name>vrna_md_defaults_special_hp_get</name></member>
      <member refid="group__model__details_1ga2f88ffc393ac9d7987849c965fd29ea8" kind="function"><name>vrna_md_defaults_noLP</name></member>
      <member refid="group__model__details_1ga934344888fbacaed538bbbfe910f2aa6" kind="function"><name>vrna_md_defaults_noLP_get</name></member>
      <member refid="group__model__details_1ga98218f85c7a957a1d1ddf4627fdf5a39" kind="function"><name>vrna_md_defaults_noGU</name></member>
      <member refid="group__model__details_1ga5faa7d4e536d7fe36ec25428c0cf2563" kind="function"><name>vrna_md_defaults_noGU_get</name></member>
      <member refid="group__model__details_1gade5b9951d71ca2fb357a4e6c0c18ccd1" kind="function"><name>vrna_md_defaults_noGUclosure</name></member>
      <member refid="group__model__details_1ga4f7fdad083243a5348d63320ddaa70f3" kind="function"><name>vrna_md_defaults_noGUclosure_get</name></member>
      <member refid="group__model__details_1ga3de50a73455d88c3957386933b8e1f90" kind="function"><name>vrna_md_defaults_logML</name></member>
      <member refid="group__model__details_1ga93f04e070d529c5d0bb87c9681f6ad29" kind="function"><name>vrna_md_defaults_logML_get</name></member>
      <member refid="group__model__details_1ga4e1deb3e91a8a99e5c6dd905a5eb0186" kind="function"><name>vrna_md_defaults_circ</name></member>
      <member refid="group__model__details_1gad3a7e58de344ad93a08925f58f94f6fb" kind="function"><name>vrna_md_defaults_circ_get</name></member>
      <member refid="group__model__details_1gae36c04033105fc519e040063341e6f4b" kind="function"><name>vrna_md_defaults_circ_penalty</name></member>
      <member refid="group__model__details_1gadd7f2da829239856a5a14f6c43d26921" kind="function"><name>vrna_md_defaults_circ_penalty_get</name></member>
      <member refid="group__model__details_1ga0685ca2aeb39af76f2421fc308163dce" kind="function"><name>vrna_md_defaults_gquad</name></member>
      <member refid="group__model__details_1gae645b8612f879eb38b45244fa9eddb9e" kind="function"><name>vrna_md_defaults_gquad_get</name></member>
      <member refid="group__model__details_1ga59b944f61c5d2babec2d4c48c820de67" kind="function"><name>vrna_md_defaults_uniq_ML</name></member>
      <member refid="group__model__details_1gab48e70fd024bf838404bcbcca0c874a0" kind="function"><name>vrna_md_defaults_uniq_ML_get</name></member>
      <member refid="group__model__details_1ga8dd29c55787a4576277e1907e92d810c" kind="function"><name>vrna_md_defaults_energy_set</name></member>
      <member refid="group__model__details_1ga017ed6afb1cba2b7f242412cab618b53" kind="function"><name>vrna_md_defaults_energy_set_get</name></member>
      <member refid="group__model__details_1ga978c468b2fe96a70d5191e3dd17d5599" kind="function"><name>vrna_md_defaults_backtrack</name></member>
      <member refid="group__model__details_1ga90da1156e6883ddd68527c2830706648" kind="function"><name>vrna_md_defaults_backtrack_get</name></member>
      <member refid="group__model__details_1ga68305274de96b56b7799575e222560d8" kind="function"><name>vrna_md_defaults_backtrack_type</name></member>
      <member refid="group__model__details_1ga1425b4ebd0e034dead66d79becd64143" kind="function"><name>vrna_md_defaults_backtrack_type_get</name></member>
      <member refid="group__model__details_1gaf1b5db10f1f476767f9a95f8a78e3132" kind="function"><name>vrna_md_defaults_compute_bpp</name></member>
      <member refid="group__model__details_1gaa3a537e61fbe0518673bf9f73fd820f3" kind="function"><name>vrna_md_defaults_compute_bpp_get</name></member>
      <member refid="group__model__details_1ga4c4bc962f09b4480cb8499f1cf8ae4ec" kind="function"><name>vrna_md_defaults_max_bp_span</name></member>
      <member refid="group__model__details_1gaa60f989e062fecd4d4bac89c1883da85" kind="function"><name>vrna_md_defaults_max_bp_span_get</name></member>
      <member refid="group__model__details_1gac152f1e78c1058a10261022c8dfda0f7" kind="function"><name>vrna_md_defaults_min_loop_size</name></member>
      <member refid="group__model__details_1ga5cc691174a75c652807dc361b617632a" kind="function"><name>vrna_md_defaults_min_loop_size_get</name></member>
      <member refid="group__model__details_1ga7b802ce0e8c3181bf5cb580de6d5b26a" kind="function"><name>vrna_md_defaults_window_size</name></member>
      <member refid="group__model__details_1ga670146a9aa3ba77f4d422d60b7c30ac9" kind="function"><name>vrna_md_defaults_window_size_get</name></member>
      <member refid="group__model__details_1ga41521d5b9fb7e0f31e7ea73f5792afab" kind="function"><name>vrna_md_defaults_oldAliEn</name></member>
      <member refid="group__model__details_1ga2374492b5019df88022fe4c05f0f3630" kind="function"><name>vrna_md_defaults_oldAliEn_get</name></member>
      <member refid="group__model__details_1ga937c45e1d06fd6168730a9b08d130be3" kind="function"><name>vrna_md_defaults_ribo</name></member>
      <member refid="group__model__details_1ga169027f0c0561ea7d87b655e4b336bfc" kind="function"><name>vrna_md_defaults_ribo_get</name></member>
      <member refid="group__model__details_1gad3a3f40baafd91a6ce80a91a68e20053" kind="function"><name>vrna_md_defaults_cv_fact</name></member>
      <member refid="group__model__details_1gae59c68393807217b0a2497adb64d3ee3" kind="function"><name>vrna_md_defaults_cv_fact_get</name></member>
      <member refid="group__model__details_1gac35e596c850dce3ad55c49119fd7d471" kind="function"><name>vrna_md_defaults_nc_fact</name></member>
      <member refid="group__model__details_1ga7ac759eaa7159bf5f022745f5da59508" kind="function"><name>vrna_md_defaults_nc_fact_get</name></member>
      <member refid="group__model__details_1ga3f73d3029d3d0025d4cc311510cd95a3" kind="function"><name>vrna_md_defaults_sfact</name></member>
      <member refid="group__model__details_1gab2df6aab954b63fd3592d18e90285dae" kind="function"><name>vrna_md_defaults_sfact_get</name></member>
      <member refid="group__model__details_1gabfb475999a35e9af42b21326a9edca12" kind="function"><name>vrna_md_defaults_salt</name></member>
      <member refid="group__model__details_1ga28eb9dd2f11828da7cc25b93884c965f" kind="function"><name>vrna_md_defaults_salt_get</name></member>
      <member refid="group__model__details_1ga807b1615aea57f61cc0a269065beface" kind="function"><name>vrna_md_defaults_saltMLLower</name></member>
      <member refid="group__model__details_1ga0813eb58f9382ae92642016960a4a781" kind="function"><name>vrna_md_defaults_saltMLLower_get</name></member>
      <member refid="group__model__details_1gaf4d0ae6115687f13d4ccabcd3b45ad7c" kind="function"><name>vrna_md_defaults_saltMLUpper</name></member>
      <member refid="group__model__details_1ga28bc6652930e82ca1b105e419f6f4595" kind="function"><name>vrna_md_defaults_saltMLUpper_get</name></member>
      <member refid="group__model__details_1gaaa7cca6b6a021221d56a7ee3b2b9b10c" kind="function"><name>vrna_md_defaults_saltDPXInit</name></member>
      <member refid="group__model__details_1ga02e0db8bf2345c12c28913af1a92186c" kind="function"><name>vrna_md_defaults_saltDPXInit_get</name></member>
      <member refid="group__model__details_1gab33bd5d2d3170e2e36ab3d7c81f4b35f" kind="function"><name>vrna_md_defaults_saltDPXInitFact</name></member>
      <member refid="group__model__details_1ga8a11417e5b8683e973effa4d874b0d68" kind="function"><name>vrna_md_defaults_saltDPXInitFact_get</name></member>
      <member refid="group__model__details_1gafdbc3fc166c2d72df0ed2609a7ec6069" kind="function"><name>vrna_md_defaults_helical_rise</name></member>
      <member refid="group__model__details_1gab9bb1dfeeb4aea4644b34d332cb5ec53" kind="function"><name>vrna_md_defaults_helical_rise_get</name></member>
      <member refid="group__model__details_1gad7cc34b70d275f5c7211dd2aa62f6c3c" kind="function"><name>vrna_md_defaults_backbone_length</name></member>
      <member refid="group__model__details_1gacdafdf6d361ee6a9abb46622986c9016" kind="function"><name>vrna_md_defaults_backbone_length_get</name></member>
      <member refid="group__model__details_1gaa9e920d3277fdbd25a240db9a7c435cc" kind="function"><name>vrna_md_defaults_circ_alpha0</name></member>
      <member refid="group__model__details_1ga53ce984830640c940f101e0cb2077ba0" kind="function"><name>vrna_md_defaults_circ_alpha0_get</name></member>
      <member refid="group__model__details_1gabad896c3650d420f3f3ddefc69e2bceb" kind="function"><name>set_model_details</name></member>
      <member refid="group__model__details_1gaff4caf2154e6f189a7c09008cefa67a8" kind="function"><name>option_string</name></member>
    </sectiondef>
    <briefdescription>
<para>The model details data structure and its corresponding modifiers. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_MODEL_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_MODEL_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="3"><highlight class="normal"></highlight></codeline>
<codeline lineno="4"><highlight class="normal"></highlight><highlight class="preprocessor">#ifdef<sp/>VRNA_WARN_DEPRECATED</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="5"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>if<sp/>defined(__clang__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="6"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(&quot;&quot;,<sp/>msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="7"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>elif<sp/>defined(__GNUC__)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="8"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func<sp/>__attribute__<sp/>((deprecated(msg)))</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="9"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="10"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/><sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="11"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="12"><highlight class="normal"></highlight><highlight class="preprocessor">#else</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="13"><highlight class="normal"></highlight><highlight class="preprocessor">#<sp/>define<sp/>DEPRECATED(func,<sp/>msg)<sp/>func</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="14"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="15"><highlight class="normal"></highlight></codeline>
<codeline lineno="21"><highlight class="normal"></highlight></codeline>
<codeline lineno="26"><highlight class="normal"></highlight></codeline>
<codeline lineno="27"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>NBASES</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="28"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>NBASES<sp/>8</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="29"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="30"><highlight class="normal"></highlight></codeline>
<codeline lineno="32" refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__md__s" kindref="compound">vrna_md_s</ref><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref>;</highlight></codeline>
<codeline lineno="33"><highlight class="normal"></highlight></codeline>
<codeline lineno="41" refid="group__model__details_1gaf47f9850b3b4763479f7a7e7a15648a2" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_TEMPERATURE<sp/><sp/><sp/><sp/>37.0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="42"><highlight class="normal"></highlight></codeline>
<codeline lineno="48" refid="group__model__details_1ga5505389cba74a18bbc116d2bb20256fa" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_PF_SCALE<sp/><sp/><sp/><sp/><sp/><sp/><sp/>-1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="49"><highlight class="normal"></highlight></codeline>
<codeline lineno="55" refid="group__model__details_1ga383d3ac8d08c3b6221754b50871c1200" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_BETA_SCALE<sp/><sp/><sp/><sp/><sp/>1.</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="56"><highlight class="normal"></highlight></codeline>
<codeline lineno="62" refid="group__model__details_1ga2aa7bc2cae774b83a5c468f824c27a42" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_DANGLES<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>2</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="63"><highlight class="normal"></highlight></codeline>
<codeline lineno="69" refid="group__model__details_1gabd1ab224e1048defd45c165ed7d1c108" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_SPECIAL_HP<sp/><sp/><sp/><sp/><sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="70"><highlight class="normal"></highlight></codeline>
<codeline lineno="76" refid="group__model__details_1gab72462726dd60ed0d43339bbf7ee08ad" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_NO_LP<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="77"><highlight class="normal"></highlight></codeline>
<codeline lineno="83" refid="group__model__details_1ga34702f7d14d38b877ba8e475281e97e2" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_NO_GU<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="84"><highlight class="normal"></highlight></codeline>
<codeline lineno="90" refid="group__model__details_1ga5308de46faaca4b9fd16045864901ee7" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_NO_GU_CLOSURE<sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="91"><highlight class="normal"></highlight></codeline>
<codeline lineno="96" refid="group__model__details_1ga22059033db7bcd875c51fec32425490a" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_CIRC<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="97"><highlight class="normal"></highlight></codeline>
<codeline lineno="103" refid="group__model__details_1ga793ed812e86f43799b14b2deee917f23" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_GQUAD<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="104"><highlight class="normal"></highlight></codeline>
<codeline lineno="110" refid="group__model__details_1ga63f6006a02ba2d89148441f406c309e7" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_UNIQ_ML<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="111"><highlight class="normal"></highlight></codeline>
<codeline lineno="117" refid="group__model__details_1ga6fcf6b2d0f89256cdbd166486c9b6e1e" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_ENERGY_SET<sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="118"><highlight class="normal"></highlight></codeline>
<codeline lineno="123" refid="group__model__details_1ga3fda8006ab84baf817bd8e5ccbc6bb35" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_BACKTRACK<sp/><sp/><sp/><sp/><sp/><sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="124"><highlight class="normal"></highlight></codeline>
<codeline lineno="130" refid="group__model__details_1gad0e81fcaca53c4a826c68e0796de2afb" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_BACKTRACK_TYPE<sp/>&apos;F&apos;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="131"><highlight class="normal"></highlight></codeline>
<codeline lineno="137" refid="group__model__details_1ga1d6cd5051940b126c248147c011bac6c" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_COMPUTE_BPP<sp/><sp/><sp/><sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="138"><highlight class="normal"></highlight></codeline>
<codeline lineno="144" refid="group__model__details_1ga7cb6f4ae8fdebff6746a4410814f2977" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_MAX_BP_SPAN<sp/><sp/><sp/><sp/>-1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="145"><highlight class="normal"></highlight></codeline>
<codeline lineno="151" refid="group__model__details_1ga8de04a9cb57e811e313b0f9f207f6bdb" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_WINDOW_SIZE<sp/><sp/><sp/><sp/>-1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="152"><highlight class="normal"></highlight></codeline>
<codeline lineno="158" refid="group__model__details_1ga938f68463e84fe060aa6502f428a517d" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_LOG_ML<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="159"><highlight class="normal"></highlight></codeline>
<codeline lineno="164" refid="group__model__details_1ga2a5bbfc1edf33077e39466d2d9807115" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_ALI_OLD_EN<sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="165"><highlight class="normal"></highlight></codeline>
<codeline lineno="171" refid="group__model__details_1ga64b3ab65a9ca42d4ad1d05e193083147" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_ALI_RIBO<sp/><sp/><sp/><sp/><sp/><sp/><sp/>0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="172"><highlight class="normal"></highlight></codeline>
<codeline lineno="178" refid="group__model__details_1gaaaf3d73d6abc18d3889676952bfedb96" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_ALI_CV_FACT<sp/><sp/><sp/><sp/>1.</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="179"><highlight class="normal"></highlight></codeline>
<codeline lineno="184" refid="group__model__details_1ga8f774daaafec28160c1ca5d09f2cbdba" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_ALI_NC_FACT<sp/><sp/><sp/><sp/>1.</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="185"><highlight class="normal"></highlight></codeline>
<codeline lineno="186"><highlight class="normal"></highlight></codeline>
<codeline lineno="187"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_PF_SMOOTH<sp/><sp/><sp/><sp/><sp/><sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="188"><highlight class="normal"></highlight></codeline>
<codeline lineno="192" refid="group__model__details_1gaa68703da9ccc5ae6da508bfda36b533f" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_SALT<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>1.021</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="193"><highlight class="normal"></highlight></codeline>
<codeline lineno="194"><highlight class="normal"></highlight></codeline>
<codeline lineno="198" refid="group__model__details_1gaec326f45e31be223d4ff2ae33e1a6ee5" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_SALT_MLLOWER<sp/><sp/><sp/><sp/>6</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="199"><highlight class="normal"></highlight></codeline>
<codeline lineno="200"><highlight class="normal"></highlight></codeline>
<codeline lineno="204" refid="group__model__details_1ga1d16fa20d2c6099957e975746f5fb610" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_SALT_MLUPPER<sp/><sp/><sp/><sp/>24</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="205"><highlight class="normal"></highlight></codeline>
<codeline lineno="206"><highlight class="normal"></highlight></codeline>
<codeline lineno="210" refid="group__model__details_1ga9fde1c2000066236e3130dda3ca71a21" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_SALT_DPXINIT<sp/><sp/><sp/><sp/><sp/><sp/><sp/>99999</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="211"><highlight class="normal"></highlight></codeline>
<codeline lineno="212"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_SALT_DPXINIT_FACT_RNA<sp/><sp/><sp/><sp/><sp/><sp/>-45.324</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="213"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_SALT_DPXINIT_FACT_DNA<sp/><sp/><sp/><sp/><sp/><sp/>-58.389</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="214"><highlight class="normal"></highlight></codeline>
<codeline lineno="215"><highlight class="normal"></highlight></codeline>
<codeline lineno="216"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_SALT_DPXINIT_FACT<sp/><sp/>VRNA_MODEL_SALT_DPXINIT_FACT_RNA</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="217"><highlight class="normal"></highlight></codeline>
<codeline lineno="218"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>Geometric<sp/>parameters<sp/>for<sp/>RNA<sp/>and<sp/>DNA<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="219"><highlight class="normal"></highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_HELICAL_RISE_RNA<sp/><sp/><sp/>2.8</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="221"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_HELICAL_RISE_DNA<sp/><sp/><sp/>3.4</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="225" refid="group__model__details_1ga6ac110e53604675da1cbed67336e9177" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_HELICAL_RISE<sp/><sp/><sp/>VRNA_MODEL_HELICAL_RISE_RNA</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="226"><highlight class="normal"></highlight></codeline>
<codeline lineno="227"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_BACKBONE_LENGTH_RNA<sp/><sp/><sp/>6.0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="228"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_BACKBONE_LENGTH_DNA<sp/><sp/><sp/>6.76</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="232" refid="group__model__details_1ga62e1e462516736e9e4482e2e4a550aab" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_BACKBONE_LENGTH<sp/><sp/><sp/>VRNA_MODEL_BACKBONE_LENGTH_RNA</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="233"><highlight class="normal"></highlight></codeline>
<codeline lineno="234"><highlight class="normal"></highlight></codeline>
<codeline lineno="235"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_CIRC_PENALTY<sp/><sp/><sp/>1</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="236"><highlight class="normal"></highlight></codeline>
<codeline lineno="237"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_MODEL_DEFAULT_CIRC_ALPHA0<sp/><sp/><sp/><sp/>4.385</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="238"><highlight class="normal"></highlight></codeline>
<codeline lineno="239"><highlight class="normal"></highlight></codeline>
<codeline lineno="240"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="241"><highlight class="normal"></highlight></codeline>
<codeline lineno="242"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>MAXALPHA</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="246" refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>MAXALPHA<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>20</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="247"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="248"><highlight class="normal"></highlight></codeline>
<codeline lineno="249"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="250"><highlight class="normal"></highlight></codeline>
<codeline lineno="260" refid="structvrna__md__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__md__s" kindref="compound">vrna_md_s</ref><sp/>{</highlight></codeline>
<codeline lineno="261" refid="structvrna__md__s_1a5f7e5c2b65bada5188443470e576aa4b" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__md__s_1a5f7e5c2b65bada5188443470e576aa4b" kindref="member">temperature</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="262" refid="structvrna__md__s_1a19524bf1d8d7ab590ed36edbbcaaba2c" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__md__s_1a19524bf1d8d7ab590ed36edbbcaaba2c" kindref="member">betaScale</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="263" refid="structvrna__md__s_1a97b9f2fa2d157c65413d33b1beb5159d" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a97b9f2fa2d157c65413d33b1beb5159d" kindref="member">pf_smooth</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="264" refid="structvrna__md__s_1adcda4ff2ea77748ae0e8700288282efc" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1adcda4ff2ea77748ae0e8700288282efc" kindref="member">dangles</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="288" refid="structvrna__md__s_1add64a96d23e77ef1d0ddf8dfc5228143" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1add64a96d23e77ef1d0ddf8dfc5228143" kindref="member">special_hp</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="289" refid="structvrna__md__s_1a753200bf21cee0ea2df64afe43999f5d" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a753200bf21cee0ea2df64afe43999f5d" kindref="member">noLP</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="290" refid="structvrna__md__s_1ad64a5eaf9c4550e7525b36a725fec4b2" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1ad64a5eaf9c4550e7525b36a725fec4b2" kindref="member">noGU</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="291" refid="structvrna__md__s_1a7e883db1f33f8f3baa5c9b140350c78e" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a7e883db1f33f8f3baa5c9b140350c78e" kindref="member">noGUclosure</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="292" refid="structvrna__md__s_1ae259f89a94acae0c7f1412603e7f57b5" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1ae259f89a94acae0c7f1412603e7f57b5" kindref="member">logML</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="293" refid="structvrna__md__s_1a92762e1008503d4623ff5c01e358a464" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a92762e1008503d4623ff5c01e358a464" kindref="member">circ</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="294" refid="structvrna__md__s_1a164a185e23c3d11492d8844da9457ce0" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a164a185e23c3d11492d8844da9457ce0" kindref="member">circ_penalty</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="295" refid="structvrna__md__s_1af88a511a2b1f526b4c6213de6cb8fd6e" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1af88a511a2b1f526b4c6213de6cb8fd6e" kindref="member">gquad</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="296" refid="structvrna__md__s_1ade065b814a4e2e72ead93ab502613ed2" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1ade065b814a4e2e72ead93ab502613ed2" kindref="member">uniq_ML</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="297" refid="structvrna__md__s_1a5eee4e3b468eb690d1407e0178dafb3f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a5eee4e3b468eb690d1407e0178dafb3f" kindref="member">energy_set</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="298" refid="structvrna__md__s_1a31f4471608cbdd03887f63c281823adb" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a31f4471608cbdd03887f63c281823adb" kindref="member">backtrack</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="299" refid="structvrna__md__s_1abb265da25121d22ed11c8435861f0e53" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1abb265da25121d22ed11c8435861f0e53" kindref="member">backtrack_type</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="300" refid="structvrna__md__s_1aa0c3e03d9064363e27adcc92b8d0380f" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1aa0c3e03d9064363e27adcc92b8d0380f" kindref="member">compute_bpp</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="301" refid="structvrna__md__s_1a3fde4ac9eaf972f503c7a76726cefb59" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a3fde4ac9eaf972f503c7a76726cefb59" kindref="member">nonstandards</ref>[64];<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="302" refid="structvrna__md__s_1a659e5fcc6e8c9f1a68e7de6548eef3b0" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a659e5fcc6e8c9f1a68e7de6548eef3b0" kindref="member">max_bp_span</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="303"><highlight class="normal"></highlight></codeline>
<codeline lineno="304" refid="structvrna__md__s_1a9ed7ba42fcc46915c5c0c524f3d255f5" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a9ed7ba42fcc46915c5c0c524f3d255f5" kindref="member">min_loop_size</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="309" refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1abea42f9229f8d8d6bcbedef316315bfc" kindref="member">window_size</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="310" refid="structvrna__md__s_1ab53aec4503130877973c6111ae6f0f76" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1ab53aec4503130877973c6111ae6f0f76" kindref="member">oldAliEn</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="311" refid="structvrna__md__s_1a3df2ae4bd9c133ef8ab92a53b1d035ec" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a3df2ae4bd9c133ef8ab92a53b1d035ec" kindref="member">ribo</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="312" refid="structvrna__md__s_1a62ebefb9d0643e5c4c8a2ec84a105ce6" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__md__s_1a62ebefb9d0643e5c4c8a2ec84a105ce6" kindref="member">cv_fact</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="313" refid="structvrna__md__s_1abcf568e6124bfcb2f847ff4eb0dfded6" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__md__s_1abcf568e6124bfcb2f847ff4eb0dfded6" kindref="member">nc_fact</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="314" refid="structvrna__md__s_1ab6f4cabaa9b4726b13592486d5bc21c7" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__md__s_1ab6f4cabaa9b4726b13592486d5bc21c7" kindref="member">sfact</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="315" refid="structvrna__md__s_1ad082d0fea31e002b90cdfe5e6382f8b0" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1ad082d0fea31e002b90cdfe5e6382f8b0" kindref="member">rtype</ref>[8];<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="316" refid="structvrna__md__s_1a66136cf9abc8ff790ec0d33245d68fd5" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">short</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="structvrna__md__s_1a66136cf9abc8ff790ec0d33245d68fd5" kindref="member">alias</ref>[<ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>+<sp/>1];<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="317" refid="structvrna__md__s_1ab4da594c638707e212f64aadb54a7454" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1ab4da594c638707e212f64aadb54a7454" kindref="member">pair</ref>[<ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>+<sp/>1][<ref refid="group__model__details_1ga05a5ffe718aa431d97419a12fb082379" kindref="member">MAXALPHA</ref><sp/>+<sp/>1];<sp/></highlight></codeline>
<codeline lineno="318" refid="structvrna__md__s_1a94bb8f9342aa99d9669c34426f6ef69c" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/><ref refid="structvrna__md__s_1a94bb8f9342aa99d9669c34426f6ef69c" kindref="member">pair_dist</ref>[7][7];<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="319" refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/><ref refid="structvrna__md__s_1a66193a872ba929c87915bcd6d7e540d2" kindref="member">salt</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="320" refid="structvrna__md__s_1acf367f80a54bd135a3f889e17bd670a3" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1acf367f80a54bd135a3f889e17bd670a3" kindref="member">saltMLLower</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="321" refid="structvrna__md__s_1a7bc6a05de301754eb5b95a620a72a60a" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a7bc6a05de301754eb5b95a620a72a60a" kindref="member">saltMLUpper</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="322" refid="structvrna__md__s_1a467b2618649b277a8843967861e2d287" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__md__s_1a467b2618649b277a8843967861e2d287" kindref="member">saltDPXInit</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="326"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/>saltDPXInitFact;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="327"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/>helical_rise;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="328"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/><sp/><sp/>backbone_length;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="329"><highlight class="normal"></highlight></codeline>
<codeline lineno="330"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><sp/>circ_alpha0;</highlight></codeline>
<codeline lineno="331"><highlight class="normal">};</highlight></codeline>
<codeline lineno="332"><highlight class="normal"></highlight></codeline>
<codeline lineno="333"><highlight class="normal"></highlight></codeline>
<codeline lineno="342"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="343" refid="group__model__details_1ga8ac6ff84936282436f822644bf841f66" refkind="member"><highlight class="normal"><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><sp/>*md);</highlight></codeline>
<codeline lineno="344"><highlight class="normal"></highlight></codeline>
<codeline lineno="345"><highlight class="normal"></highlight></codeline>
<codeline lineno="358"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="359" refid="group__model__details_1ga36ae40b8c3b82362f5798ad5b047b814" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga36ae40b8c3b82362f5798ad5b047b814" kindref="member">vrna_md_update</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md);</highlight></codeline>
<codeline lineno="360"><highlight class="normal"></highlight></codeline>
<codeline lineno="361"><highlight class="normal"></highlight></codeline>
<codeline lineno="372"><highlight class="normal"><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*</highlight></codeline>
<codeline lineno="373" refid="group__model__details_1gaa7c753fefc98866d5dc0dae3e6bd4486" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaa7c753fefc98866d5dc0dae3e6bd4486" kindref="member">vrna_md_copy</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*md_to,</highlight></codeline>
<codeline lineno="374"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>*md_from);</highlight></codeline>
<codeline lineno="375"><highlight class="normal"></highlight></codeline>
<codeline lineno="376"><highlight class="normal"></highlight></codeline>
<codeline lineno="382"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="383" refid="group__model__details_1ga2207e3b40295825655c629421fe8f349" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga2207e3b40295825655c629421fe8f349" kindref="member">vrna_md_option_string</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md);</highlight></codeline>
<codeline lineno="384"><highlight class="normal"></highlight></codeline>
<codeline lineno="385"><highlight class="normal"></highlight></codeline>
<codeline lineno="386"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="387"><highlight class="normal">vrna_md_set_nonstandards(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/><sp/>*md,</highlight></codeline>
<codeline lineno="388"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*ns_bases);</highlight></codeline>
<codeline lineno="389"><highlight class="normal"></highlight></codeline>
<codeline lineno="390"><highlight class="normal"></highlight></codeline>
<codeline lineno="410"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="411" refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga70834424cf804d149937de89f80ceb45" kindref="member">vrna_md_defaults_reset</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md_p);</highlight></codeline>
<codeline lineno="412"><highlight class="normal"></highlight></codeline>
<codeline lineno="413"><highlight class="normal"></highlight></codeline>
<codeline lineno="421"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="422" refid="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaf9e527e9a2f7e6fd6e42bc6e602f5445" kindref="member">vrna_md_defaults_temperature</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>T);</highlight></codeline>
<codeline lineno="423"><highlight class="normal"></highlight></codeline>
<codeline lineno="424"><highlight class="normal"></highlight></codeline>
<codeline lineno="432"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="433" refid="group__model__details_1ga96b24a74437f9ba46c4e06343155bf46" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga96b24a74437f9ba46c4e06343155bf46" kindref="member">vrna_md_defaults_temperature_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="434"><highlight class="normal"></highlight></codeline>
<codeline lineno="435"><highlight class="normal"></highlight></codeline>
<codeline lineno="445"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="446" refid="group__model__details_1gae984567db36c3f9b8731ecc917abf3a2" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gae984567db36c3f9b8731ecc917abf3a2" kindref="member">vrna_md_defaults_betaScale</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>b);</highlight></codeline>
<codeline lineno="447"><highlight class="normal"></highlight></codeline>
<codeline lineno="448"><highlight class="normal"></highlight></codeline>
<codeline lineno="456"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="457" refid="group__model__details_1gabb8780f5410c52f970d75b044059bd09" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gabb8780f5410c52f970d75b044059bd09" kindref="member">vrna_md_defaults_betaScale_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="458"><highlight class="normal"></highlight></codeline>
<codeline lineno="459"><highlight class="normal"></highlight></codeline>
<codeline lineno="460"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="461"><highlight class="normal">vrna_md_defaults_pf_smooth(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>s);</highlight></codeline>
<codeline lineno="462"><highlight class="normal"></highlight></codeline>
<codeline lineno="463"><highlight class="normal"></highlight></codeline>
<codeline lineno="464"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="465"><highlight class="normal">vrna_md_defaults_pf_smooth_get(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="466"><highlight class="normal"></highlight></codeline>
<codeline lineno="467"><highlight class="normal"></highlight></codeline>
<codeline lineno="475"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="476" refid="group__model__details_1gac76a5374def8e5e4e644ff6e4cc72dee" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gac76a5374def8e5e4e644ff6e4cc72dee" kindref="member">vrna_md_defaults_dangles</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>d);</highlight></codeline>
<codeline lineno="477"><highlight class="normal"></highlight></codeline>
<codeline lineno="478"><highlight class="normal"></highlight></codeline>
<codeline lineno="486"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="487" refid="group__model__details_1ga67ca06f95ae133778c79a4493c9817b8" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga67ca06f95ae133778c79a4493c9817b8" kindref="member">vrna_md_defaults_dangles_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="488"><highlight class="normal"></highlight></codeline>
<codeline lineno="489"><highlight class="normal"></highlight></codeline>
<codeline lineno="497"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="498" refid="group__model__details_1gafff6449a02744add0308e653230c15fc" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gafff6449a02744add0308e653230c15fc" kindref="member">vrna_md_defaults_special_hp</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="499"><highlight class="normal"></highlight></codeline>
<codeline lineno="500"><highlight class="normal"></highlight></codeline>
<codeline lineno="508"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="509" refid="group__model__details_1ga1d68a6efdaa1253cc63fd9cd06452559" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga1d68a6efdaa1253cc63fd9cd06452559" kindref="member">vrna_md_defaults_special_hp_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="510"><highlight class="normal"></highlight></codeline>
<codeline lineno="511"><highlight class="normal"></highlight></codeline>
<codeline lineno="519"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="520" refid="group__model__details_1ga2f88ffc393ac9d7987849c965fd29ea8" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga2f88ffc393ac9d7987849c965fd29ea8" kindref="member">vrna_md_defaults_noLP</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="521"><highlight class="normal"></highlight></codeline>
<codeline lineno="522"><highlight class="normal"></highlight></codeline>
<codeline lineno="530"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="531" refid="group__model__details_1ga934344888fbacaed538bbbfe910f2aa6" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga934344888fbacaed538bbbfe910f2aa6" kindref="member">vrna_md_defaults_noLP_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="532"><highlight class="normal"></highlight></codeline>
<codeline lineno="533"><highlight class="normal"></highlight></codeline>
<codeline lineno="541"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="542" refid="group__model__details_1ga98218f85c7a957a1d1ddf4627fdf5a39" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga98218f85c7a957a1d1ddf4627fdf5a39" kindref="member">vrna_md_defaults_noGU</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="543"><highlight class="normal"></highlight></codeline>
<codeline lineno="544"><highlight class="normal"></highlight></codeline>
<codeline lineno="552"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="553" refid="group__model__details_1ga5faa7d4e536d7fe36ec25428c0cf2563" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga5faa7d4e536d7fe36ec25428c0cf2563" kindref="member">vrna_md_defaults_noGU_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="554"><highlight class="normal"></highlight></codeline>
<codeline lineno="555"><highlight class="normal"></highlight></codeline>
<codeline lineno="563"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="564" refid="group__model__details_1gade5b9951d71ca2fb357a4e6c0c18ccd1" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gade5b9951d71ca2fb357a4e6c0c18ccd1" kindref="member">vrna_md_defaults_noGUclosure</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="565"><highlight class="normal"></highlight></codeline>
<codeline lineno="566"><highlight class="normal"></highlight></codeline>
<codeline lineno="574"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="575" refid="group__model__details_1ga4f7fdad083243a5348d63320ddaa70f3" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga4f7fdad083243a5348d63320ddaa70f3" kindref="member">vrna_md_defaults_noGUclosure_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="576"><highlight class="normal"></highlight></codeline>
<codeline lineno="577"><highlight class="normal"></highlight></codeline>
<codeline lineno="585"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="586" refid="group__model__details_1ga3de50a73455d88c3957386933b8e1f90" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga3de50a73455d88c3957386933b8e1f90" kindref="member">vrna_md_defaults_logML</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="587"><highlight class="normal"></highlight></codeline>
<codeline lineno="588"><highlight class="normal"></highlight></codeline>
<codeline lineno="596"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="597" refid="group__model__details_1ga93f04e070d529c5d0bb87c9681f6ad29" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga93f04e070d529c5d0bb87c9681f6ad29" kindref="member">vrna_md_defaults_logML_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="598"><highlight class="normal"></highlight></codeline>
<codeline lineno="599"><highlight class="normal"></highlight></codeline>
<codeline lineno="607"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="608" refid="group__model__details_1ga4e1deb3e91a8a99e5c6dd905a5eb0186" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga4e1deb3e91a8a99e5c6dd905a5eb0186" kindref="member">vrna_md_defaults_circ</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="609"><highlight class="normal"></highlight></codeline>
<codeline lineno="610"><highlight class="normal"></highlight></codeline>
<codeline lineno="618"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="619" refid="group__model__details_1gad3a7e58de344ad93a08925f58f94f6fb" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gad3a7e58de344ad93a08925f58f94f6fb" kindref="member">vrna_md_defaults_circ_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="620"><highlight class="normal"></highlight></codeline>
<codeline lineno="621"><highlight class="normal"></highlight></codeline>
<codeline lineno="629"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="630" refid="group__model__details_1gae36c04033105fc519e040063341e6f4b" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gae36c04033105fc519e040063341e6f4b" kindref="member">vrna_md_defaults_circ_penalty</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="631"><highlight class="normal"></highlight></codeline>
<codeline lineno="632"><highlight class="normal"></highlight></codeline>
<codeline lineno="640"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="641" refid="group__model__details_1gadd7f2da829239856a5a14f6c43d26921" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gadd7f2da829239856a5a14f6c43d26921" kindref="member">vrna_md_defaults_circ_penalty_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="642"><highlight class="normal"></highlight></codeline>
<codeline lineno="643"><highlight class="normal"></highlight></codeline>
<codeline lineno="651"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="652" refid="group__model__details_1ga0685ca2aeb39af76f2421fc308163dce" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga0685ca2aeb39af76f2421fc308163dce" kindref="member">vrna_md_defaults_gquad</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="653"><highlight class="normal"></highlight></codeline>
<codeline lineno="654"><highlight class="normal"></highlight></codeline>
<codeline lineno="662"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="663" refid="group__model__details_1gae645b8612f879eb38b45244fa9eddb9e" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gae645b8612f879eb38b45244fa9eddb9e" kindref="member">vrna_md_defaults_gquad_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="664"><highlight class="normal"></highlight></codeline>
<codeline lineno="665"><highlight class="normal"></highlight></codeline>
<codeline lineno="675"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="676" refid="group__model__details_1ga59b944f61c5d2babec2d4c48c820de67" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga59b944f61c5d2babec2d4c48c820de67" kindref="member">vrna_md_defaults_uniq_ML</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="677"><highlight class="normal"></highlight></codeline>
<codeline lineno="678"><highlight class="normal"></highlight></codeline>
<codeline lineno="686"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="687" refid="group__model__details_1gab48e70fd024bf838404bcbcca0c874a0" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gab48e70fd024bf838404bcbcca0c874a0" kindref="member">vrna_md_defaults_uniq_ML_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="688"><highlight class="normal"></highlight></codeline>
<codeline lineno="689"><highlight class="normal"></highlight></codeline>
<codeline lineno="697"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="698" refid="group__model__details_1ga8dd29c55787a4576277e1907e92d810c" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga8dd29c55787a4576277e1907e92d810c" kindref="member">vrna_md_defaults_energy_set</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>e);</highlight></codeline>
<codeline lineno="699"><highlight class="normal"></highlight></codeline>
<codeline lineno="700"><highlight class="normal"></highlight></codeline>
<codeline lineno="708"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="709" refid="group__model__details_1ga017ed6afb1cba2b7f242412cab618b53" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga017ed6afb1cba2b7f242412cab618b53" kindref="member">vrna_md_defaults_energy_set_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="710"><highlight class="normal"></highlight></codeline>
<codeline lineno="711"><highlight class="normal"></highlight></codeline>
<codeline lineno="719"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="720" refid="group__model__details_1ga978c468b2fe96a70d5191e3dd17d5599" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga978c468b2fe96a70d5191e3dd17d5599" kindref="member">vrna_md_defaults_backtrack</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="721"><highlight class="normal"></highlight></codeline>
<codeline lineno="722"><highlight class="normal"></highlight></codeline>
<codeline lineno="730"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="731" refid="group__model__details_1ga90da1156e6883ddd68527c2830706648" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga90da1156e6883ddd68527c2830706648" kindref="member">vrna_md_defaults_backtrack_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="732"><highlight class="normal"></highlight></codeline>
<codeline lineno="733"><highlight class="normal"></highlight></codeline>
<codeline lineno="741"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="742" refid="group__model__details_1ga68305274de96b56b7799575e222560d8" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga68305274de96b56b7799575e222560d8" kindref="member">vrna_md_defaults_backtrack_type</ref>(</highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>t);</highlight></codeline>
<codeline lineno="743"><highlight class="normal"></highlight></codeline>
<codeline lineno="744"><highlight class="normal"></highlight></codeline>
<codeline lineno="752"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="753" refid="group__model__details_1ga1425b4ebd0e034dead66d79becd64143" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga1425b4ebd0e034dead66d79becd64143" kindref="member">vrna_md_defaults_backtrack_type_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="754"><highlight class="normal"></highlight></codeline>
<codeline lineno="755"><highlight class="normal"></highlight></codeline>
<codeline lineno="763"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="764" refid="group__model__details_1gaf1b5db10f1f476767f9a95f8a78e3132" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaf1b5db10f1f476767f9a95f8a78e3132" kindref="member">vrna_md_defaults_compute_bpp</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="765"><highlight class="normal"></highlight></codeline>
<codeline lineno="766"><highlight class="normal"></highlight></codeline>
<codeline lineno="774"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="775" refid="group__model__details_1gaa3a537e61fbe0518673bf9f73fd820f3" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaa3a537e61fbe0518673bf9f73fd820f3" kindref="member">vrna_md_defaults_compute_bpp_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="776"><highlight class="normal"></highlight></codeline>
<codeline lineno="777"><highlight class="normal"></highlight></codeline>
<codeline lineno="785"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="786" refid="group__model__details_1ga4c4bc962f09b4480cb8499f1cf8ae4ec" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga4c4bc962f09b4480cb8499f1cf8ae4ec" kindref="member">vrna_md_defaults_max_bp_span</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>span);</highlight></codeline>
<codeline lineno="787"><highlight class="normal"></highlight></codeline>
<codeline lineno="788"><highlight class="normal"></highlight></codeline>
<codeline lineno="796"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="797" refid="group__model__details_1gaa60f989e062fecd4d4bac89c1883da85" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaa60f989e062fecd4d4bac89c1883da85" kindref="member">vrna_md_defaults_max_bp_span_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="798"><highlight class="normal"></highlight></codeline>
<codeline lineno="799"><highlight class="normal"></highlight></codeline>
<codeline lineno="807"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="808" refid="group__model__details_1gac152f1e78c1058a10261022c8dfda0f7" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gac152f1e78c1058a10261022c8dfda0f7" kindref="member">vrna_md_defaults_min_loop_size</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>size);</highlight></codeline>
<codeline lineno="809"><highlight class="normal"></highlight></codeline>
<codeline lineno="810"><highlight class="normal"></highlight></codeline>
<codeline lineno="818"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="819" refid="group__model__details_1ga5cc691174a75c652807dc361b617632a" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga5cc691174a75c652807dc361b617632a" kindref="member">vrna_md_defaults_min_loop_size_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="820"><highlight class="normal"></highlight></codeline>
<codeline lineno="821"><highlight class="normal"></highlight></codeline>
<codeline lineno="829"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="830" refid="group__model__details_1ga7b802ce0e8c3181bf5cb580de6d5b26a" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga7b802ce0e8c3181bf5cb580de6d5b26a" kindref="member">vrna_md_defaults_window_size</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>size);</highlight></codeline>
<codeline lineno="831"><highlight class="normal"></highlight></codeline>
<codeline lineno="832"><highlight class="normal"></highlight></codeline>
<codeline lineno="840"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="841" refid="group__model__details_1ga670146a9aa3ba77f4d422d60b7c30ac9" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga670146a9aa3ba77f4d422d60b7c30ac9" kindref="member">vrna_md_defaults_window_size_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="842"><highlight class="normal"></highlight></codeline>
<codeline lineno="843"><highlight class="normal"></highlight></codeline>
<codeline lineno="854"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="855" refid="group__model__details_1ga41521d5b9fb7e0f31e7ea73f5792afab" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga41521d5b9fb7e0f31e7ea73f5792afab" kindref="member">vrna_md_defaults_oldAliEn</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="856"><highlight class="normal"></highlight></codeline>
<codeline lineno="857"><highlight class="normal"></highlight></codeline>
<codeline lineno="865"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="866" refid="group__model__details_1ga2374492b5019df88022fe4c05f0f3630" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga2374492b5019df88022fe4c05f0f3630" kindref="member">vrna_md_defaults_oldAliEn_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="867"><highlight class="normal"></highlight></codeline>
<codeline lineno="868"><highlight class="normal"></highlight></codeline>
<codeline lineno="876"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="877" refid="group__model__details_1ga937c45e1d06fd6168730a9b08d130be3" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga937c45e1d06fd6168730a9b08d130be3" kindref="member">vrna_md_defaults_ribo</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>flag);</highlight></codeline>
<codeline lineno="878"><highlight class="normal"></highlight></codeline>
<codeline lineno="879"><highlight class="normal"></highlight></codeline>
<codeline lineno="887"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="888" refid="group__model__details_1ga169027f0c0561ea7d87b655e4b336bfc" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga169027f0c0561ea7d87b655e4b336bfc" kindref="member">vrna_md_defaults_ribo_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="889"><highlight class="normal"></highlight></codeline>
<codeline lineno="890"><highlight class="normal"></highlight></codeline>
<codeline lineno="898"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="899" refid="group__model__details_1gad3a3f40baafd91a6ce80a91a68e20053" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gad3a3f40baafd91a6ce80a91a68e20053" kindref="member">vrna_md_defaults_cv_fact</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>factor);</highlight></codeline>
<codeline lineno="900"><highlight class="normal"></highlight></codeline>
<codeline lineno="901"><highlight class="normal"></highlight></codeline>
<codeline lineno="909"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="910" refid="group__model__details_1gae59c68393807217b0a2497adb64d3ee3" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gae59c68393807217b0a2497adb64d3ee3" kindref="member">vrna_md_defaults_cv_fact_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="911"><highlight class="normal"></highlight></codeline>
<codeline lineno="912"><highlight class="normal"></highlight></codeline>
<codeline lineno="920"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="921" refid="group__model__details_1gac35e596c850dce3ad55c49119fd7d471" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gac35e596c850dce3ad55c49119fd7d471" kindref="member">vrna_md_defaults_nc_fact</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>factor);</highlight></codeline>
<codeline lineno="922"><highlight class="normal"></highlight></codeline>
<codeline lineno="923"><highlight class="normal"></highlight></codeline>
<codeline lineno="931"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="932" refid="group__model__details_1ga7ac759eaa7159bf5f022745f5da59508" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga7ac759eaa7159bf5f022745f5da59508" kindref="member">vrna_md_defaults_nc_fact_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="933"><highlight class="normal"></highlight></codeline>
<codeline lineno="934"><highlight class="normal"></highlight></codeline>
<codeline lineno="942"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="943" refid="group__model__details_1ga3f73d3029d3d0025d4cc311510cd95a3" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga3f73d3029d3d0025d4cc311510cd95a3" kindref="member">vrna_md_defaults_sfact</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>factor);</highlight></codeline>
<codeline lineno="944"><highlight class="normal"></highlight></codeline>
<codeline lineno="945"><highlight class="normal"></highlight></codeline>
<codeline lineno="953"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="954" refid="group__model__details_1gab2df6aab954b63fd3592d18e90285dae" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gab2df6aab954b63fd3592d18e90285dae" kindref="member">vrna_md_defaults_sfact_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="955"><highlight class="normal"></highlight></codeline>
<codeline lineno="956"><highlight class="normal"></highlight></codeline>
<codeline lineno="962"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="963" refid="group__model__details_1gabfb475999a35e9af42b21326a9edca12" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gabfb475999a35e9af42b21326a9edca12" kindref="member">vrna_md_defaults_salt</ref>(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga59bc4fe917f2ad11376d083260e289da" kindref="member">salt</ref>);</highlight></codeline>
<codeline lineno="964"><highlight class="normal"></highlight></codeline>
<codeline lineno="965"><highlight class="normal"></highlight></codeline>
<codeline lineno="970"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="971" refid="group__model__details_1ga28eb9dd2f11828da7cc25b93884c965f" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga28eb9dd2f11828da7cc25b93884c965f" kindref="member">vrna_md_defaults_salt_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="972"><highlight class="normal"></highlight></codeline>
<codeline lineno="973"><highlight class="normal"></highlight></codeline>
<codeline lineno="979"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="980" refid="group__model__details_1ga807b1615aea57f61cc0a269065beface" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga807b1615aea57f61cc0a269065beface" kindref="member">vrna_md_defaults_saltMLLower</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>lower);</highlight></codeline>
<codeline lineno="981"><highlight class="normal"></highlight></codeline>
<codeline lineno="982"><highlight class="normal"></highlight></codeline>
<codeline lineno="987"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="988" refid="group__model__details_1ga0813eb58f9382ae92642016960a4a781" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga0813eb58f9382ae92642016960a4a781" kindref="member">vrna_md_defaults_saltMLLower_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="989"><highlight class="normal"></highlight></codeline>
<codeline lineno="990"><highlight class="normal"></highlight></codeline>
<codeline lineno="996"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="997" refid="group__model__details_1gaf4d0ae6115687f13d4ccabcd3b45ad7c" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaf4d0ae6115687f13d4ccabcd3b45ad7c" kindref="member">vrna_md_defaults_saltMLUpper</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>upper);</highlight></codeline>
<codeline lineno="998"><highlight class="normal"></highlight></codeline>
<codeline lineno="999"><highlight class="normal"></highlight></codeline>
<codeline lineno="1004"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1005" refid="group__model__details_1ga28bc6652930e82ca1b105e419f6f4595" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga28bc6652930e82ca1b105e419f6f4595" kindref="member">vrna_md_defaults_saltMLUpper_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1006"><highlight class="normal"></highlight></codeline>
<codeline lineno="1007"><highlight class="normal"></highlight></codeline>
<codeline lineno="1014"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1015" refid="group__model__details_1gaaa7cca6b6a021221d56a7ee3b2b9b10c" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gaaa7cca6b6a021221d56a7ee3b2b9b10c" kindref="member">vrna_md_defaults_saltDPXInit</ref>(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>value);</highlight></codeline>
<codeline lineno="1016"><highlight class="normal"></highlight></codeline>
<codeline lineno="1017"><highlight class="normal"></highlight></codeline>
<codeline lineno="1024"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1025" refid="group__model__details_1ga02e0db8bf2345c12c28913af1a92186c" refkind="member"><highlight class="normal"><ref refid="group__model__details_1ga02e0db8bf2345c12c28913af1a92186c" kindref="member">vrna_md_defaults_saltDPXInit_get</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1026"><highlight class="normal"></highlight></codeline>
<codeline lineno="1027"><highlight class="normal"></highlight></codeline>
<codeline lineno="1028"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1029"><highlight class="normal">vrna_md_defaults_saltDPXInitFact(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>value);</highlight></codeline>
<codeline lineno="1030"><highlight class="normal"></highlight></codeline>
<codeline lineno="1031"><highlight class="normal"></highlight></codeline>
<codeline lineno="1032"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1033"><highlight class="normal">vrna_md_defaults_saltDPXInitFact_get(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1034"><highlight class="normal"></highlight></codeline>
<codeline lineno="1035"><highlight class="normal"></highlight></codeline>
<codeline lineno="1036"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1037"><highlight class="normal">vrna_md_defaults_helical_rise(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>value);</highlight></codeline>
<codeline lineno="1038"><highlight class="normal"></highlight></codeline>
<codeline lineno="1039"><highlight class="normal"></highlight></codeline>
<codeline lineno="1040"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1041"><highlight class="normal">vrna_md_defaults_helical_rise_get(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1042"><highlight class="normal"></highlight></codeline>
<codeline lineno="1043"><highlight class="normal"></highlight></codeline>
<codeline lineno="1044"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1045"><highlight class="normal">vrna_md_defaults_backbone_length(</highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>value);</highlight></codeline>
<codeline lineno="1046"><highlight class="normal"></highlight></codeline>
<codeline lineno="1047"><highlight class="normal"></highlight></codeline>
<codeline lineno="1048"><highlight class="normal"></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1049"><highlight class="normal">vrna_md_defaults_backbone_length_get(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1050"><highlight class="normal"></highlight></codeline>
<codeline lineno="1051"><highlight class="normal"></highlight></codeline>
<codeline lineno="1052"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1053"><highlight class="normal">vrna_md_defaults_circ_alpha0(</highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/>a0);</highlight></codeline>
<codeline lineno="1054"><highlight class="normal"></highlight></codeline>
<codeline lineno="1055"><highlight class="normal"></highlight></codeline>
<codeline lineno="1056"><highlight class="normal"></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1057"><highlight class="normal">vrna_md_defaults_circ_alpha0_get(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1058"><highlight class="normal"></highlight></codeline>
<codeline lineno="1059"><highlight class="normal"></highlight></codeline>
<codeline lineno="1060"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1061"><highlight class="normal"></highlight></codeline>
<codeline lineno="1062"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>model_detailsT<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>vrna_md_t<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="comment">/*<sp/>restore<sp/>compatibility<sp/>of<sp/>struct<sp/>rename<sp/>*/</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1063"><highlight class="normal"></highlight></codeline>
<codeline lineno="1064"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>BEGIN<sp/>deprecated<sp/>global<sp/>variables:<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1065"><highlight class="normal"></highlight></codeline>
<codeline lineno="1077"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gab4b11c8d9c758430960896bc3fe82ead" kindref="member">temperature</ref>,</highlight></codeline>
<codeline lineno="1078"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>temperature<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_temperature()<sp/>and<sp/>vrna_md_defaults_temperature_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1079"><highlight class="normal"></highlight></codeline>
<codeline lineno="1080"><highlight class="normal"></highlight></codeline>
<codeline lineno="1092"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gad3b22044065acc6dee0af68931b52cfd" kindref="member">pf_scale</ref>,</highlight></codeline>
<codeline lineno="1093"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>pf_scale<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_pf_scale()<sp/>and<sp/>vrna_md_defaults_pf_scale_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1094"><highlight class="normal"></highlight></codeline>
<codeline lineno="1116"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga72b511ed1201f7e23ec437e468790d74" kindref="member">dangles</ref>,</highlight></codeline>
<codeline lineno="1117"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>dangles<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_dangles()<sp/>and<sp/>vrna_md_defaults_dangles_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1118"><highlight class="normal"></highlight></codeline>
<codeline lineno="1124"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga4f6265bdf0ead7ff4628a360adbfd77e" kindref="member">tetra_loop</ref>,</highlight></codeline>
<codeline lineno="1125"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>tetra_loop<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_tetra_loop()<sp/>and<sp/>vrna_md_defaults_tetra_loop_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1126"><highlight class="normal"></highlight></codeline>
<codeline lineno="1134"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga097eccaabd6ae8b4fef83cccff85bb5d" kindref="member">noLonelyPairs</ref>,</highlight></codeline>
<codeline lineno="1135"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>noLP<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_noLP()<sp/>and<sp/>vrna_md_defaults_noLP_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1136"><highlight class="normal"></highlight></codeline>
<codeline lineno="1140"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gabf380d09e4f1ab94fc6af57cf0ad5d32" kindref="member">noGU</ref>,</highlight></codeline>
<codeline lineno="1141"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>noGU<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_noGU()<sp/>and<sp/>vrna_md_defaults_noGU_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1142"><highlight class="normal"></highlight></codeline>
<codeline lineno="1146"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gaa8d1c7b92489179e1eafa562b7bdd259" kindref="member">no_closingGU</ref>,</highlight></codeline>
<codeline lineno="1147"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>noGU_closure<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_noGU_closure()<sp/>and<sp/>vrna_md_defaults_noGU_closure_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1148"><highlight class="normal"></highlight></codeline>
<codeline lineno="1152"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gaf9202a1a09f5828dc731e2d9a10fa111" kindref="member">circ</ref>,</highlight></codeline>
<codeline lineno="1153"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>circ<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_circ()<sp/>and<sp/>vrna_md_defaults_circ_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1154"><highlight class="normal"></highlight></codeline>
<codeline lineno="1158"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga25f2bdcdf56e813d288845484a13d704" kindref="member">gquad</ref>,</highlight></codeline>
<codeline lineno="1159"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>gquad<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_gquad()<sp/>and<sp/>vrna_md_defaults_gquad_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1160"><highlight class="normal"></highlight></codeline>
<codeline lineno="1164"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga6c5655c8b272e3e6cab74dd0f540294f" kindref="member">uniq_ML</ref>,</highlight></codeline>
<codeline lineno="1165"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>uniq_ML<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_uniq_ML()<sp/>and<sp/>vrna_md_defaults_uniq_ML_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1166"><highlight class="normal"></highlight></codeline>
<codeline lineno="1174"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gafb1ef1166da85092ae8a325e02dcae71" kindref="member">energy_set</ref>,</highlight></codeline>
<codeline lineno="1175"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>energy_set<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_energy_set()<sp/>and<sp/>vrna_md_defaults_energy_set_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1176"><highlight class="normal"></highlight></codeline>
<codeline lineno="1183"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gad512b5dd4dbec60faccfe137bb474489" kindref="member">do_backtrack</ref>,</highlight></codeline>
<codeline lineno="1184"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>backtrack<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_backtrack()<sp/>and<sp/>vrna_md_defaults_backtrack_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1185"><highlight class="normal"></highlight></codeline>
<codeline lineno="1193"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga83bdb43472a259c71e69fa9f70f420c3" kindref="member">backtrack_type</ref>,</highlight></codeline>
<codeline lineno="1194"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>backtrack_type<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_backtrack_type()<sp/>and<sp/>vrna_md_defaults_backtrack_type_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1195"><highlight class="normal"></highlight></codeline>
<codeline lineno="1203"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*<ref refid="group__model__details_1ga2695d91cc535d09c2eae5c3884e2ec64" kindref="member">nonstandards</ref>,</highlight></codeline>
<codeline lineno="1204"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>nonstandards<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_nonstandards()<sp/>and<sp/>vrna_md_defaults_nonstandards_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1205"><highlight class="normal"></highlight></codeline>
<codeline lineno="1211"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga18df869af0d70101106458fc3f027806" kindref="member">max_bp_span</ref>,</highlight></codeline>
<codeline lineno="1212"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>max_bp_span<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_max_bp_span()<sp/>and<sp/>vrna_md_defaults_max_bp_span_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1213"><highlight class="normal"></highlight></codeline>
<codeline lineno="1217"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gac408868ba00671cbc7d1d535105af045" kindref="member">oldAliEn</ref>,</highlight></codeline>
<codeline lineno="1218"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>oldAliEn<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_oldAliEn()<sp/>and<sp/>vrna_md_defaults_oldAliEn_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1219"><highlight class="normal"></highlight></codeline>
<codeline lineno="1223"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga0656afca1d2853f9ee6591172f5638de" kindref="member">ribo</ref>,</highlight></codeline>
<codeline lineno="1224"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>ribo<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_ribo()<sp/>and<sp/>vrna_md_defaults_ribo_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1225"><highlight class="normal"></highlight></codeline>
<codeline lineno="1226"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gaf3cbac6ff5d706d6e414677841ddf94c" kindref="member">cv_fact</ref>,</highlight></codeline>
<codeline lineno="1227"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>cv_fact<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_cv_fact()<sp/>and<sp/>vrna_md_defaults_cv_fact_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1228"><highlight class="normal"></highlight></codeline>
<codeline lineno="1229"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga502948a122a2af5b914355b1f3ea2f61" kindref="member">nc_fact</ref>,</highlight></codeline>
<codeline lineno="1230"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>nc_fact<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_nc_fact()<sp/>and<sp/>vrna_md_defaults_nc_fact_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1231"><highlight class="normal"></highlight></codeline>
<codeline lineno="1233"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="fold__vars_8h_1a80c3c5fd35e7479704cc91d2d0367743" kindref="member">logML</ref>,</highlight></codeline>
<codeline lineno="1234"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>logML<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_logML()<sp/>and<sp/>vrna_md_defaults_logML_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1235"><highlight class="normal"></highlight></codeline>
<codeline lineno="1237"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">double</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1ga59bc4fe917f2ad11376d083260e289da" kindref="member">salt</ref>,</highlight></codeline>
<codeline lineno="1238"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>salt<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_salt()<sp/>and<sp/>vrna_md_defaults_salt_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1239"><highlight class="normal"></highlight></codeline>
<codeline lineno="1241"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="group__model__details_1gafd2b9a6a1d42a6bf2b8be99a4b44dc7e" kindref="member">saltDPXInit</ref>,</highlight></codeline>
<codeline lineno="1242"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>saltDPXInit<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_saltDPXInit()<sp/>and<sp/>vrna_md_defaults_saltDPXInit_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1243"><highlight class="normal"></highlight></codeline>
<codeline lineno="1244"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>helical_rise,</highlight></codeline>
<codeline lineno="1245"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>helical_rise<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_helical_rise()<sp/>and<sp/>vrna_md_defaults_helical_rise_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1246"><highlight class="normal"></highlight></codeline>
<codeline lineno="1247"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">extern</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">float</highlight><highlight class="normal"><sp/>backbone_length,</highlight></codeline>
<codeline lineno="1248"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>backbone_length<sp/>field<sp/>in<sp/>model_details<sp/>data<sp/>structure<sp/>as<sp/>well<sp/>as<sp/>vrna_md_defaults_backbone_length()<sp/>and<sp/>vrna_md_defaults_backbone_length_get()<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1249"><highlight class="normal"></highlight></codeline>
<codeline lineno="1250"><highlight class="normal"></highlight><highlight class="comment">/*<sp/>END<sp/>deprecated<sp/>global<sp/>variables:<sp/>*/</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1251"><highlight class="normal"></highlight></codeline>
<codeline lineno="1265"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1266" refid="group__model__details_1gabad896c3650d420f3f3ddefc69e2bceb" refkind="member"><highlight class="normal"><ref refid="group__model__details_1gabad896c3650d420f3f3ddefc69e2bceb" kindref="member">set_model_details</ref>(<ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref><sp/>*md);</highlight></codeline>
<codeline lineno="1267"><highlight class="normal"></highlight></codeline>
<codeline lineno="1268"><highlight class="normal"></highlight></codeline>
<codeline lineno="1269"><highlight class="normal"></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>*</highlight></codeline>
<codeline lineno="1270"><highlight class="normal">option_string(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="1271"><highlight class="normal"></highlight></codeline>
<codeline lineno="1272"><highlight class="normal"></highlight></codeline>
<codeline lineno="1273"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="1277"><highlight class="normal"></highlight></codeline>
<codeline lineno="1278"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/model.h"/>
  </compounddef>
</doxygen>
