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  <compounddef id="group__energy__parameters__salt" kind="group">
    <compoundname>energy_parameters_salt</compoundname>
    <title>Salt corrections for energy parameters</title>
    <innerfile refid="salt_8h">salt.h</innerfile>
    <sectiondef kind="func">
      <memberdef kind="function" id="group__energy__parameters__salt_1gae83764d58e98e05ea49530775bcba104" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>double</type>
        <definition>double vrna_salt_loop</definition>
        <argsstring>(int L, double salt, double T, double backbonelen)</argsstring>
        <name>vrna_salt_loop</name>
        <param>
          <type>int</type>
          <declname>L</declname>
        </param>
        <param>
          <type>double</type>
          <declname>salt</declname>
        </param>
        <param>
          <type>double</type>
          <declname>T</declname>
        </param>
        <param>
          <type>double</type>
          <declname>backbonelen</declname>
        </param>
        <briefdescription>
<para>Get salt correction for a loop at a given salt concentration and temperature. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>L</parametername>
</parameternamelist>
<parameterdescription>
<para>backbone number in loop </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>salt</parametername>
</parameternamelist>
<parameterdescription>
<para>salt concentration (M) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>T</parametername>
</parameternamelist>
<parameterdescription>
<para>absolute temperature (K) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>backbonelen</parametername>
</parameternamelist>
<parameterdescription>
<para>Backbone Length, phosphate-to-phosphate distance (typically 6 for RNA, 6.76 for DNA)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>Salt correction for loop in dcal/mol </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/salt.h" line="31" column="1" declfile="ViennaRNA/params/salt.h" declline="31" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__energy__parameters__salt_1ga79eb7c0dcb7e08dd37437c19be4a7751" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_salt_loop_int</definition>
        <argsstring>(int L, double salt, double T, double backbonelen)</argsstring>
        <name>vrna_salt_loop_int</name>
        <param>
          <type>int</type>
          <declname>L</declname>
        </param>
        <param>
          <type>double</type>
          <declname>salt</declname>
        </param>
        <param>
          <type>double</type>
          <declname>T</declname>
        </param>
        <param>
          <type>double</type>
          <declname>backbonelen</declname>
        </param>
        <briefdescription>
<para>Get salt correction for a loop at a given salt concentration and temperature. </para>
        </briefdescription>
        <detaileddescription>
<para>This functions is same as vrna_salt_loop but returns rounded salt correction in integer</para>
<para><simplesect kind="see"><para><ref refid="group__energy__parameters__salt_1gae83764d58e98e05ea49530775bcba104" kindref="member">vrna_salt_loop</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>L</parametername>
</parameternamelist>
<parameterdescription>
<para>backbone number in loop </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>salt</parametername>
</parameternamelist>
<parameterdescription>
<para>salt concentration (M) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>T</parametername>
</parameternamelist>
<parameterdescription>
<para>absolute temperature (K) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>backbonelen</parametername>
</parameternamelist>
<parameterdescription>
<para>Backbone Length, phosphate-to-phosphate distance (typically 6 for RNA, 6.76 for DNA)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>Rounded salt correction for loop in dcal/mol </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/salt.h" line="49" column="1" declfile="ViennaRNA/params/salt.h" declline="49" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__energy__parameters__salt_1gab1b3e5d8995b1688765e4244038f157f" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_salt_stack</definition>
        <argsstring>(double salt, double T, double hrise)</argsstring>
        <name>vrna_salt_stack</name>
        <param>
          <type>double</type>
          <declname>salt</declname>
        </param>
        <param>
          <type>double</type>
          <declname>T</declname>
        </param>
        <param>
          <type>double</type>
          <declname>hrise</declname>
        </param>
        <briefdescription>
<para>Get salt correction for a stack at a given salt concentration and temperature. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>salt</parametername>
</parameternamelist>
<parameterdescription>
<para>salt concentration (M) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>T</parametername>
</parameternamelist>
<parameterdescription>
<para>absolute temperature (K) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>hrise</parametername>
</parameternamelist>
<parameterdescription>
<para>Helical Rise (typically 2.8 for RNA, 3.4 for DNA)</para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>Rounded salt correction for stack in dcal/mol </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/salt.h" line="62" column="1" declfile="ViennaRNA/params/salt.h" declline="62" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__energy__parameters__salt_1ga1099cd74de693d0aecc7b471342e1a31" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_salt_ml</definition>
        <argsstring>(double saltLoop[], int lower, int upper, int *m, int *b)</argsstring>
        <name>vrna_salt_ml</name>
        <param>
          <type>double</type>
          <declname>saltLoop</declname>
          <array>[]</array>
        </param>
        <param>
          <type>int</type>
          <declname>lower</declname>
        </param>
        <param>
          <type>int</type>
          <declname>upper</declname>
        </param>
        <param>
          <type>int *</type>
          <declname>m</declname>
        </param>
        <param>
          <type>int *</type>
          <declname>b</declname>
        </param>
        <briefdescription>
<para>Fit linear function to loop salt correction. </para>
        </briefdescription>
        <detaileddescription>
<para>For a given range of loop size (backbone number), we perform a linear fitting on loop salt correction</para>
<para><formula id="127">\[ \text{Loop correction} \approx m \cdot L + b. \]</formula></para>
<para><simplesect kind="see"><para><ref refid="group__energy__parameters__salt_1gae83764d58e98e05ea49530775bcba104" kindref="member">vrna_salt_loop()</ref></para>
</simplesect>
<parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>saltLoop</parametername>
</parameternamelist>
<parameterdescription>
<para>List of loop salt correction of size from 1 </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>lower</parametername>
</parameternamelist>
<parameterdescription>
<para>Define the size lower bound for fitting </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>upper</parametername>
</parameternamelist>
<parameterdescription>
<para>Define the size upper bound for fitting </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>m</parametername>
</parameternamelist>
<parameterdescription>
<para>pointer to store the parameter m in fitting result </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>b</parametername>
</parameternamelist>
<parameterdescription>
<para>pointer to store the parameter b in fitting result </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/salt.h" line="82" column="1" declfile="ViennaRNA/params/salt.h" declline="82" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="group__energy__parameters__salt_1ga157f362ca309f306c66bc668edb3aceb" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_salt_duplex_init</definition>
        <argsstring>(vrna_md_t *md)</argsstring>
        <name>vrna_salt_duplex_init</name>
        <param>
          <type><ref refid="group__model__details_1ga1f8a10e12a0a1915f2a4eff0b28ea17c" kindref="member">vrna_md_t</ref> *</type>
          <declname>md</declname>
        </param>
        <briefdescription>
<para>Get salt correction for duplex initialization at a given salt concentration. </para>
        </briefdescription>
        <detaileddescription>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>md</parametername>
</parameternamelist>
<parameterdescription>
<para>Model details data structure that specfifies salt concentration in buffer (M) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
<simplesect kind="return"><para>Rounded correction for duplex initialization in dcal/mol </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/params/salt.h" line="92" column="1" declfile="ViennaRNA/params/salt.h" declline="92" declcolumn="1"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
  </compounddef>
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