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        </childnode>
        <childnode refid="109" relation="include">
        </childnode>
      </node>
      <node id="143">
        <label>ViennaRNA/utils/strings.h</label>
        <link refid="strings_8h"/>
        <childnode refid="144" relation="include">
        </childnode>
        <childnode refid="109" relation="include">
        </childnode>
      </node>
      <node id="140">
        <label>ViennaRNA/utils/structures.h</label>
        <link refid="utils_2structures_8h"/>
        <childnode refid="109" relation="include">
        </childnode>
      </node>
      <node id="59">
        <label>ViennaRNA/walk.h</label>
        <link refid="walk_8h"/>
      </node>
    </invincdepgraph>
    <innerclass refid="structvrna__hc__s" prot="public">vrna_hc_s</innerclass>
    <innerclass refid="structvrna__hc__up__s" prot="public">vrna_hc_up_s</innerclass>
    <sectiondef kind="define">
      <memberdef kind="define" id="hard_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/constraints/hard.h" line="13" column="11" bodyfile="ViennaRNA/constraints/hard.h" bodystart="13" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="hard_8h_1a08d12a9a846ea593b7171d277c9f033f" prot="public" static="no">
        <name>VRNA_CONSTRAINT_NO_HEADER</name>
        <initializer>0</initializer>
        <briefdescription>
<para>do not print the header information line </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000132"><xreftitle>Deprecated</xreftitle><xrefdescription><para>This mode is not supported anymore!</para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="110" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="110" bodyend="-1"/>
      </memberdef>
      <member refid="group__hard__constraints_1ga4bfc2f15c4f261c62a11af9d2aa80c90" kind="define"><name>VRNA_CONSTRAINT_DB</name></member>
      <member refid="group__hard__constraints_1ga29ebe940110d60ab798fdacbcdbbfb7d" kind="define"><name>VRNA_CONSTRAINT_DB_ENFORCE_BP</name></member>
      <member refid="group__hard__constraints_1ga13053547a2de5532b64b64d35e097ae1" kind="define"><name>VRNA_CONSTRAINT_DB_PIPE</name></member>
      <member refid="group__hard__constraints_1ga369bea82eae75fbe626f409fa425747e" kind="define"><name>VRNA_CONSTRAINT_DB_DOT</name></member>
      <member refid="group__hard__constraints_1ga7283bbe0f8954f7b030ecc3f2d1932b2" kind="define"><name>VRNA_CONSTRAINT_DB_X</name></member>
      <memberdef kind="define" id="hard_8h_1ad54c1315a47d55653dcaa5de6e544b77" prot="public" static="no">
        <name>VRNA_CONSTRAINT_DB_ANG_BRACK</name>
        <initializer>524288U</initializer>
        <briefdescription>
<para>angle brackets &apos;&lt;&apos;, &apos;&gt;&apos; switch for structure constraint (paired downstream/upstream) </para>
        </briefdescription>
        <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__hard__constraints_1gadfe1b73edc675a5c0363b81d55173144" kindref="member">vrna_hc_add_from_db()</ref>, <ref refid="group__hard__constraints_1ga74dd0cf2be4b70680a48488923d4cdec" kindref="member">vrna_constraints_add()</ref>, <ref refid="group__constraints_1gaa1f20b53bf09ac2e6b0dbb13f7d89670" kindref="member">vrna_message_constraint_options()</ref>, <ref refid="group__constraints_1gaec7e13fa0465c2acc7a621d1aecb709f" kindref="member">vrna_message_constraint_options_all()</ref> </para>
</simplesect>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="172" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="172" bodyend="-1"/>
      </memberdef>
      <member refid="group__hard__constraints_1gac17b034852c914bc5879954c65d7e74b" kind="define"><name>VRNA_CONSTRAINT_DB_RND_BRACK</name></member>
      <member refid="group__hard__constraints_1ga5c17253f5a39d1d49b0fb11f5196982a" kind="define"><name>VRNA_CONSTRAINT_DB_INTRAMOL</name></member>
      <member refid="group__hard__constraints_1ga31d0ebb9755ca8a4acafc14f00ca755d" kind="define"><name>VRNA_CONSTRAINT_DB_INTERMOL</name></member>
      <member refid="group__hard__constraints_1ga75cfab03cdc97c95b3ce8bb29f52b08e" kind="define"><name>VRNA_CONSTRAINT_DB_GQUAD</name></member>
      <memberdef kind="define" id="hard_8h_1a10fadeec2d291a851fe2197051cf842c" prot="public" static="no">
        <name>VRNA_CONSTRAINT_DB_CANONICAL_BP</name>
        <initializer>16777216U</initializer>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="221" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="221" bodyend="-1"/>
      </memberdef>
      <member refid="group__hard__constraints_1ga10ce6bd2355945f3c8161b7a30a2c322" kind="define"><name>VRNA_CONSTRAINT_DB_WUSS</name></member>
      <member refid="group__hard__constraints_1ga1c3864bdc92147a4d93de2b1b4356177" kind="define"><name>VRNA_CONSTRAINT_DB_DEFAULT</name></member>
      <memberdef kind="define" id="hard_8h_1addb99fd07ad9acc0201fd07eada8f661" prot="public" static="no">
        <name>VRNA_CONSTRAINT_CONTEXT_NONE</name>
        <initializer>(unsigned char)0</initializer>
        <briefdescription>
<para>Constraint context flag that forbids a nucleotide or base pair to appear in any loop. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="261" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="261" bodyend="-1"/>
      </memberdef>
      <member refid="group__hard__constraints_1ga9418eda62a5dec070896702c279d2548" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_EXT_LOOP</name></member>
      <member refid="group__hard__constraints_1ga79203702b197b6b9d3b78eed40663eb1" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_HP_LOOP</name></member>
      <member refid="group__hard__constraints_1ga21feeab3a9e5fa5a9e3d9ac0fcf5994f" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_INT_LOOP</name></member>
      <member refid="group__hard__constraints_1ga0536288e04ff6332ecdc23ca4705402b" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC</name></member>
      <member refid="group__hard__constraints_1ga456ecd2ff00056bb64da8dd4f61bbfc5" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_MB_LOOP</name></member>
      <member refid="group__hard__constraints_1ga02a3d703ddbcfce393e4bbfcb9db7077" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC</name></member>
      <memberdef kind="define" id="hard_8h_1a1aa55f2c6347e670e003b1a765632dad" prot="public" static="no">
        <name>VRNA_CONSTRAINT_CONTEXT_ENFORCE</name>
        <initializer>(unsigned char)(1 &lt;&lt; 6)</initializer>
        <briefdescription>
<para>Hard constraint flag to indicate enforcement of constraints. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="314" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="314" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="hard_8h_1a9fcac36535850ff612c7e6b1305304a1" prot="public" static="no">
        <name>VRNA_CONSTRAINT_CONTEXT_NO_REMOVE</name>
        <initializer>(unsigned char)(1 &lt;&lt; 7)</initializer>
        <briefdescription>
<para>Hard constraint flag to indicate not to remove base pairs that conflict with a given constraint. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="319" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="319" bodyend="-1"/>
      </memberdef>
      <memberdef kind="define" id="hard_8h_1a10675929fdc14c5f81df49d77933067a" prot="public" static="no">
        <name>VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS</name>
        <initializer>                                                              (unsigned char)(<ref refid="group__hard__constraints_1ga9418eda62a5dec070896702c279d2548" kindref="member">VRNA_CONSTRAINT_CONTEXT_EXT_LOOP</ref> | \
                                                              <ref refid="group__hard__constraints_1ga79203702b197b6b9d3b78eed40663eb1" kindref="member">VRNA_CONSTRAINT_CONTEXT_HP_LOOP</ref> | \
                                                              <ref refid="group__hard__constraints_1ga21feeab3a9e5fa5a9e3d9ac0fcf5994f" kindref="member">VRNA_CONSTRAINT_CONTEXT_INT_LOOP</ref> | \
                                                              <ref refid="group__hard__constraints_1ga456ecd2ff00056bb64da8dd4f61bbfc5" kindref="member">VRNA_CONSTRAINT_CONTEXT_MB_LOOP</ref>)</initializer>
        <briefdescription>
<para>Constraint context flag indicating base pairs that close any loop. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="324" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="324" bodyend="327"/>
      </memberdef>
      <memberdef kind="define" id="hard_8h_1ae03ed6ba25cf3cefdf36516e4081eb17" prot="public" static="no">
        <name>VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS</name>
        <initializer>                                                                (unsigned char)(<ref refid="group__hard__constraints_1ga0536288e04ff6332ecdc23ca4705402b" kindref="member">VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC</ref> | \
                                                                <ref refid="group__hard__constraints_1ga02a3d703ddbcfce393e4bbfcb9db7077" kindref="member">VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC</ref>)</initializer>
        <briefdescription>
<para>Constraint context flag indicating base pairs enclosed by any loop. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="332" column="9" bodyfile="ViennaRNA/constraints/hard.h" bodystart="332" bodyend="333"/>
      </memberdef>
      <member refid="group__hard__constraints_1ga886d9127c49bb982a4b67cd7581e8a5a" kind="define"><name>VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS</name></member>
    </sectiondef>
    <sectiondef kind="enum">
      <memberdef kind="enum" id="hard_8h_1a0fcb8bda9b3712e14f8f513def112435" prot="public" static="no" strong="no">
        <type></type>
        <name>vrna_hc_type_e</name>
        <enumvalue id="hard_8h_1a0fcb8bda9b3712e14f8f513def112435a030a42722f849b10dd5780ceed7dfedd" prot="public">
          <name>VRNA_HC_DEFAULT</name>
          <briefdescription>
<para>Default Hard Constraints. </para>
          </briefdescription>
          <detaileddescription>
          </detaileddescription>
        </enumvalue>
        <enumvalue id="hard_8h_1a0fcb8bda9b3712e14f8f513def112435a876c110b3de8e8c89ba5824b08cadb74" prot="public">
          <name>VRNA_HC_WINDOW</name>
          <briefdescription>
<para>Hard Constraints suitable for local structure prediction using window approach. </para>
          </briefdescription>
          <detaileddescription>
<para><simplesect kind="see"><para><ref refid="group__mfe__window_1gacdbc049dcfc7a0e2eb37a327efab91e2" kindref="member">vrna_mfe_window()</ref>, <ref refid="group__mfe__window_1ga90d3756f07aa78a47ffac187ead3c0aa" kindref="member">vrna_mfe_window_zscore()</ref>, <ref refid="group__part__func__window__deprecated_1gaf6d77f10775c1d58c8199d5ec95d4228" kindref="member">pfl_fold()</ref> </para>
</simplesect>
</para>
          </detaileddescription>
        </enumvalue>
        <briefdescription>
<para>The hard constraints type. </para>
        </briefdescription>
        <detaileddescription>
<para>Global and local structure prediction methods use a slightly different way to handle hard constraints internally. This enum is used to distinguish both types. </para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="351" column="1" bodyfile="ViennaRNA/constraints/hard.h" bodystart="351" bodyend="357"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="typedef">
      <member refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kind="typedef"><name>vrna_hc_t</name></member>
      <member refid="group__hard__constraints_1ga8cd53427a942a81c87ec526bbff32ef9" kind="typedef"><name>vrna_hc_up_t</name></member>
      <memberdef kind="typedef" id="hard_8h_1a66d2e80f252082924d1e1dcff3e578c7" prot="public" static="no">
        <type>struct vrna_hc_depot_s</type>
        <definition>typedef struct vrna_hc_depot_s vrna_hc_depot_t</definition>
        <argsstring></argsstring>
        <name>vrna_hc_depot_t</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="35" column="30" bodyfile="ViennaRNA/constraints/hard.h" bodystart="35" bodyend="-1"/>
      </memberdef>
      <member refid="group__hard__constraints_1ga23a523332de2867a1568a0229345ab80" kind="typedef"><name>vrna_hc_eval_f</name></member>
      <memberdef kind="typedef" id="hard_8h_1ae591b5f9d17bfabe878ffb17b5993490" prot="public" static="no">
        <type>unsigned char(*</type>
        <definition>typedef unsigned char(* vrna_hc_eval_loop_f) (int i, int j, int k, int l, unsigned char d, vrna_hc_t *hc)</definition>
        <argsstring>)(int i, int j, int k, int l, unsigned char d, vrna_hc_t *hc)</argsstring>
        <name>vrna_hc_eval_loop_f</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="79" column="18" bodyfile="ViennaRNA/constraints/hard.h" bodystart="79" bodyend="-1"/>
      </memberdef>
      <memberdef kind="typedef" id="hard_8h_1a6aa5e7ef23163aeae81e480b4a63a720" prot="public" static="no">
        <type>unsigned char(*</type>
        <definition>typedef unsigned char(* vrna_hc_eval_hp_f) (int i, int j, vrna_hc_t *hc)</definition>
        <argsstring>)(int i, int j, vrna_hc_t *hc)</argsstring>
        <name>vrna_hc_eval_hp_f</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="86" column="18" bodyfile="ViennaRNA/constraints/hard.h" bodystart="86" bodyend="-1"/>
      </memberdef>
      <memberdef kind="typedef" id="hard_8h_1a3d5f0ac50ca54a086e98ec155a2317ba" prot="public" static="no">
        <type>unsigned char(*</type>
        <definition>typedef unsigned char(* vrna_hc_eval_int_f) (int i, int j, int k, int l, vrna_hc_t *hc)</definition>
        <argsstring>)(int i, int j, int k, int l, vrna_hc_t *hc)</argsstring>
        <name>vrna_hc_eval_int_f</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="90" column="18" bodyfile="ViennaRNA/constraints/hard.h" bodystart="90" bodyend="-1"/>
      </memberdef>
      <memberdef kind="typedef" id="hard_8h_1aae21ef0240b3de516841c6e4f63943b4" prot="public" static="no">
        <type>unsigned char</type>
        <definition>typedef unsigned char vrna_callback_hc_evaluate(int i, int j, int k, int l, unsigned char d, void *data)</definition>
        <argsstring>(int i, int j, int k, int l, unsigned char d, void *data)</argsstring>
        <name>vrna_callback_hc_evaluate</name>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="102" column="19" bodyfile="ViennaRNA/constraints/hard.h" bodystart="102" bodyend="-1"/>
      </memberdef>
    </sectiondef>
    <sectiondef kind="func">
      <member refid="group__constraints_1gaa1f20b53bf09ac2e6b0dbb13f7d89670" kind="function"><name>vrna_message_constraint_options</name></member>
      <member refid="group__constraints_1gaec7e13fa0465c2acc7a621d1aecb709f" kind="function"><name>vrna_message_constraint_options_all</name></member>
      <member refid="group__hard__constraints_1ga4fdb1e98f0d1a2d5728dd3a3aae4a357" kind="function"><name>vrna_hc_init</name></member>
      <memberdef kind="function" id="hard_8h_1a23ce9c3572e8915a1a244c066aeb4439" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_hc_init_window</definition>
        <argsstring>(vrna_fold_compound_t *fc)</argsstring>
        <name>vrna_hc_init_window</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="506" column="1" declfile="ViennaRNA/constraints/hard.h" declline="506" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="hard_8h_1acba6575e3d7d3da35ca5a29d83b955b9" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_hc_prepare</definition>
        <argsstring>(vrna_fold_compound_t *fc, unsigned int options)</argsstring>
        <name>vrna_hc_prepare</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="510" column="1" declfile="ViennaRNA/constraints/hard.h" declline="510" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="hard_8h_1a44ad7f93e0449ad824d88a3629d2cbd4" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_hc_update</definition>
        <argsstring>(vrna_fold_compound_t *fc, unsigned int i, unsigned int options)</argsstring>
        <name>vrna_hc_update</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>i</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>options</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="515" column="1" declfile="ViennaRNA/constraints/hard.h" declline="515" declcolumn="1"/>
      </memberdef>
      <member refid="group__hard__constraints_1gaed20a31c4143ffb6b4835cff46d400b0" kind="function"><name>vrna_hc_add_up</name></member>
      <member refid="group__hard__constraints_1gaec15e527103f5b68258ea4c636fa90d7" kind="function"><name>vrna_hc_add_up_strand</name></member>
      <member refid="group__hard__constraints_1gafe5379c54a6450f028f41d1e78ea5feb" kind="function"><name>vrna_hc_add_up_batch</name></member>
      <memberdef kind="function" id="hard_8h_1ac590474592bbbe5b2c540c78465426b4" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>int</type>
        <definition>int vrna_hc_add_up_strand_batch</definition>
        <argsstring>(vrna_fold_compound_t *fc, vrna_hc_up_t *constraints)</argsstring>
        <name>vrna_hc_add_up_strand_batch</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type><ref refid="group__hard__constraints_1ga8cd53427a942a81c87ec526bbff32ef9" kindref="member">vrna_hc_up_t</ref> *</type>
          <declname>constraints</declname>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="587" column="1" declfile="ViennaRNA/constraints/hard.h" declline="587" declcolumn="1"/>
      </memberdef>
      <member refid="group__hard__constraints_1ga08b90109b99e3e3916e319bf3e424ec1" kind="function"><name>vrna_hc_add_bp</name></member>
      <member refid="group__hard__constraints_1ga4c5149492fdd45ef138f3796e05cefea" kind="function"><name>vrna_hc_add_bp_strand</name></member>
      <member refid="group__hard__constraints_1ga719fd082b5c7c6b222916d4378c715a6" kind="function"><name>vrna_hc_add_bp_nonspecific</name></member>
      <member refid="group__hard__constraints_1ga696dcf77887d856c6f21ea266d8b9ca2" kind="function"><name>vrna_hc_free</name></member>
      <memberdef kind="function" id="hard_8h_1ac30609e180b7ac6fe26f8a59bafbb03e" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void vrna_hc_add_f</definition>
        <argsstring>(vrna_fold_compound_t *fc, vrna_hc_eval_f f)</argsstring>
        <name>vrna_hc_add_f</name>
        <param>
          <type><ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref> *</type>
          <declname>fc</declname>
        </param>
        <param>
          <type><ref refid="group__hard__constraints_1ga23a523332de2867a1568a0229345ab80" kindref="member">vrna_hc_eval_f</ref></type>
          <declname>f</declname>
        </param>
        <briefdescription>
<para>Add a function pointer pointer for the generic hard constraint feature. </para>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="697" column="1" declfile="ViennaRNA/constraints/hard.h" declline="697" declcolumn="1"/>
      </memberdef>
      <member refid="group__hard__constraints_1gaba4f4528b605d0b18ac5b3153ee93eae" kind="function"><name>vrna_hc_add_data</name></member>
      <member refid="group__hard__constraints_1gadfe1b73edc675a5c0363b81d55173144" kind="function"><name>vrna_hc_add_from_db</name></member>
      <memberdef kind="function" id="hard_8h_1a000c04a5393131260e0a8f7bfa4dc690" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type></type>
        <definition>vrna_smx_csr</definition>
        <argsstring>(vrna_uchar) *vrna_hc_nondefaults(vrna_fold_compound_t *fc)</argsstring>
        <name>vrna_smx_csr</name>
        <param>
          <type>vrna_uchar</type>
        </param>
        <briefdescription>
        </briefdescription>
        <detaileddescription>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="742" column="1" declfile="ViennaRNA/constraints/hard.h" declline="742" declcolumn="1"/>
      </memberdef>
      <memberdef kind="function" id="hard_8h_1a4d167deb70bb51723e44374dc981deb2" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void print_tty_constraint</definition>
        <argsstring>(unsigned int option)</argsstring>
        <name>print_tty_constraint</name>
        <param>
          <type>unsigned int</type>
          <declname>option</declname>
        </param>
        <briefdescription>
<para>Print structure constraint characters to stdout. (constraint support is specified by option parameter). </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000133"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use vrna_message_constraints() instead! </para>
</xrefdescription></xrefsect><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>option</parametername>
</parameternamelist>
<parameterdescription>
<para>Option switch that tells which constraint help will be printed </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="757" column="18" declfile="ViennaRNA/constraints/hard.h" declline="757" declcolumn="18"/>
      </memberdef>
      <memberdef kind="function" id="hard_8h_1ae8ae8a34962b9959be3f6c40f0a80ac1" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void print_tty_constraint_full</definition>
        <argsstring>(void)</argsstring>
        <name>print_tty_constraint_full</name>
        <param>
          <type>void</type>
        </param>
        <briefdescription>
<para>Print structure constraint characters to stdout (full constraint support). </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000134"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Use <ref refid="group__constraints_1gaec7e13fa0465c2acc7a621d1aecb709f" kindref="member">vrna_message_constraint_options_all()</ref> instead! </para>
</xrefdescription></xrefsect></para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="767" column="18" declfile="ViennaRNA/constraints/hard.h" declline="767" declcolumn="18"/>
      </memberdef>
      <memberdef kind="function" id="hard_8h_1a36c3a6c3218b041f992052767bc74549" prot="public" static="no" const="no" explicit="no" inline="no" virt="non-virtual">
        <type>void</type>
        <definition>void constrain_ptypes</definition>
        <argsstring>(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type)</argsstring>
        <name>constrain_ptypes</name>
        <param>
          <type>const char *</type>
          <declname>constraint</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>length</declname>
        </param>
        <param>
          <type>char *</type>
          <declname>ptype</declname>
        </param>
        <param>
          <type>int *</type>
          <declname>BP</declname>
        </param>
        <param>
          <type>int</type>
          <declname>min_loop_size</declname>
        </param>
        <param>
          <type>unsigned int</type>
          <declname>idx_type</declname>
        </param>
        <briefdescription>
<para>Insert constraining pair types according to constraint structure string. </para>
        </briefdescription>
        <detaileddescription>
<para><xrefsect id="deprecated_1_deprecated000135"><xreftitle>Deprecated</xreftitle><xrefdescription><para>Do not use this function anymore! Structure constraints are now handled through <ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref> and related functions.</para>
</xrefdescription></xrefsect></para>
<para><parameterlist kind="param"><parameteritem>
<parameternamelist>
<parametername>constraint</parametername>
</parameternamelist>
<parameterdescription>
<para>The structure constraint string </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>length</parametername>
</parameternamelist>
<parameterdescription>
<para>The actual length of the sequence (constraint may be shorter) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>ptype</parametername>
</parameternamelist>
<parameterdescription>
<para>A pointer to the basepair type array </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>BP</parametername>
</parameternamelist>
<parameterdescription>
<para>(not used anymore) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>min_loop_size</parametername>
</parameternamelist>
<parameterdescription>
<para>The minimal loop size (usually <ref refid="constants_8h_1ae646250fd59311356c7e5722a81c3a96" kindref="member">TURN</ref> ) </para>
</parameterdescription>
</parameteritem>
<parameteritem>
<parameternamelist>
<parametername>idx_type</parametername>
</parameternamelist>
<parameterdescription>
<para>Define the access type for base pair type array (0 = indx, 1 = iindx) </para>
</parameterdescription>
</parameteritem>
</parameterlist>
</para>
        </detaileddescription>
        <inbodydescription>
        </inbodydescription>
        <location file="ViennaRNA/constraints/hard.h" line="788" column="18" declfile="ViennaRNA/constraints/hard.h" declline="788" declcolumn="18"/>
      </memberdef>
    </sectiondef>
    <briefdescription>
<para>Functions and data structures for handling of secondary structure hard constraints. </para>
    </briefdescription>
    <detaileddescription>
    </detaileddescription>
    <programlisting>
<codeline lineno="1"><highlight class="preprocessor">#ifndef<sp/>VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="2"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_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="16"><highlight class="normal"></highlight></codeline>
<codeline lineno="22"><highlight class="normal"></highlight></codeline>
<codeline lineno="27" refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/><sp/></highlight><highlight class="normal"><ref refid="structvrna__hc__s" kindref="compound">vrna_hc_s</ref><sp/><ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref>;</highlight></codeline>
<codeline lineno="28"><highlight class="normal"></highlight></codeline>
<codeline lineno="33" refid="group__hard__constraints_1ga8cd53427a942a81c87ec526bbff32ef9" 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__hc__up__s" kindref="compound">vrna_hc_up_s</ref><sp/><ref refid="group__hard__constraints_1ga8cd53427a942a81c87ec526bbff32ef9" kindref="member">vrna_hc_up_t</ref>;</highlight></codeline>
<codeline lineno="34"><highlight class="normal"></highlight></codeline>
<codeline lineno="35"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal">vrna_hc_depot_s<sp/>vrna_hc_depot_t;</highlight></codeline>
<codeline lineno="36"><highlight class="normal"></highlight></codeline>
<codeline lineno="37"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="fold__compound_8h" kindref="compound">ViennaRNA/fold_compound.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="38"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;<ref refid="constraints_2basic_8h" kindref="compound">ViennaRNA/constraints/basic.h</ref>&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="39"><highlight class="normal"></highlight><highlight class="preprocessor">#include<sp/>&lt;ViennaRNA/datastructures/sparse_mx.h&gt;</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="40"><highlight class="normal"></highlight></codeline>
<codeline lineno="72" refid="group__hard__constraints_1ga23a523332de2867a1568a0229345ab80" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/>char<sp/>(*<ref refid="group__hard__constraints_1ga23a523332de2867a1568a0229345ab80" kindref="member">vrna_hc_eval_f</ref>)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="73"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="74"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k,</highlight></codeline>
<codeline lineno="75"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>l,</highlight></codeline>
<codeline lineno="76"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>d,</highlight></codeline>
<codeline lineno="77"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data);</highlight></codeline>
<codeline lineno="78"><highlight class="normal"></highlight></codeline>
<codeline lineno="79"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/>char<sp/>(*vrna_hc_eval_loop_f)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="80"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="81"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k,</highlight></codeline>
<codeline lineno="82"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>l,</highlight></codeline>
<codeline lineno="83"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>d,</highlight></codeline>
<codeline lineno="84"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref><sp/><sp/><sp/><sp/><sp/>*hc);</highlight></codeline>
<codeline lineno="85"><highlight class="normal"></highlight></codeline>
<codeline lineno="86"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/>char<sp/>(*vrna_hc_eval_hp_f)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="87"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="88"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref><sp/><sp/><sp/><sp/><sp/>*hc);</highlight></codeline>
<codeline lineno="89"><highlight class="normal"></highlight></codeline>
<codeline lineno="90"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/>char<sp/>(*vrna_hc_eval_int_f)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="91"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="92"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>k,</highlight></codeline>
<codeline lineno="93"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>l,</highlight></codeline>
<codeline lineno="94"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref><sp/><sp/><sp/><sp/><sp/>*hc);</highlight></codeline>
<codeline lineno="95"><highlight class="normal"></highlight></codeline>
<codeline lineno="96"><highlight class="normal">DEPRECATED(</highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>(vrna_callback_hc_evaluate)(</highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>i,</highlight></codeline>
<codeline lineno="97"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>j,</highlight></codeline>
<codeline lineno="98"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>k,</highlight></codeline>
<codeline lineno="99"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>l,</highlight></codeline>
<codeline lineno="100"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/>d,</highlight></codeline>
<codeline lineno="101"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/>*data),</highlight></codeline>
<codeline lineno="102"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_hc_eval_f<sp/>instead!&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="103"><highlight class="normal"></highlight></codeline>
<codeline lineno="104"><highlight class="normal"></highlight></codeline>
<codeline lineno="110" refid="hard_8h_1a08d12a9a846ea593b7171d277c9f033f" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_NO_HEADER<sp/><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="120" refid="group__hard__constraints_1ga4bfc2f15c4f261c62a11af9d2aa80c90" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>16384U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="121"><highlight class="normal"></highlight></codeline>
<codeline lineno="133" refid="group__hard__constraints_1ga29ebe940110d60ab798fdacbcdbbfb7d" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_ENFORCE_BP<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>32768U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="134"><highlight class="normal"></highlight></codeline>
<codeline lineno="146" refid="group__hard__constraints_1ga13053547a2de5532b64b64d35e097ae1" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_PIPE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>65536U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="147"><highlight class="normal"></highlight></codeline>
<codeline lineno="156" refid="group__hard__constraints_1ga369bea82eae75fbe626f409fa425747e" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_DOT<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>131072U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="165" refid="group__hard__constraints_1ga7283bbe0f8954f7b030ecc3f2d1932b2" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_X<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>262144U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="172" refid="hard_8h_1ad54c1315a47d55653dcaa5de6e544b77" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_ANG_BRACK<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>524288U</highlight><highlight class="preprocessor"></highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="181" refid="group__hard__constraints_1gac17b034852c914bc5879954c65d7e74b" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_RND_BRACK<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>1048576U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="182"><highlight class="normal"></highlight></codeline>
<codeline lineno="194" refid="group__hard__constraints_1ga5c17253f5a39d1d49b0fb11f5196982a" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_INTRAMOL<sp/><sp/><sp/><sp/>2097152U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="195"><highlight class="normal"></highlight></codeline>
<codeline lineno="207" refid="group__hard__constraints_1ga31d0ebb9755ca8a4acafc14f00ca755d" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_INTERMOL<sp/><sp/><sp/><sp/>4194304U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="208"><highlight class="normal"></highlight></codeline>
<codeline lineno="219" refid="group__hard__constraints_1ga75cfab03cdc97c95b3ce8bb29f52b08e" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_GQUAD<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>8388608U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="220"><highlight class="normal"></highlight></codeline>
<codeline lineno="221"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_CANONICAL_BP<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>16777216U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="222"><highlight class="normal"></highlight></codeline>
<codeline lineno="231" refid="group__hard__constraints_1ga10ce6bd2355945f3c8161b7a30a2c322" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_WUSS<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>33554432U</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="232"><highlight class="normal"></highlight></codeline>
<codeline lineno="233"><highlight class="normal"></highlight></codeline>
<codeline lineno="245" refid="group__hard__constraints_1ga1c3864bdc92147a4d93de2b1b4356177" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_DB_DEFAULT<sp/>\</highlight></codeline>
<codeline lineno="246"><highlight class="preprocessor"><sp/><sp/>(VRNA_CONSTRAINT_DB<sp/>\</highlight></codeline>
<codeline lineno="247"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_PIPE<sp/>\</highlight></codeline>
<codeline lineno="248"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_DOT<sp/>\</highlight></codeline>
<codeline lineno="249"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_X<sp/>\</highlight></codeline>
<codeline lineno="250"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_ANG_BRACK<sp/>\</highlight></codeline>
<codeline lineno="251"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_RND_BRACK<sp/>\</highlight></codeline>
<codeline lineno="252"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_INTRAMOL<sp/>\</highlight></codeline>
<codeline lineno="253"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_INTERMOL<sp/>\</highlight></codeline>
<codeline lineno="254"><highlight class="preprocessor"><sp/><sp/><sp/>|<sp/>VRNA_CONSTRAINT_DB_GQUAD<sp/>\</highlight></codeline>
<codeline lineno="255"><highlight class="preprocessor"><sp/><sp/>)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="256"><highlight class="normal"></highlight></codeline>
<codeline lineno="257"><highlight class="normal"></highlight></codeline>
<codeline lineno="261" refid="hard_8h_1addb99fd07ad9acc0201fd07eada8f661" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_NONE<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)0</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="262"><highlight class="normal"></highlight></codeline>
<codeline lineno="269" refid="group__hard__constraints_1ga9418eda62a5dec070896702c279d2548" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_EXT_LOOP<sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>0)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="270"><highlight class="normal"></highlight></codeline>
<codeline lineno="277" refid="group__hard__constraints_1ga79203702b197b6b9d3b78eed40663eb1" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_HP_LOOP<sp/><sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>1)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="278"><highlight class="normal"></highlight></codeline>
<codeline lineno="285" refid="group__hard__constraints_1ga21feeab3a9e5fa5a9e3d9ac0fcf5994f" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_INT_LOOP<sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>2)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="286"><highlight class="normal"></highlight></codeline>
<codeline lineno="293" refid="group__hard__constraints_1ga0536288e04ff6332ecdc23ca4705402b" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC<sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>3)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="294"><highlight class="normal"></highlight></codeline>
<codeline lineno="301" refid="group__hard__constraints_1ga456ecd2ff00056bb64da8dd4f61bbfc5" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_MB_LOOP<sp/><sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>4)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="302"><highlight class="normal"></highlight></codeline>
<codeline lineno="309" refid="group__hard__constraints_1ga02a3d703ddbcfce393e4bbfcb9db7077" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC<sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>5)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="310"><highlight class="normal"></highlight></codeline>
<codeline lineno="314" refid="hard_8h_1a1aa55f2c6347e670e003b1a765632dad" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_ENFORCE<sp/><sp/><sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>6)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="315"><highlight class="normal"></highlight></codeline>
<codeline lineno="319" refid="hard_8h_1a9fcac36535850ff612c7e6b1305304a1" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_NO_REMOVE<sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(1<sp/>&lt;&lt;<sp/>7)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="320"><highlight class="normal"></highlight></codeline>
<codeline lineno="324" refid="hard_8h_1a10675929fdc14c5f81df49d77933067a" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS<sp/>(unsigned<sp/>char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP<sp/>|<sp/>\</highlight></codeline>
<codeline lineno="325"><highlight class="preprocessor"><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/><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/><sp/><sp/><sp/><sp/>VRNA_CONSTRAINT_CONTEXT_HP_LOOP<sp/>|<sp/>\</highlight></codeline>
<codeline lineno="326"><highlight class="preprocessor"><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/><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/><sp/><sp/><sp/><sp/>VRNA_CONSTRAINT_CONTEXT_INT_LOOP<sp/>|<sp/>\</highlight></codeline>
<codeline lineno="327"><highlight class="preprocessor"><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/><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/><sp/><sp/><sp/><sp/>VRNA_CONSTRAINT_CONTEXT_MB_LOOP)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="328"><highlight class="normal"></highlight></codeline>
<codeline lineno="332" refid="hard_8h_1ae03ed6ba25cf3cefdf36516e4081eb17" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS<sp/><sp/>(unsigned<sp/>char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC<sp/>|<sp/>\</highlight></codeline>
<codeline lineno="333"><highlight class="preprocessor"><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/><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/><sp/><sp/><sp/><sp/><sp/><sp/>VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="334"><highlight class="normal"></highlight></codeline>
<codeline lineno="341" refid="group__hard__constraints_1ga886d9127c49bb982a4b67cd7581e8a5a" refkind="member"><highlight class="normal"></highlight><highlight class="preprocessor">#define<sp/>VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS<sp/><sp/><sp/><sp/><sp/>(unsigned<sp/>char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS<sp/>|<sp/>\</highlight></codeline>
<codeline lineno="342"><highlight class="preprocessor"><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/><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/><sp/><sp/><sp/><sp/>VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="343"><highlight class="normal"></highlight></codeline>
<codeline lineno="344"><highlight class="normal"></highlight></codeline>
<codeline lineno="351" refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435" refkind="member"><highlight class="normal"></highlight><highlight class="keyword">typedef</highlight><highlight class="normal"><sp/></highlight><highlight class="keyword">enum</highlight><highlight class="normal"><sp/>{</highlight></codeline>
<codeline lineno="352" refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435a030a42722f849b10dd5780ceed7dfedd" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435a030a42722f849b10dd5780ceed7dfedd" kindref="member">VRNA_HC_DEFAULT</ref>,<sp/><sp/></highlight></codeline>
<codeline lineno="353" refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435a876c110b3de8e8c89ba5824b08cadb74" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435a876c110b3de8e8c89ba5824b08cadb74" kindref="member">VRNA_HC_WINDOW</ref><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="357"><highlight class="normal">}<sp/><ref refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435" kindref="member">vrna_hc_type_e</ref>;</highlight></codeline>
<codeline lineno="358"><highlight class="normal"></highlight></codeline>
<codeline lineno="359"><highlight class="normal"></highlight></codeline>
<codeline lineno="384" refid="structvrna__hc__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__hc__s" kindref="compound">vrna_hc_s</ref><sp/>{</highlight></codeline>
<codeline lineno="385"><highlight class="normal"><sp/><sp/><ref refid="hard_8h_1a0fcb8bda9b3712e14f8f513def112435" kindref="member">vrna_hc_type_e</ref><sp/><sp/><sp/><sp/><sp/><sp/>type;</highlight></codeline>
<codeline lineno="386"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>n;</highlight></codeline>
<codeline lineno="387"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>strands;</highlight></codeline>
<codeline lineno="388"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*sn;</highlight></codeline>
<codeline lineno="389"><highlight class="normal"></highlight></codeline>
<codeline lineno="390"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>state;</highlight></codeline>
<codeline lineno="391"><highlight class="normal"></highlight></codeline>
<codeline lineno="392"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*mx;</highlight></codeline>
<codeline lineno="393"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/>**matrix_local;</highlight></codeline>
<codeline lineno="394"><highlight class="normal"></highlight></codeline>
<codeline lineno="395" refid="structvrna__hc__s_1a1eeb78354751034653cae0e8d9479606" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__hc__s_1a1eeb78354751034653cae0e8d9479606" kindref="member">up_ext</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="398" refid="structvrna__hc__s_1a3e2c015ab854e4840ab2fbf9fec67ee4" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__hc__s_1a3e2c015ab854e4840ab2fbf9fec67ee4" kindref="member">up_hp</ref>;<sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="401" refid="structvrna__hc__s_1a43c7f642a9abbbe3b711ab2b6d9d9df8" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__hc__s_1a43c7f642a9abbbe3b711ab2b6d9d9df8" kindref="member">up_int</ref>;<sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="404" refid="structvrna__hc__s_1a77747a921caf4a31779d7b8d1081ce9e" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__hc__s_1a77747a921caf4a31779d7b8d1081ce9e" kindref="member">up_ml</ref>;<sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="407"><highlight class="normal"></highlight></codeline>
<codeline lineno="408" refid="structvrna__hc__s_1ab8e78449185c98024fca57720e0db1f0" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__hard__constraints_1ga23a523332de2867a1568a0229345ab80" kindref="member">vrna_hc_eval_f</ref><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="structvrna__hc__s_1ab8e78449185c98024fca57720e0db1f0" kindref="member">f</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="411"><highlight class="normal"></highlight></codeline>
<codeline lineno="412" refid="structvrna__hc__s_1acef3d722142cb5f4a8e114e5fbce3b1a" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*<ref refid="structvrna__hc__s_1acef3d722142cb5f4a8e114e5fbce3b1a" kindref="member">data</ref>;<sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="416"><highlight class="normal"></highlight></codeline>
<codeline lineno="417" refid="structvrna__hc__s_1aae5cddf2662f6a2027ac89ff5deaf6ab" refkind="member"><highlight class="normal"><sp/><sp/><ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f</ref><sp/><ref refid="structvrna__hc__s_1aae5cddf2662f6a2027ac89ff5deaf6ab" kindref="member">free_data</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="427"><highlight class="normal"></highlight></codeline>
<codeline lineno="428"><highlight class="normal"><sp/><sp/>vrna_hc_depot_t<sp/>*depot;</highlight></codeline>
<codeline lineno="429"><highlight class="normal"></highlight></codeline>
<codeline lineno="430"><highlight class="normal"><sp/><sp/>vrna_hc_eval_loop_f<sp/>eval_ext;</highlight></codeline>
<codeline lineno="431"><highlight class="normal"><sp/><sp/>vrna_hc_eval_hp_f<sp/><sp/><sp/>eval_hp;</highlight></codeline>
<codeline lineno="432"><highlight class="normal"><sp/><sp/>vrna_hc_eval_int_f<sp/><sp/>eval_int;</highlight></codeline>
<codeline lineno="433"><highlight class="normal"><sp/><sp/>vrna_hc_eval_loop_f<sp/>eval_mb;</highlight></codeline>
<codeline lineno="434"><highlight class="normal">};</highlight></codeline>
<codeline lineno="435"><highlight class="normal"></highlight></codeline>
<codeline lineno="441" refid="structvrna__hc__up__s" refkind="compound"><highlight class="normal"></highlight><highlight class="keyword">struct<sp/></highlight><highlight class="normal"><ref refid="structvrna__hc__up__s" kindref="compound">vrna_hc_up_s</ref><sp/>{</highlight></codeline>
<codeline lineno="442" refid="structvrna__hc__up__s_1a67a98def263c534a8c57298098da16e8" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><ref refid="structvrna__hc__up__s_1a67a98def263c534a8c57298098da16e8" kindref="member">position</ref>;<sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight></codeline>
<codeline lineno="443"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>strand;</highlight></codeline>
<codeline lineno="444" refid="structvrna__hc__up__s_1a468414760f373f7dc0eb1fd47cf708d0" refkind="member"><highlight class="normal"><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><ref refid="structvrna__hc__up__s_1a468414760f373f7dc0eb1fd47cf708d0" kindref="member">options</ref>;<sp/><sp/></highlight></codeline>
<codeline lineno="445"><highlight class="normal">};</highlight></codeline>
<codeline lineno="446"><highlight class="normal"></highlight></codeline>
<codeline lineno="469"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="470" refid="group__constraints_1gaa1f20b53bf09ac2e6b0dbb13f7d89670" refkind="member"><highlight class="normal"><ref refid="group__constraints_1gaa1f20b53bf09ac2e6b0dbb13f7d89670" kindref="member">vrna_message_constraint_options</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>option);</highlight></codeline>
<codeline lineno="471"><highlight class="normal"></highlight></codeline>
<codeline lineno="472"><highlight class="normal"></highlight></codeline>
<codeline lineno="483"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="484" refid="group__constraints_1gaec7e13fa0465c2acc7a621d1aecb709f" refkind="member"><highlight class="normal"><ref refid="group__constraints_1gaec7e13fa0465c2acc7a621d1aecb709f" kindref="member">vrna_message_constraint_options_all</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="485"><highlight class="normal"></highlight></codeline>
<codeline lineno="486"><highlight class="normal"></highlight></codeline>
<codeline lineno="501"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="502" refid="group__hard__constraints_1ga4fdb1e98f0d1a2d5728dd3a3aae4a357" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1ga4fdb1e98f0d1a2d5728dd3a3aae4a357" kindref="member">vrna_hc_init</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="503"><highlight class="normal"></highlight></codeline>
<codeline lineno="504"><highlight class="normal"></highlight></codeline>
<codeline lineno="505"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="506"><highlight class="normal">vrna_hc_init_window(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="507"><highlight class="normal"></highlight></codeline>
<codeline lineno="508"><highlight class="normal"></highlight></codeline>
<codeline lineno="509"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="510"><highlight class="normal">vrna_hc_prepare(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="511"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="512"><highlight class="normal"></highlight></codeline>
<codeline lineno="513"><highlight class="normal"></highlight></codeline>
<codeline lineno="514"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="515"><highlight class="normal">vrna_hc_update(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="516"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="517"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="518"><highlight class="normal"></highlight></codeline>
<codeline lineno="519"><highlight class="normal"></highlight></codeline>
<codeline lineno="534"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="535" refid="group__hard__constraints_1gaed20a31c4143ffb6b4835cff46d400b0" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1gaed20a31c4143ffb6b4835cff46d400b0" kindref="member">vrna_hc_add_up</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="536"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="537"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>option);</highlight></codeline>
<codeline lineno="538"><highlight class="normal"></highlight></codeline>
<codeline lineno="539"><highlight class="normal"></highlight></codeline>
<codeline lineno="565"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="566" refid="group__hard__constraints_1gaec15e527103f5b68258ea4c636fa90d7" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1gaec15e527103f5b68258ea4c636fa90d7" kindref="member">vrna_hc_add_up_strand</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="567"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="568"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>strand,</highlight></codeline>
<codeline lineno="569"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>option);</highlight></codeline>
<codeline lineno="570"><highlight class="normal"></highlight></codeline>
<codeline lineno="571"><highlight class="normal"></highlight></codeline>
<codeline lineno="581"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="582" refid="group__hard__constraints_1gafe5379c54a6450f028f41d1e78ea5feb" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1gafe5379c54a6450f028f41d1e78ea5feb" kindref="member">vrna_hc_add_up_batch</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="583"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__hard__constraints_1ga8cd53427a942a81c87ec526bbff32ef9" kindref="member">vrna_hc_up_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*constraints);</highlight></codeline>
<codeline lineno="584"><highlight class="normal"></highlight></codeline>
<codeline lineno="585"><highlight class="normal"></highlight></codeline>
<codeline lineno="586"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="587"><highlight class="normal">vrna_hc_add_up_strand_batch(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="588"><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/><sp/><sp/><sp/><ref refid="group__hard__constraints_1ga8cd53427a942a81c87ec526bbff32ef9" kindref="member">vrna_hc_up_t</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*constraints);</highlight></codeline>
<codeline lineno="589"><highlight class="normal"></highlight></codeline>
<codeline lineno="590"><highlight class="normal"></highlight></codeline>
<codeline lineno="607"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="608" refid="group__hard__constraints_1ga08b90109b99e3e3916e319bf3e424ec1" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1ga08b90109b99e3e3916e319bf3e424ec1" kindref="member">vrna_hc_add_bp</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="609"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="610"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="611"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>option);</highlight></codeline>
<codeline lineno="612"><highlight class="normal"></highlight></codeline>
<codeline lineno="613"><highlight class="normal"></highlight></codeline>
<codeline lineno="644"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="645" refid="group__hard__constraints_1ga4c5149492fdd45ef138f3796e05cefea" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1ga4c5149492fdd45ef138f3796e05cefea" kindref="member">vrna_hc_add_bp_strand</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="646"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="647"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>j,</highlight></codeline>
<codeline lineno="648"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>strand_i,</highlight></codeline>
<codeline lineno="649"><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/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>strand_j,</highlight></codeline>
<codeline lineno="650"><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/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>option);</highlight></codeline>
<codeline lineno="651"><highlight class="normal"></highlight></codeline>
<codeline lineno="652"><highlight class="normal"></highlight></codeline>
<codeline lineno="670"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="671" refid="group__hard__constraints_1ga719fd082b5c7c6b222916d4378c715a6" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1ga719fd082b5c7c6b222916d4378c715a6" kindref="member">vrna_hc_add_bp_nonspecific</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="672"><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/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>i,</highlight></codeline>
<codeline lineno="673"><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/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>d,</highlight></codeline>
<codeline lineno="674"><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/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>option);</highlight></codeline>
<codeline lineno="675"><highlight class="normal"></highlight></codeline>
<codeline lineno="676"><highlight class="normal"></highlight></codeline>
<codeline lineno="688"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="689" refid="group__hard__constraints_1ga696dcf77887d856c6f21ea266d8b9ca2" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1ga696dcf77887d856c6f21ea266d8b9ca2" kindref="member">vrna_hc_free</ref>(<ref refid="group__hard__constraints_1gac7e4c4f8abe3163a68110c5bff24e01d" kindref="member">vrna_hc_t</ref><sp/>*hc);</highlight></codeline>
<codeline lineno="690"><highlight class="normal"></highlight></codeline>
<codeline lineno="691"><highlight class="normal"></highlight></codeline>
<codeline lineno="696"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="697" refid="hard_8h_1ac30609e180b7ac6fe26f8a59bafbb03e" refkind="member"><highlight class="normal"><ref refid="hard_8h_1ac30609e180b7ac6fe26f8a59bafbb03e" kindref="member">vrna_hc_add_f</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="698"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__hard__constraints_1ga23a523332de2867a1568a0229345ab80" kindref="member">vrna_hc_eval_f</ref><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>f);</highlight></codeline>
<codeline lineno="699"><highlight class="normal"></highlight></codeline>
<codeline lineno="700"><highlight class="normal"></highlight></codeline>
<codeline lineno="712"><highlight class="normal"></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="713" refid="group__hard__constraints_1gaba4f4528b605d0b18ac5b3153ee93eae" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1gaba4f4528b605d0b18ac5b3153ee93eae" kindref="member">vrna_hc_add_data</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc,</highlight></codeline>
<codeline lineno="714"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">void</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*data,</highlight></codeline>
<codeline lineno="715"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="group__fold__compound_1gab4e75b7511179095ef41dc1a8656433a" kindref="member">vrna_auxdata_free_f</ref><sp/><sp/>f);</highlight></codeline>
<codeline lineno="716"><highlight class="normal"></highlight></codeline>
<codeline lineno="717"><highlight class="normal"></highlight></codeline>
<codeline lineno="736"><highlight class="normal"></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="737" refid="group__hard__constraints_1gadfe1b73edc675a5c0363b81d55173144" refkind="member"><highlight class="normal"><ref refid="group__hard__constraints_1gadfe1b73edc675a5c0363b81d55173144" kindref="member">vrna_hc_add_from_db</ref>(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/><sp/>*fc,</highlight></codeline>
<codeline lineno="738"><highlight class="normal"><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/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*constraint,</highlight></codeline>
<codeline lineno="739"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>options);</highlight></codeline>
<codeline lineno="740"><highlight class="normal"></highlight></codeline>
<codeline lineno="741"><highlight class="normal"></highlight></codeline>
<codeline lineno="742"><highlight class="normal">vrna_smx_csr(vrna_uchar)<sp/>*</highlight></codeline>
<codeline lineno="743"><highlight class="normal">vrna_hc_nondefaults(<ref refid="group__fold__compound_1ga1b0cef17fd40466cef5968eaeeff6166" kindref="member">vrna_fold_compound_t</ref><sp/>*fc);</highlight></codeline>
<codeline lineno="744"><highlight class="normal"></highlight></codeline>
<codeline lineno="745"><highlight class="normal"></highlight></codeline>
<codeline lineno="746"><highlight class="normal"></highlight><highlight class="preprocessor">#ifndef<sp/>VRNA_DISABLE_BACKWARD_COMPATIBILITY</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="747"><highlight class="normal"></highlight></codeline>
<codeline lineno="755"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="756"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="hard_8h_1a4d167deb70bb51723e44374dc981deb2" kindref="member">print_tty_constraint</ref>(</highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/>option),</highlight></codeline>
<codeline lineno="757" refid="hard_8h_1a4d167deb70bb51723e44374dc981deb2" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_message_constraint_options()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="758"><highlight class="normal"></highlight></codeline>
<codeline lineno="765"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="766"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="hard_8h_1ae8ae8a34962b9959be3f6c40f0a80ac1" kindref="member">print_tty_constraint_full</ref>(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal">),</highlight></codeline>
<codeline lineno="767" refid="hard_8h_1ae8ae8a34962b9959be3f6c40f0a80ac1" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>vrna_message_constraint_options_all()<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="768"><highlight class="normal"></highlight></codeline>
<codeline lineno="781"><highlight class="normal">DEPRECATED(</highlight><highlight class="keywordtype">void</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="782"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><ref refid="hard_8h_1a36c3a6c3218b041f992052767bc74549" kindref="member">constrain_ptypes</ref>(</highlight><highlight class="keyword">const</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/>*constraint,</highlight></codeline>
<codeline lineno="783"><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/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>length,</highlight></codeline>
<codeline lineno="784"><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/><sp/><sp/><sp/></highlight><highlight class="keywordtype">char</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*ptype,</highlight></codeline>
<codeline lineno="785"><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/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>*BP,</highlight></codeline>
<codeline lineno="786"><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/><sp/><sp/><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/>min_loop_size,</highlight></codeline>
<codeline lineno="787"><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/><sp/><sp/><sp/></highlight><highlight class="keywordtype">unsigned</highlight><highlight class="normal"><sp/></highlight><highlight class="keywordtype">int</highlight><highlight class="normal"><sp/><sp/>idx_type),</highlight></codeline>
<codeline lineno="788" refid="hard_8h_1a36c3a6c3218b041f992052767bc74549" refkind="member"><highlight class="normal"><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/><sp/></highlight><highlight class="stringliteral">&quot;Use<sp/>the<sp/>new<sp/>API<sp/>and<sp/>the<sp/>hard<sp/>constraint<sp/>framework<sp/>instead&quot;</highlight><highlight class="normal">);</highlight></codeline>
<codeline lineno="789"><highlight class="normal"></highlight></codeline>
<codeline lineno="790"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight><highlight class="normal"></highlight></codeline>
<codeline lineno="791"><highlight class="normal"></highlight></codeline>
<codeline lineno="792"><highlight class="normal"></highlight><highlight class="preprocessor">#endif</highlight></codeline>
    </programlisting>
    <location file="ViennaRNA/constraints/hard.h"/>
  </compounddef>
</doxygen>
