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+<h1>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func.h File Reference</h1>
<p>Partition function of single RNA sequences.
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<p><a href="part__func_8h_source.html">Go to the source code of this file.</a></p>
-<table class="memberdecls">
-<tr class="heading"><td colspan="2"><h2><a name="func-members"></a>
-Functions</h2></td></tr>
-<tr class="memitem:ga1839c61275760944b3a007c41d5c0823"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823">pf_fold_par</a> (const char *sequence, char *structure, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
-<tr class="memdesc:ga1839c61275760944b3a007c41d5c0823"><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function <img class="formulaInl" alt="$Q$" src="form_18.png"/> for a given RNA sequence. <a href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823"></a><br/></td></tr>
-<tr class="memitem:gadc3db3d98742427e7001a7fd36ef28c2"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2">pf_fold</a> (const char *sequence, char *structure)</td></tr>
-<tr class="memdesc:gadc3db3d98742427e7001a7fd36ef28c2"><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function <img class="formulaInl" alt="$Q$" src="form_18.png"/> of an RNA sequence. <a href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2"></a><br/></td></tr>
-<tr class="memitem:ga819ce5fca8984004ac81c4a3b04cb735"><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735">pf_circ_fold</a> (const char *sequence, char *structure)</td></tr>
-<tr class="memdesc:ga819ce5fca8984004ac81c4a3b04cb735"><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function of a circular RNA sequence. <a href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735"></a><br/></td></tr>
-<tr class="memitem:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack</a> (char *sequence)</td></tr>
-<tr class="memdesc:gac03ca6db186bb3bf0a2a326d7fb3ba03"><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
+<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__pf__fold.html#ga1839c61275760944b3a007c41d5c0823">pf_fold_par</a> (const char *sequence, char *structure, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters, int calculate_bppm, int is_constrained, int is_circular)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function <img class="formulaInl" alt="$Q$" src="form_18.png"/> for a given RNA sequence. <a href="group__pf__fold.html#ga1839c61275760944b3a007c41d5c0823"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2">pf_fold</a> (const char *sequence, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function <img class="formulaInl" alt="$Q$" src="form_18.png"/> of an RNA sequence. <a href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">float </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735">pf_circ_fold</a> (const char *sequence, char *structure)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Compute the partition function of a circular RNA sequence. <a href="group__pf__fold.html#ga819ce5fca8984004ac81c4a3b04cb735"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03">pbacktrack</a> (char *sequence)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure from the Boltzmann ensemble according its probability<br/>
. <a href="group__subopt__stochbt.html#gac03ca6db186bb3bf0a2a326d7fb3ba03"></a><br/></td></tr>
-<tr class="memitem:ga00474051204ac9ad576b3e45174d03ff"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">pbacktrack_circ</a> (char *sequence)</td></tr>
-<tr class="memdesc:ga00474051204ac9ad576b3e45174d03ff"><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. <a href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff"></a><br/></td></tr>
-<tr class="memitem:gae73db3f49a94f0f72e067ecd12681dbd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd">free_pf_arrays</a> (void)</td></tr>
-<tr class="memdesc:gae73db3f49a94f0f72e067ecd12681dbd"><td class="mdescLeft"> </td><td class="mdescRight">Free arrays for the partition function recursions. <a href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd"></a><br/></td></tr>
-<tr class="memitem:ga384e927890f9c034ff09fa66da102d28"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28">update_pf_params</a> (int length)</td></tr>
-<tr class="memdesc:ga384e927890f9c034ff09fa66da102d28"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28"></a><br/></td></tr>
-<tr class="memitem:ga0733527a94de3b79eee3c3c03c99c1bc"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga0733527a94de3b79eee3c3c03c99c1bc"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc">update_pf_params_par</a> (int length, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
-<tr class="memdesc:ga0733527a94de3b79eee3c3c03c99c1bc"><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <br/></td></tr>
-<tr class="memitem:ga6d463707d5f64bdc4d21515b7dd9b115"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115">export_bppm</a> (void)</td></tr>
-<tr class="memdesc:ga6d463707d5f64bdc4d21515b7dd9b115"><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i,j) is achieved by. <a href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115"></a><br/></td></tr>
-<tr class="memitem:ga03e15e831a31b1154855ab47edbdb019"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr</a> (<a class="el" href="structplist.html">plist</a> **pl, double *probs, int length, double cutoff)</td></tr>
-<tr class="memdesc:ga03e15e831a31b1154855ab47edbdb019"><td class="mdescLeft"> </td><td class="mdescRight">Create a plist from a probability matrix. <a href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019"></a><br/></td></tr>
-<tr class="memitem:ga18607e79e106cad827f482eedd2f632e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e">get_pf_arrays</a> (short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)</td></tr>
-<tr class="memdesc:ga18607e79e106cad827f482eedd2f632e"><td class="mdescLeft"> </td><td class="mdescRight">Get the pointers to (almost) all relavant computation arrays used in partition function computation. <a href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e"></a><br/></td></tr>
-<tr class="memitem:a189e2a1ec6cc32c53ea72f7543b0441e"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a189e2a1ec6cc32c53ea72f7543b0441e"></a>
-double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e">get_subseq_F</a> (int i, int j)</td></tr>
-<tr class="memdesc:a189e2a1ec6cc32c53ea72f7543b0441e"><td class="mdescLeft"> </td><td class="mdescRight">Get the free energy of a subsequence from the q[] array. <br/></td></tr>
-<tr class="memitem:ga9aba0ba1433a6d259331e0fe9fc4a9a6"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6">get_centroid_struct_pl</a> (int length, double *dist, <a class="el" href="structplist.html">plist</a> *pl)</td></tr>
-<tr class="memdesc:ga9aba0ba1433a6d259331e0fe9fc4a9a6"><td class="mdescLeft"> </td><td class="mdescRight">Get the centroid structure of the ensemble. <a href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6"></a><br/></td></tr>
-<tr class="memitem:gacdabece4aa1e20c9eaa97acb4c4dcc38"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38">get_centroid_struct_pr</a> (int length, double *dist, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
-<tr class="memdesc:gacdabece4aa1e20c9eaa97acb4c4dcc38"><td class="mdescLeft"> </td><td class="mdescRight">Get the centroid structure of the ensemble. <a href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38"></a><br/></td></tr>
-<tr class="memitem:ga79cbc375af65f11609feb6b055269e7d"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance</a> (int length)</td></tr>
-<tr class="memdesc:ga79cbc375af65f11609feb6b055269e7d"><td class="mdescLeft"> </td><td class="mdescRight">Get the mean base pair distance of the last partition function computation. <a href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d"></a><br/></td></tr>
-<tr class="memitem:ga72d84525f0afd3a9d60d830a2f501fa5"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5">mean_bp_distance_pr</a> (int length, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
-<tr class="memdesc:ga72d84525f0afd3a9d60d830a2f501fa5"><td class="mdescLeft"> </td><td class="mdescRight">Get the mean base pair distance in the thermodynamic ensemble. <a href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5"></a><br/></td></tr>
-<tr class="memitem:a1f562d463c14d4703d9656056200eb38"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a1f562d463c14d4703d9656056200eb38"></a>
-void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38">bppm_to_structure</a> (char *structure, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>, unsigned int length)</td></tr>
-<tr class="memdesc:a1f562d463c14d4703d9656056200eb38"><td class="mdescLeft"> </td><td class="mdescRight">Create a dot-bracket like structure string from base pair probability matrix. <br/></td></tr>
-<tr class="memitem:a49962ad6242b8c628de6ca16bb831c1d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a49962ad6242b8c628de6ca16bb831c1d"></a>
-char </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d">bppm_symbol</a> (const float *x)</td></tr>
-<tr class="memdesc:a49962ad6242b8c628de6ca16bb831c1d"><td class="mdescLeft"> </td><td class="mdescRight">Get a pseudo dot bracket notation for a given probability information. <br/></td></tr>
-<tr class="memitem:a15176e23eceeff8c7d14eabcfec8a2af"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af">init_pf_fold</a> (int length)</td></tr>
-<tr class="memdesc:a15176e23eceeff8c7d14eabcfec8a2af"><td class="mdescLeft"> </td><td class="mdescRight">Allocate space for <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> <a href="#a15176e23eceeff8c7d14eabcfec8a2af"></a><br/></td></tr>
-<tr class="memitem:ae89a63bd83e75a80b2ba36d20b31ce81"><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a> (int length, double *dist)</td></tr>
-<tr class="memitem:ae9556ba7ded44fe2321b6f67c3fc02a3"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a> (int length)</td></tr>
-<tr class="memitem:a68ba6f3a48e08ca131ab54621ce3a2d7"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a> (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</td></tr>
-<tr class="memitem:a7b6ab474cc80accc48010ccfcc59f96b"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a> (int u, int type, short si1, short sj1, const char *string)</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:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td></tr>
-<tr class="memdesc:gacd79b1a570e6ad9be24cb11fe8cae30a"><td class="mdescLeft"> </td><td class="mdescRight">Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. <a href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff">pbacktrack_circ</a> (char *sequence)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. <a href="group__subopt__stochbt.html#ga00474051204ac9ad576b3e45174d03ff"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd">free_pf_arrays</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Free arrays for the partition function recursions. <a href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28">update_pf_params</a> (int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <a href="group__pf__fold.html#ga384e927890f9c034ff09fa66da102d28"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="ga0733527a94de3b79eee3c3c03c99c1bc"></a><!-- doxytag: member="part_func.h::update_pf_params_par" ref="ga0733527a94de3b79eee3c3c03c99c1bc" args="(int length, pf_paramT *parameters)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga0733527a94de3b79eee3c3c03c99c1bc">update_pf_params_par</a> (int length, <a class="el" href="structpf__paramT.html">pf_paramT</a> *parameters)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Recalculate energy parameters. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115">export_bppm</a> (void)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i,j) is achieved by. <a href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019">assign_plist_from_pr</a> (<a class="el" href="structplist.html">plist</a> **pl, double *probs, int length, double cutoff)</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 probability matrix. <a href="group__pf__fold.html#ga03e15e831a31b1154855ab47edbdb019"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e">get_pf_arrays</a> (short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the pointers to (almost) all relavant computation arrays used in partition function computation. <a href="group__pf__fold.html#ga18607e79e106cad827f482eedd2f632e"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a189e2a1ec6cc32c53ea72f7543b0441e"></a><!-- doxytag: member="part_func.h::get_subseq_F" ref="a189e2a1ec6cc32c53ea72f7543b0441e" args="(int i, int j)" -->
+double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a189e2a1ec6cc32c53ea72f7543b0441e">get_subseq_F</a> (int i, int j)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the free energy of a subsequence from the q[] array. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6">get_centroid_struct_pl</a> (int length, double *dist, <a class="el" href="structplist.html">plist</a> *pl)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the centroid structure of the ensemble. <a href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38">get_centroid_struct_pr</a> (int length, double *dist, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the centroid structure of the ensemble. <a href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance</a> (int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the mean base pair distance of the last partition function computation. <a href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5">mean_bp_distance_pr</a> (int length, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the mean base pair distance in the thermodynamic ensemble. <a href="group__pf__fold.html#ga72d84525f0afd3a9d60d830a2f501fa5"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a1f562d463c14d4703d9656056200eb38"></a><!-- doxytag: member="part_func.h::bppm_to_structure" ref="a1f562d463c14d4703d9656056200eb38" args="(char *structure, double *pr, unsigned int length)" -->
+void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a1f562d463c14d4703d9656056200eb38">bppm_to_structure</a> (char *structure, double *<a class="el" href="fold__vars_8h.html#a0f5757427fd5f2f79d6fca0081cd5a52">pr</a>, unsigned int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Create a dot-bracket like structure string from base pair probability matrix. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a49962ad6242b8c628de6ca16bb831c1d"></a><!-- doxytag: member="part_func.h::bppm_symbol" ref="a49962ad6242b8c628de6ca16bb831c1d" args="(const float *x)" -->
+char </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a49962ad6242b8c628de6ca16bb831c1d">bppm_symbol</a> (const float *x)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Get a pseudo dot bracket notation for a given probability information. <br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a15176e23eceeff8c7d14eabcfec8a2af">init_pf_fold</a> (int length)</td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Allocate space for <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a>. <a href="#a15176e23eceeff8c7d14eabcfec8a2af"></a><br/></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">char * </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#ae89a63bd83e75a80b2ba36d20b31ce81">centroid</a> (int length, double *dist)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#ae9556ba7ded44fe2321b6f67c3fc02a3">mean_bp_dist</a> (int length)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a68ba6f3a48e08ca131ab54621ce3a2d7">expLoopEnergy</a> (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)</td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="part__func_8h.html#a7b6ab474cc80accc48010ccfcc59f96b">expHairpinEnergy</a> (int u, int type, short si1, short sj1, const char *string)</td></tr>
+<tr><td colspan="2"><h2>Variables</h2></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a">st_back</a></td></tr>
+<tr><td class="mdescLeft"> </td><td class="mdescRight">Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. <a href="group__subopt__stochbt.html#gacd79b1a570e6ad9be24cb11fe8cae30a"></a><br/></td></tr>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
-<div class="textblock"><p>Partition function of single RNA sequences. </p>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
+<p>Partition function of single RNA sequences. </p>
<p>This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to Partion function folding... </p>
-</div><hr/><h2>Function Documentation</h2>
-<a class="anchor" id="a15176e23eceeff8c7d14eabcfec8a2af"></a>
+<hr/><h2>Function Documentation</h2>
+<a class="anchor" id="a15176e23eceeff8c7d14eabcfec8a2af"></a><!-- doxytag: member="part_func.h::init_pf_fold" ref="a15176e23eceeff8c7d14eabcfec8a2af" args="(int length)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void init_pf_fold </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em></td><td>)</td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em></td>
+ <td> ) </td>
<td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
-<p>Allocate space for <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a> </p>
+<p>Allocate space for <a class="el" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold()</a>. </p>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000011">Deprecated:</a></b></dt><dd>This function is obsolete and will be removed soon! </dd></dl>
</div>
</div>
-<a class="anchor" id="ae89a63bd83e75a80b2ba36d20b31ce81"></a>
+<a class="anchor" id="ae89a63bd83e75a80b2ba36d20b31ce81"></a><!-- doxytag: member="part_func.h::centroid" ref="ae89a63bd83e75a80b2ba36d20b31ce81" args="(int length, double *dist)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">char* centroid </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">double * </td>
- <td class="paramname"><em>dist</em> </td>
+ <td class="paramtype">double * </td>
+ <td class="paramname"> <em>dist</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000012">Deprecated:</a></b></dt><dd>This function is deprecated and should not be used anymore as it is not threadsafe! </dd></dl>
-<dl class="section see"><dt>See also:</dt><dd><a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6" title="Get the centroid structure of the ensemble.">get_centroid_struct_pl()</a>, <a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38" title="Get the centroid structure of the ensemble.">get_centroid_struct_pr()</a> </dd></dl>
+<dl class="see"><dt><b>See also:</b></dt><dd><a class="el" href="group__centroid__fold.html#ga9aba0ba1433a6d259331e0fe9fc4a9a6" title="Get the centroid structure of the ensemble.">get_centroid_struct_pl()</a>, <a class="el" href="group__centroid__fold.html#gacdabece4aa1e20c9eaa97acb4c4dcc38" title="Get the centroid structure of the ensemble.">get_centroid_struct_pr()</a> </dd></dl>
</div>
</div>
-<a class="anchor" id="ae9556ba7ded44fe2321b6f67c3fc02a3"></a>
+<a class="anchor" id="ae9556ba7ded44fe2321b6f67c3fc02a3"></a><!-- doxytag: member="part_func.h::mean_bp_dist" ref="ae9556ba7ded44fe2321b6f67c3fc02a3" args="(int length)" -->
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<td class="memname">double mean_bp_dist </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>length</em></td><td>)</td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>length</em></td>
+ <td> ) </td>
<td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<p>get the mean pair distance of ensemble</p>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000013">Deprecated:</a></b></dt><dd>This function is not threadsafe and should not be used anymore. Use <a class="el" href="group__pf__fold.html#ga79cbc375af65f11609feb6b055269e7d">mean_bp_distance()</a> instead! </dd></dl>
</div>
</div>
-<a class="anchor" id="a68ba6f3a48e08ca131ab54621ce3a2d7"></a>
+<a class="anchor" id="a68ba6f3a48e08ca131ab54621ce3a2d7"></a><!-- doxytag: member="part_func.h::expLoopEnergy" ref="a68ba6f3a48e08ca131ab54621ce3a2d7" args="(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)" -->
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<td class="memname">double expLoopEnergy </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>u1</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>u1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>u2</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>u2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>type</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>type</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>type2</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>type2</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short </td>
- <td class="paramname"><em>si1</em>, </td>
+ <td class="paramtype">short </td>
+ <td class="paramname"> <em>si1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short </td>
- <td class="paramname"><em>sj1</em>, </td>
+ <td class="paramtype">short </td>
+ <td class="paramname"> <em>sj1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short </td>
- <td class="paramname"><em>sp1</em>, </td>
+ <td class="paramtype">short </td>
+ <td class="paramname"> <em>sp1</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short </td>
- <td class="paramname"><em>sq1</em> </td>
+ <td class="paramtype">short </td>
+ <td class="paramname"> <em>sq1</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
- <td></td><td></td>
+ <td></td><td></td><td></td>
</tr>
</table>
-</div><div class="memdoc">
+</div>
+<div class="memdoc">
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000014">Deprecated:</a></b></dt><dd>Use <a class="el" href="loop__energies_8h.html#aa5e98e524e2a41e290b942b09544bc9e">exp_E_IntLoop()</a> from <a class="el" href="loop__energies_8h.html" title="Energy evaluation for MFE and partition function calculations.">loop_energies.h</a> instead </dd></dl>
</div>
</div>
-<a class="anchor" id="a7b6ab474cc80accc48010ccfcc59f96b"></a>
+<a class="anchor" id="a7b6ab474cc80accc48010ccfcc59f96b"></a><!-- doxytag: member="part_func.h::expHairpinEnergy" ref="a7b6ab474cc80accc48010ccfcc59f96b" args="(int u, int type, short si1, short sj1, const char *string)" -->
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<td class="memname">double expHairpinEnergy </td>
<td>(</td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>u</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>u</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">int </td>
- <td class="paramname"><em>type</em>, </td>
+ <td class="paramtype">int </td>
+ <td class="paramname"> <em>type</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
- <td class="paramtype">short </td>
- <td class="paramname"><em>si1</em>, </td>
+ <td class="paramtype">short </td>
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