-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:gadb973133c241d57c04b253df35e4d34e"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e">fold_par</a> (const char *sequence, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int is_constrained, int is_circular)</td></tr>
-<tr class="memdesc:gadb973133c241d57c04b253df35e4d34e"><td class="mdescLeft"> </td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of an RNA sequence. <a href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e"></a><br/></td></tr>
-<tr class="memitem:gaadafcb0f140795ae62e5ca027e335a9b"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b">fold</a> (const char *sequence, char *structure)</td></tr>
-<tr class="memdesc:gaadafcb0f140795ae62e5ca027e335a9b"><td class="mdescLeft"> </td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of an RNA sequence. <a href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b"></a><br/></td></tr>
-<tr class="memitem:ga4ac63ab3e8d9a80ced28b8052d94e423"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423">circfold</a> (const char *sequence, char *structure)</td></tr>
-<tr class="memdesc:ga4ac63ab3e8d9a80ced28b8052d94e423"><td class="mdescLeft"> </td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. <a href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423"></a><br/></td></tr>
-<tr class="memitem:gaf93986cb3cb29770ec9cca69c9fab8cf"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">energy_of_structure</a> (const char *string, const char *structure, int verbosity_level)</td></tr>
-<tr class="memdesc:gaf93986cb3cb29770ec9cca69c9fab8cf"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA using global model detail settings. <a href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf"></a><br/></td></tr>
-<tr class="memitem:gab5169ea4f72f250e43811463a33f4e40"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40">energy_of_struct_par</a> (const char *string, const char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
-<tr class="memdesc:gab5169ea4f72f250e43811463a33f4e40"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
-<tr class="memitem:gaeb14f3664aec67fc03268ac75253f0f8"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">energy_of_circ_structure</a> (const char *string, const char *structure, int verbosity_level)</td></tr>
-<tr class="memdesc:gaeb14f3664aec67fc03268ac75253f0f8"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
-<tr class="memitem:ga75dc765ee4a1177832bc817c94cf88e5"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5">energy_of_circ_struct_par</a> (const char *string, const char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
-<tr class="memdesc:ga75dc765ee4a1177832bc817c94cf88e5"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
-<tr class="memitem:ga8831445966b761417e713360791299d8"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">energy_of_structure_pt</a> (const char *string, short *ptable, short *s, short *s1, int verbosity_level)</td></tr>
-<tr class="memdesc:ga8831445966b761417e713360791299d8"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="group__eval.html#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
-<tr class="memitem:gada4701dd7519b29da75ceac147601f4e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e">energy_of_struct_pt_par</a> (const char *string, short *ptable, short *s, short *s1, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
-<tr class="memdesc:gada4701dd7519b29da75ceac147601f4e"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="group__eval.html#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
-<tr class="memitem:ga107fdfe5fd641868156bfd849f6866c7"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga107fdfe5fd641868156bfd849f6866c7"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7">free_arrays</a> (void)</td></tr>
-<tr class="memdesc:ga107fdfe5fd641868156bfd849f6866c7"><td class="mdescLeft"> </td><td class="mdescRight">Free arrays for mfe folding. <br/></td></tr>
-<tr class="memitem:a87b7869bd1d8dc79c60775c74e009e9b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a87b7869bd1d8dc79c60775c74e009e9b">parenthesis_structure</a> (char *structure, <a class="el" href="structbondT.html">bondT</a> *bp, int length)</td></tr>
-<tr class="memdesc:a87b7869bd1d8dc79c60775c74e009e9b"><td class="mdescLeft"> </td><td class="mdescRight">Create a dot-backet/parenthesis structure from backtracking stack. <a href="#a87b7869bd1d8dc79c60775c74e009e9b"></a><br/></td></tr>
-<tr class="memitem:a325f3835c68f34fe833b2b7a5828857f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a325f3835c68f34fe833b2b7a5828857f">parenthesis_zuker</a> (char *structure, <a class="el" href="structbondT.html">bondT</a> *bp, int length)</td></tr>
-<tr class="memdesc:a325f3835c68f34fe833b2b7a5828857f"><td class="mdescLeft"> </td><td class="mdescRight">Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. <a href="#a325f3835c68f34fe833b2b7a5828857f"></a><br/></td></tr>
-<tr class="memitem:ga41bf8f6fa15b94471f7095cad9f0ccf3"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga41bf8f6fa15b94471f7095cad9f0ccf3"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga41bf8f6fa15b94471f7095cad9f0ccf3">update_fold_params</a> (void)</td></tr>
-<tr class="memdesc:ga41bf8f6fa15b94471f7095cad9f0ccf3"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <br/></td></tr>
-<tr class="memitem:a539ecaed89730f7644c202f304d7529b"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a539ecaed89730f7644c202f304d7529b">energy_of_move</a> (const char *string, const char *structure, int m1, int m2)</td></tr>
-<tr class="memdesc:a539ecaed89730f7644c202f304d7529b"><td class="mdescLeft"> </td><td class="mdescRight">Calculate energy of a move (closing or opening of a base pair) <a href="#a539ecaed89730f7644c202f304d7529b"></a><br/></td></tr>
-<tr class="memitem:a49e0ee561be69faf0568213546f6a53f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a49e0ee561be69faf0568213546f6a53f">energy_of_move_pt</a> (short *pt, short *s, short *s1, int m1, int m2)</td></tr>
-<tr class="memdesc:a49e0ee561be69faf0568213546f6a53f"><td class="mdescLeft"> </td><td class="mdescRight">Calculate energy of a move (closing or opening of a base pair) <a href="#a49e0ee561be69faf0568213546f6a53f"></a><br/></td></tr>
-<tr class="memitem:a507d4fd93f4b398d793ba2402731388d"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a507d4fd93f4b398d793ba2402731388d">loop_energy</a> (short *ptable, short *s, short *s1, int i)</td></tr>
-<tr class="memdesc:a507d4fd93f4b398d793ba2402731388d"><td class="mdescLeft"> </td><td class="mdescRight">Calculate energy of a loop. <a href="#a507d4fd93f4b398d793ba2402731388d"></a><br/></td></tr>
-<tr class="memitem:adaa59b81664e2e36cb9932e891558fae"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#adaa59b81664e2e36cb9932e891558fae">assign_plist_from_db</a> (<a class="el" href="structplist.html">plist</a> **pl, const char *struc, float <a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
-<tr class="memdesc:adaa59b81664e2e36cb9932e891558fae"><td class="mdescLeft"> </td><td class="mdescRight">Create a plist from a dot-bracket string. <a href="#adaa59b81664e2e36cb9932e891558fae"></a><br/></td></tr>
-<tr class="memitem:a2163034a25c6115d894b199e97e03f6c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a> (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)</td></tr>
-<tr class="memitem:ab327ce11972f5ac069d52c8dedfdb700"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a> (int size, int type, int si1, int sj1, const char *string)</td></tr>
-<tr class="memitem:ac3f0a28d9cb609d388b155445073fd20"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a> (int length)</td></tr>
-<tr class="memitem:ac2b37fea2145c94d925a3f33378ef87b"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a> (const char *string, const char *structure)</td></tr>
-<tr class="memitem:a27ce6f68512d43bf1fe14a06c9d76d5c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a> (const char *string, short *ptable, short *s, short *s1)</td></tr>
-<tr class="memitem:a657222e2758c46bf13b416ef3032e417"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a> (const char *string, const char *structure)</td></tr>
-</table><table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="var-members"></a>
-Variables</h2></td></tr>
-<tr class="memitem:a80c3c5fd35e7479704cc91d2d0367743"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a80c3c5fd35e7479704cc91d2d0367743"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743">logML</a></td></tr>
-<tr class="memdesc:a80c3c5fd35e7479704cc91d2d0367743"><td class="mdescLeft"> </td><td class="mdescRight">if nonzero use logarithmic ML energy in energy_of_struct <br/></td></tr>
-<tr class="memitem:a6c5655c8b272e3e6cab74dd0f540294f"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6c5655c8b272e3e6cab74dd0f540294f"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a6c5655c8b272e3e6cab74dd0f540294f">uniq_ML</a></td></tr>
-<tr class="memdesc:a6c5655c8b272e3e6cab74dd0f540294f"><td class="mdescLeft"> </td><td class="mdescRight">do ML decomposition uniquely (for subopt) <br/></td></tr>
-<tr class="memitem:ab9b2c3a37a5516614c06d0ab54b97cda"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ab9b2c3a37a5516614c06d0ab54b97cda"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda">cut_point</a></td></tr>
-<tr class="memdesc:ab9b2c3a37a5516614c06d0ab54b97cda"><td class="mdescLeft"> </td><td class="mdescRight">set to first pos of second seq for cofolding <br/></td></tr>
-<tr class="memitem:ga567530678f6260a1a649a5beca5da4c5"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a>
-int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
-<tr class="memdesc:ga567530678f6260a1a649a5beca5da4c5"><td class="mdescLeft"> </td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>
+<table border="0" cellpadding="0" cellspacing="0">
+<tr><td colspan="2"><h2>Functions</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e">fold_par</a> (const char *sequence, char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int is_constrained, int is_circular)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of an RNA sequence. <a href="group__mfe__fold.html#gadb973133c241d57c04b253df35e4d34e"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b">fold</a> (const char *sequence, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of an RNA sequence. <a href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423">circfold</a> (const char *sequence, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. <a href="group__mfe__fold.html#ga4ac63ab3e8d9a80ced28b8052d94e423"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf">energy_of_structure</a> (const char *string, const char *structure, int verbosity_level)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA using global model detail settings. <a href="group__eval.html#gaf93986cb3cb29770ec9cca69c9fab8cf"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40">energy_of_struct_par</a> (const char *string, const char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="group__eval.html#gab5169ea4f72f250e43811463a33f4e40"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8">energy_of_circ_structure</a> (const char *string, const char *structure, int verbosity_level)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="group__eval.html#gaeb14f3664aec67fc03268ac75253f0f8"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5">energy_of_circ_struct_par</a> (const char *string, const char *structure, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded circular RNA. <a href="group__eval.html#ga75dc765ee4a1177832bc817c94cf88e5"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga8831445966b761417e713360791299d8">energy_of_structure_pt</a> (const char *string, short *ptable, short *s, short *s1, int verbosity_level)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="group__eval.html#ga8831445966b761417e713360791299d8"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#gada4701dd7519b29da75ceac147601f4e">energy_of_struct_pt_par</a> (const char *string, short *ptable, short *s, short *s1, <a class="el" href="structparamT.html">paramT</a> *parameters, int verbosity_level)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate the free energy of an already folded RNA. <a href="group__eval.html#gada4701dd7519b29da75ceac147601f4e"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga107fdfe5fd641868156bfd849f6866c7"></a><!-- doxytag: member="fold.h::free_arrays" ref="ga107fdfe5fd641868156bfd849f6866c7" args="(void)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7">free_arrays</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free arrays for mfe folding. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a87b7869bd1d8dc79c60775c74e009e9b">parenthesis_structure</a> (char *structure, <a class="el" href="structbondT.html">bondT</a> *bp, int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Create a dot-backet/parenthesis structure from backtracking stack. <a href="#a87b7869bd1d8dc79c60775c74e009e9b"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a325f3835c68f34fe833b2b7a5828857f">parenthesis_zuker</a> (char *structure, <a class="el" href="structbondT.html">bondT</a> *bp, int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c. <a href="#a325f3835c68f34fe833b2b7a5828857f"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga41bf8f6fa15b94471f7095cad9f0ccf3"></a><!-- doxytag: member="fold.h::update_fold_params" ref="ga41bf8f6fa15b94471f7095cad9f0ccf3" args="(void)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__fold.html#ga41bf8f6fa15b94471f7095cad9f0ccf3">update_fold_params</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a539ecaed89730f7644c202f304d7529b">energy_of_move</a> (const char *string, const char *structure, int m1, int m2)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate energy of a move (closing or opening of a base pair). <a href="#a539ecaed89730f7644c202f304d7529b"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a49e0ee561be69faf0568213546f6a53f">energy_of_move_pt</a> (short *pt, short *s, short *s1, int m1, int m2)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate energy of a move (closing or opening of a base pair). <a href="#a49e0ee561be69faf0568213546f6a53f"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a507d4fd93f4b398d793ba2402731388d">loop_energy</a> (short *ptable, short *s, short *s1, int i)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Calculate energy of a loop. <a href="#a507d4fd93f4b398d793ba2402731388d"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#adaa59b81664e2e36cb9932e891558fae">assign_plist_from_db</a> (<a class="el" href="structplist.html">plist</a> **pl, const char *struc, float <a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Create a <a class="el" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others...">plist</a> from a dot-bracket string. <a href="#adaa59b81664e2e36cb9932e891558fae"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a2163034a25c6115d894b199e97e03f6c">LoopEnergy</a> (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ab327ce11972f5ac069d52c8dedfdb700">HairpinE</a> (int size, int type, int si1, int sj1, const char *string)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ac3f0a28d9cb609d388b155445073fd20">initialize_fold</a> (int length)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ac2b37fea2145c94d925a3f33378ef87b">energy_of_struct</a> (const char *string, const char *structure)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a27ce6f68512d43bf1fe14a06c9d76d5c">energy_of_struct_pt</a> (const char *string, short *ptable, short *s, short *s1)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a657222e2758c46bf13b416ef3032e417">energy_of_circ_struct</a> (const char *string, const char *structure)</td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a80c3c5fd35e7479704cc91d2d0367743"></a><!-- doxytag: member="fold.h::logML" ref="a80c3c5fd35e7479704cc91d2d0367743" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a80c3c5fd35e7479704cc91d2d0367743">logML</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">if nonzero use logarithmic ML energy in energy_of_struct <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a6c5655c8b272e3e6cab74dd0f540294f"></a><!-- doxytag: member="fold.h::uniq_ML" ref="a6c5655c8b272e3e6cab74dd0f540294f" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#a6c5655c8b272e3e6cab74dd0f540294f">uniq_ML</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">do ML decomposition uniquely (for subopt) <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ab9b2c3a37a5516614c06d0ab54b97cda"></a><!-- doxytag: member="fold.h::cut_point" ref="ab9b2c3a37a5516614c06d0ab54b97cda" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="fold_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda">cut_point</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">set to first pos of second seq for cofolding <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga567530678f6260a1a649a5beca5da4c5"></a><!-- doxytag: member="fold.h::eos_debug" ref="ga567530678f6260a1a649a5beca5da4c5" args="" -->
+int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__eval.html#ga567530678f6260a1a649a5beca5da4c5">eos_debug</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">verbose info from energy_of_struct <br/></td></tr>