1\hypertarget{part__func_8h_source}{}\doxysection{part\+\_\+func.\+h} 2\label{part__func_8h_source}\index{ViennaRNA/part\_func.h@{ViennaRNA/part\_func.h}} 3 4\begin{DoxyCode}{0} 5\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00001}\mbox{\hyperlink{group__pf__cofold_ga5445d8d96a40e9e79b1fa5a7f1a6b7ea}{00001}} \textcolor{preprocessor}{\#ifndef VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H}} 6\DoxyCodeLine{00002 \textcolor{preprocessor}{\#define VIENNA\_RNA\_PACKAGE\_PART\_FUNC\_H}} 7\DoxyCodeLine{00003 } 8\DoxyCodeLine{00008 \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{vrna\_dimer\_pf\_s}} \mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{vrna\_dimer\_pf\_t}};} 9\DoxyCodeLine{00009 } 10\DoxyCodeLine{00010 } 11\DoxyCodeLine{00011 \textcolor{preprocessor}{\#ifndef VRNA\_DISABLE\_BACKWARD\_COMPATIBILITY}} 12\DoxyCodeLine{00012 } 13\DoxyCodeLine{00017 \textcolor{keyword}{typedef} \textcolor{keyword}{struct }\mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{vrna\_dimer\_pf\_s}} \mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{cofoldF}};} 14\DoxyCodeLine{00018 } 15\DoxyCodeLine{00019 \textcolor{preprocessor}{\#endif}} 16\DoxyCodeLine{00020 } 17\DoxyCodeLine{00021 } 18\DoxyCodeLine{00022 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{datastructures_2basic_8h}{ViennaRNA/datastructures/basic.h}}>}} 19\DoxyCodeLine{00023 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{fold__compound_8h}{ViennaRNA/fold\_compound.h}}>}} 20\DoxyCodeLine{00024 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{utils_2structures_8h}{ViennaRNA/utils/structures.h}}>}} 21\DoxyCodeLine{00025 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{params_2basic_8h}{ViennaRNA/params/basic.h}}>}} 22\DoxyCodeLine{00026 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{centroid_8h}{ViennaRNA/centroid.h}}>}} 23\DoxyCodeLine{00027 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{equilibrium__probs_8h}{ViennaRNA/equilibrium\_probs.h}}>}} 24\DoxyCodeLine{00028 \textcolor{preprocessor}{\#include <\mbox{\hyperlink{boltzmann__sampling_8h}{ViennaRNA/boltzmann\_sampling.h}}>}} 25\DoxyCodeLine{00029 } 26\DoxyCodeLine{00030 \textcolor{preprocessor}{\#ifdef VRNA\_WARN\_DEPRECATED}} 27\DoxyCodeLine{00031 \textcolor{preprocessor}{\# if defined(\_\_clang\_\_)}} 28\DoxyCodeLine{00032 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func \_\_attribute\_\_ ((deprecated("{}"{}}, msg)))} 29\DoxyCodeLine{00033 \textcolor{preprocessor}{\# elif defined(\_\_GNUC\_\_)}} 30\DoxyCodeLine{00034 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func \_\_attribute\_\_ ((deprecated(msg)))}} 31\DoxyCodeLine{00035 \textcolor{preprocessor}{\# else}} 32\DoxyCodeLine{00036 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func}} 33\DoxyCodeLine{00037 \textcolor{preprocessor}{\# endif}} 34\DoxyCodeLine{00038 \textcolor{preprocessor}{\#else}} 35\DoxyCodeLine{00039 \textcolor{preprocessor}{\# define DEPRECATED(func, msg) func}} 36\DoxyCodeLine{00040 \textcolor{preprocessor}{\#endif}} 37\DoxyCodeLine{00041 } 38\DoxyCodeLine{00051 \textcolor{comment}{/*}} 39\DoxyCodeLine{00052 \textcolor{comment}{ \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#}} 40\DoxyCodeLine{00053 \textcolor{comment}{ \# PARTITION FUNCTION COMPUTATION \#}} 41\DoxyCodeLine{00054 \textcolor{comment}{ \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#}} 42\DoxyCodeLine{00055 \textcolor{comment}{ */}} 43\DoxyCodeLine{00056 } 44\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00097}\mbox{\hyperlink{group__part__func__global}{00097}} \textcolor{keyword}{struct }\mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{vrna\_dimer\_pf\_s}} \{} 45\DoxyCodeLine{00098 \textcolor{comment}{/* free energies for: */}} 46\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00099}\mbox{\hyperlink{group__part__func__global_a82e31d1fb6e95923fab6036f52c370af}{00099}} \textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global_a82e31d1fb6e95923fab6036f52c370af}{F0AB}}; } 47\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00100}\mbox{\hyperlink{group__part__func__global_a01a87f59db2b7fbf883b056e6f6c673a}{00100}} \textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global_a01a87f59db2b7fbf883b056e6f6c673a}{FAB}}; } 48\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00101}\mbox{\hyperlink{group__part__func__global_a7b01cea5721f61badebc29cf0a9c4266}{00101}} \textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global_a7b01cea5721f61badebc29cf0a9c4266}{FcAB}}; } 49\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00102}\mbox{\hyperlink{group__part__func__global_a1aca57247f2c023d08028b1919005b0a}{00102}} \textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global_a1aca57247f2c023d08028b1919005b0a}{FA}}; } 50\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00103}\mbox{\hyperlink{group__part__func__global_ab4d307be5400604d3c1d84d58a9981df}{00103}} \textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global_ab4d307be5400604d3c1d84d58a9981df}{FB}}; } 51\DoxyCodeLine{00104 \};} 52\DoxyCodeLine{00105 } 53\DoxyCodeLine{00139 \textcolor{keywordtype}{float}} 54\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00140}\mbox{\hyperlink{group__part__func__global_ga29e256d688ad221b78d37f427e0e99bc}{00140}} \mbox{\hyperlink{group__part__func__global_ga29e256d688ad221b78d37f427e0e99bc}{vrna\_pf}}(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *vc,} 55\DoxyCodeLine{00141 \textcolor{keywordtype}{char} *structure);} 56\DoxyCodeLine{00142 } 57\DoxyCodeLine{00143 } 58\DoxyCodeLine{00162 \mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{vrna\_dimer\_pf\_t}}} 59\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00163}\mbox{\hyperlink{group__part__func__global_ga4e5c7d06c302a7c59fc0d64dc142ca63}{00163}} \mbox{\hyperlink{group__part__func__global_ga4e5c7d06c302a7c59fc0d64dc142ca63}{vrna\_pf\_dimer}}(\mbox{\hyperlink{group__fold__compound_structvrna__fc__s}{vrna\_fold\_compound\_t}} *vc,} 60\DoxyCodeLine{00164 \textcolor{keywordtype}{char} *structure);} 61\DoxyCodeLine{00165 } 62\DoxyCodeLine{00166 } 63\DoxyCodeLine{00167 \textcolor{comment}{/* End basic global interface */}} 64\DoxyCodeLine{00196 \textcolor{keywordtype}{float}} 65\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00197}\mbox{\hyperlink{group__part__func__global_gac4a2a74a79e49818bc35412a2b392c7e}{00197}} \mbox{\hyperlink{group__part__func__global_gac4a2a74a79e49818bc35412a2b392c7e}{vrna\_pf\_fold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,} 66\DoxyCodeLine{00198 \textcolor{keywordtype}{char} *structure,} 67\DoxyCodeLine{00199 \mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} **pl);} 68\DoxyCodeLine{00200 } 69\DoxyCodeLine{00201 } 70\DoxyCodeLine{00226 \textcolor{keywordtype}{float}} 71\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00227}\mbox{\hyperlink{group__part__func__global_ga87e5a77b6e50dd54e9d032a9b92973be}{00227}} \mbox{\hyperlink{group__part__func__global_ga87e5a77b6e50dd54e9d032a9b92973be}{vrna\_pf\_circfold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,} 72\DoxyCodeLine{00228 \textcolor{keywordtype}{char} *structure,} 73\DoxyCodeLine{00229 \mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} **pl);} 74\DoxyCodeLine{00230 } 75\DoxyCodeLine{00231 } 76\DoxyCodeLine{00253 \textcolor{keywordtype}{float}} 77\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00254}\mbox{\hyperlink{group__part__func__global_ga374e31a0f326b2c5da5b84e143a63f38}{00254}} \mbox{\hyperlink{group__part__func__global_ga374e31a0f326b2c5da5b84e143a63f38}{vrna\_pf\_alifold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,} 78\DoxyCodeLine{00255 \textcolor{keywordtype}{char} *structure,} 79\DoxyCodeLine{00256 \mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} **pl);} 80\DoxyCodeLine{00257 } 81\DoxyCodeLine{00258 } 82\DoxyCodeLine{00283 \textcolor{keywordtype}{float}} 83\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00284}\mbox{\hyperlink{group__part__func__global_gab70fe6c9a78b79cc5669881720926e1d}{00284}} \mbox{\hyperlink{group__part__func__global_gab70fe6c9a78b79cc5669881720926e1d}{vrna\_pf\_circalifold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} **sequences,} 84\DoxyCodeLine{00285 \textcolor{keywordtype}{char} *structure,} 85\DoxyCodeLine{00286 \mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} **pl);} 86\DoxyCodeLine{00287 } 87\DoxyCodeLine{00288 } 88\DoxyCodeLine{00315 \mbox{\hyperlink{group__part__func__global_structvrna__dimer__pf__s}{vrna\_dimer\_pf\_t}}} 89\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00316}\mbox{\hyperlink{group__part__func__global_gaf2b846f7ac382686f35ff7b9202fdd5c}{00316}} \mbox{\hyperlink{group__part__func__global_gaf2b846f7ac382686f35ff7b9202fdd5c}{vrna\_pf\_co\_fold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *seq,} 90\DoxyCodeLine{00317 \textcolor{keywordtype}{char} *structure,} 91\DoxyCodeLine{00318 \mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} **pl);} 92\DoxyCodeLine{00319 } 93\DoxyCodeLine{00320 } 94\DoxyCodeLine{00321 \textcolor{comment}{/* End simplified global interface */}} 95\DoxyCodeLine{00326 \textcolor{comment}{/*}} 96\DoxyCodeLine{00327 \textcolor{comment}{ \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#}} 97\DoxyCodeLine{00328 \textcolor{comment}{ \# OTHER PARTITION FUNCTION RELATED DECLARATIONS \#}} 98\DoxyCodeLine{00329 \textcolor{comment}{ \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#}} 99\DoxyCodeLine{00330 \textcolor{comment}{ */}} 100\DoxyCodeLine{00331 } 101\DoxyCodeLine{00341 \textcolor{keywordtype}{int}} 102\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00342}\mbox{\hyperlink{group__pf__fold_gad2b3594f0b50b68029e0f54fdce59313}{00342}} \mbox{\hyperlink{group__pf__fold_gad2b3594f0b50b68029e0f54fdce59313}{vrna\_pf\_float\_precision}}(\textcolor{keywordtype}{void});} 103\DoxyCodeLine{00343 } 104\DoxyCodeLine{00344 } 105\DoxyCodeLine{00345 \textcolor{preprocessor}{\#ifndef VRNA\_DISABLE\_BACKWARD\_COMPATIBILITY}} 106\DoxyCodeLine{00346 } 107\DoxyCodeLine{00347 \textcolor{comment}{/*}} 108\DoxyCodeLine{00348 \textcolor{comment}{ \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#}} 109\DoxyCodeLine{00349 \textcolor{comment}{ \# DEPRECATED FUNCTIONS \#}} 110\DoxyCodeLine{00350 \textcolor{comment}{ \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#}} 111\DoxyCodeLine{00351 \textcolor{comment}{ */}} 112\DoxyCodeLine{00352 } 113\DoxyCodeLine{00365 \textcolor{keyword}{extern} \textcolor{keywordtype}{int} \mbox{\hyperlink{group__subopt__stochbt__deprecated_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\_back}};} 114\DoxyCodeLine{00366 } 115\DoxyCodeLine{00407 DEPRECATED(\textcolor{keywordtype}{float} \mbox{\hyperlink{group__part__func__global__deprecated_gac4f95bee734b2563a3d6e9932117ebdf}{pf\_fold\_par}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,} 116\DoxyCodeLine{00408 \textcolor{keywordtype}{char} *structure,} 117\DoxyCodeLine{00409 \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{vrna\_exp\_param\_t}} *parameters,} 118\DoxyCodeLine{00410 \textcolor{keywordtype}{int} calculate\_bppm,} 119\DoxyCodeLine{00411 \textcolor{keywordtype}{int} is\_constrained,} 120\DoxyCodeLine{00412 \textcolor{keywordtype}{int} is\_circular),} 121\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00413}\mbox{\hyperlink{group__part__func__global__deprecated_gac4f95bee734b2563a3d6e9932117ebdf}{00413}} \textcolor{stringliteral}{"{}Use the new API and vrna\_pf() instead"{}});} 122\DoxyCodeLine{00414 } 123\DoxyCodeLine{00454 DEPRECATED(\textcolor{keywordtype}{float} \mbox{\hyperlink{group__part__func__global__deprecated_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,} 124\DoxyCodeLine{00455 \textcolor{keywordtype}{char} *structure),} 125\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00456}\mbox{\hyperlink{group__part__func__global__deprecated_gadc3db3d98742427e7001a7fd36ef28c2}{00456}} \textcolor{stringliteral}{"{}Use vrna\_pf\_fold() or vrna\_pf() instead"{}});} 126\DoxyCodeLine{00457 } 127\DoxyCodeLine{00484 DEPRECATED(\textcolor{keywordtype}{float} \mbox{\hyperlink{group__part__func__global__deprecated_ga819ce5fca8984004ac81c4a3b04cb735}{pf\_circ\_fold}}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence,} 128\DoxyCodeLine{00485 \textcolor{keywordtype}{char} *structure),} 129\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00486}\mbox{\hyperlink{group__part__func__global__deprecated_ga819ce5fca8984004ac81c4a3b04cb735}{00486}} \textcolor{stringliteral}{"{}Use vrna\_pf\_circfold() or vrna\_pf() instead"{}});} 130\DoxyCodeLine{00487 } 131\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00499}\mbox{\hyperlink{group__subopt__stochbt__deprecated_gac03ca6db186bb3bf0a2a326d7fb3ba03}{00499}} DEPRECATED(\textcolor{keywordtype}{char} *\mbox{\hyperlink{group__subopt__stochbt__deprecated_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack}}(\textcolor{keywordtype}{char} *sequence), \textcolor{stringliteral}{"{}Use vrna\_pbacktrack() instead"{}});} 132\DoxyCodeLine{00500 } 133\DoxyCodeLine{00506 DEPRECATED(\textcolor{keywordtype}{char} *\mbox{\hyperlink{group__subopt__stochbt__deprecated_gaf2e614b8beb4ddf3e8751433b76f39db}{pbacktrack5}}(\textcolor{keywordtype}{char} *sequence,} 134\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00507}\mbox{\hyperlink{group__subopt__stochbt__deprecated_gaf2e614b8beb4ddf3e8751433b76f39db}{00507}} \textcolor{keywordtype}{int} length), \textcolor{stringliteral}{"{}Use vrna\_pbacktrack5() instead"{}});} 135\DoxyCodeLine{00508 } 136\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00524}\mbox{\hyperlink{group__subopt__stochbt__deprecated_ga00474051204ac9ad576b3e45174d03ff}{00524}} DEPRECATED(\textcolor{keywordtype}{char} *\mbox{\hyperlink{group__subopt__stochbt__deprecated_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_circ}}(\textcolor{keywordtype}{char} *sequence), \textcolor{stringliteral}{"{}Use vrna\_pbacktrack() instead"{}});} 137\DoxyCodeLine{00525 } 138\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00544}\mbox{\hyperlink{group__part__func__global__deprecated_gae73db3f49a94f0f72e067ecd12681dbd}{00544}} DEPRECATED(\textcolor{keywordtype}{void} \mbox{\hyperlink{group__part__func__global__deprecated_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}}(\textcolor{keywordtype}{void}), \textcolor{stringliteral}{"{}This function is obsolete"{}});} 139\DoxyCodeLine{00545 } 140\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00557}\mbox{\hyperlink{group__part__func__global__deprecated_ga384e927890f9c034ff09fa66da102d28}{00557}} DEPRECATED(\textcolor{keywordtype}{void} \mbox{\hyperlink{group__part__func__global__deprecated_ga384e927890f9c034ff09fa66da102d28}{update\_pf\_params}}(\textcolor{keywordtype}{int} length), \textcolor{stringliteral}{"{}This function is obsolete"{}});} 141\DoxyCodeLine{00558 } 142\DoxyCodeLine{00567 DEPRECATED(\textcolor{keywordtype}{void} \mbox{\hyperlink{group__part__func__global__deprecated_gaafe2d1b21f5418b123b088aa395e827d}{update\_pf\_params\_par}}(\textcolor{keywordtype}{int} length,} 143\DoxyCodeLine{00568 \mbox{\hyperlink{group__energy__parameters_structvrna__exp__param__s}{vrna\_exp\_param\_t}} *parameters),} 144\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00569}\mbox{\hyperlink{group__part__func__global__deprecated_gaafe2d1b21f5418b123b088aa395e827d}{00569}} \textcolor{stringliteral}{"{}Use the new API with vrna\_fold\_compound\_t instead"{}});} 145\DoxyCodeLine{00570 } 146\DoxyCodeLine{00588 DEPRECATED(\mbox{\hyperlink{group__data__structures_ga31125aeace516926bf7f251f759b6126}{FLT\_OR\_DBL}} *\mbox{\hyperlink{group__part__func__global__deprecated_gac5ac7ee281aae1c5cc5898a841178073}{export\_bppm}}(\textcolor{keywordtype}{void}),} 147\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00589}\mbox{\hyperlink{group__part__func__global__deprecated_gac5ac7ee281aae1c5cc5898a841178073}{00589}} \textcolor{stringliteral}{"{}Use the new API with vrna\_fold\_compound\_t instead"{}});} 148\DoxyCodeLine{00590 } 149\DoxyCodeLine{00591 } 150\DoxyCodeLine{00608 DEPRECATED(\textcolor{keywordtype}{int} \mbox{\hyperlink{group__part__func__global__deprecated_ga42faebdfce6f070c5f89adfc8427525c}{get\_pf\_arrays}}(\textcolor{keywordtype}{short} **S\_p,} 151\DoxyCodeLine{00609 \textcolor{keywordtype}{short} **S1\_p,} 152\DoxyCodeLine{00610 \textcolor{keywordtype}{char} **ptype\_p,} 153\DoxyCodeLine{00611 \mbox{\hyperlink{group__data__structures_ga31125aeace516926bf7f251f759b6126}{FLT\_OR\_DBL}} **qb\_p,} 154\DoxyCodeLine{00612 \mbox{\hyperlink{group__data__structures_ga31125aeace516926bf7f251f759b6126}{FLT\_OR\_DBL}} **qm\_p,} 155\DoxyCodeLine{00613 \mbox{\hyperlink{group__data__structures_ga31125aeace516926bf7f251f759b6126}{FLT\_OR\_DBL}} **q1k\_p,} 156\DoxyCodeLine{00614 \mbox{\hyperlink{group__data__structures_ga31125aeace516926bf7f251f759b6126}{FLT\_OR\_DBL}} **qln\_p),} 157\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00615}\mbox{\hyperlink{group__part__func__global__deprecated_ga42faebdfce6f070c5f89adfc8427525c}{00615}} \textcolor{stringliteral}{"{}Use the new API with vrna\_fold\_compound\_t instead"{}});} 158\DoxyCodeLine{00616 } 159\DoxyCodeLine{00622 DEPRECATED(\textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global__deprecated_ga189e2a1ec6cc32c53ea72f7543b0441e}{get\_subseq\_F}}(\textcolor{keywordtype}{int} i,} 160\DoxyCodeLine{00623 \textcolor{keywordtype}{int} j),} 161\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00624}\mbox{\hyperlink{group__part__func__global__deprecated_ga189e2a1ec6cc32c53ea72f7543b0441e}{00624}} \textcolor{stringliteral}{"{}Use the new API with vrna\_fold\_compound\_t instead"{}});} 162\DoxyCodeLine{00625 } 163\DoxyCodeLine{00626 } 164\DoxyCodeLine{00638 DEPRECATED(\textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global__deprecated_ga79cbc375af65f11609feb6b055269e7d}{mean\_bp\_distance}}(\textcolor{keywordtype}{int} length),} 165\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00639}\mbox{\hyperlink{group__part__func__global__deprecated_ga79cbc375af65f11609feb6b055269e7d}{00639}} \textcolor{stringliteral}{"{}Use vrna\_mean\_bp\_distance() or vrna\_mean\_bp\_distance\_pr() instead"{}});} 166\DoxyCodeLine{00640 } 167\DoxyCodeLine{00658 DEPRECATED(\textcolor{keywordtype}{double} \mbox{\hyperlink{group__part__func__global__deprecated_gad5ba36cef8d01cf4244cc09b9bf1ce1d}{mean\_bp\_distance\_pr}}(\textcolor{keywordtype}{int} length,} 168\DoxyCodeLine{00659 \mbox{\hyperlink{group__data__structures_ga31125aeace516926bf7f251f759b6126}{FLT\_OR\_DBL}} *\mbox{\hyperlink{fold__vars_8h_ac98ec419070aee6831b44e5c700f090f}{pr}}),} 169\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00660}\mbox{\hyperlink{group__part__func__global__deprecated_gad5ba36cef8d01cf4244cc09b9bf1ce1d}{00660}} \textcolor{stringliteral}{"{}Use vrna\_mean\_bp\_distance() or vrna\_mean\_bp\_distance\_pr() instead"{}});} 170\DoxyCodeLine{00661 } 171\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00669}\mbox{\hyperlink{group__part__func__global__deprecated_ga8f18624bcd0b47d1a266d9e5527e5362}{00669}} DEPRECATED(\mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} *\mbox{\hyperlink{group__part__func__global__deprecated_ga8f18624bcd0b47d1a266d9e5527e5362}{stackProb}}(\textcolor{keywordtype}{double} cutoff), \textcolor{stringliteral}{"{}Use vrna\_stack\_prob() instead"{}});} 172\DoxyCodeLine{00670 } 173\DoxyCodeLine{00671 } 174\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00679}\mbox{\hyperlink{group__part__func__global__deprecated_ga15176e23eceeff8c7d14eabcfec8a2af}{00679}} DEPRECATED(\textcolor{keywordtype}{void} \mbox{\hyperlink{group__part__func__global__deprecated_ga15176e23eceeff8c7d14eabcfec8a2af}{init\_pf\_fold}}(\textcolor{keywordtype}{int} length), \textcolor{stringliteral}{"{}This function is obsolete"{}});} 175\DoxyCodeLine{00680 } 176\DoxyCodeLine{00685 DEPRECATED(\textcolor{keywordtype}{char} *\mbox{\hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid}}(\textcolor{keywordtype}{int} length,} 177\DoxyCodeLine{00686 \textcolor{keywordtype}{double} *dist),} 178\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00687}\mbox{\hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{00687}} \textcolor{stringliteral}{"{}Use vrna\_centroid() instead"{}});} 179\DoxyCodeLine{00688 } 180\DoxyCodeLine{00693 DEPRECATED(\textcolor{keywordtype}{char} *\mbox{\hyperlink{part__func_8h_a4e99e951dfdc006fe56c3a59374378ed}{get\_centroid\_struct\_gquad\_pr}}(\textcolor{keywordtype}{int} length,} 181\DoxyCodeLine{00694 \textcolor{keywordtype}{double} *dist),} 182\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00695}\mbox{\hyperlink{part__func_8h_a4e99e951dfdc006fe56c3a59374378ed}{00695}} \textcolor{stringliteral}{"{}Use vrna\_centroid() instead"{}});} 183\DoxyCodeLine{00696 } 184\DoxyCodeLine{00702 DEPRECATED(\textcolor{keywordtype}{double} \mbox{\hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\_bp\_dist}}(\textcolor{keywordtype}{int} length),} 185\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00703}\mbox{\hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{00703}} \textcolor{stringliteral}{"{}Use vrna\_mean\_bp\_distance() or vrna\_mean\_bp\_distance\_pr() instead"{}});} 186\DoxyCodeLine{00704 } 187\DoxyCodeLine{00708 DEPRECATED(\textcolor{keywordtype}{double} \mbox{\hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy}}(\textcolor{keywordtype}{int} u1,} 188\DoxyCodeLine{00709 \textcolor{keywordtype}{int} u2,} 189\DoxyCodeLine{00710 \textcolor{keywordtype}{int} type,} 190\DoxyCodeLine{00711 \textcolor{keywordtype}{int} type2,} 191\DoxyCodeLine{00712 \textcolor{keywordtype}{short} si1,} 192\DoxyCodeLine{00713 \textcolor{keywordtype}{short} sj1,} 193\DoxyCodeLine{00714 \textcolor{keywordtype}{short} sp1,} 194\DoxyCodeLine{00715 \textcolor{keywordtype}{short} sq1),} 195\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00716}\mbox{\hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{00716}} \textcolor{stringliteral}{"{}"{}});} 196\DoxyCodeLine{00717 } 197\DoxyCodeLine{00721 DEPRECATED(\textcolor{keywordtype}{double} \mbox{\hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy}}(\textcolor{keywordtype}{int} u,} 198\DoxyCodeLine{00722 \textcolor{keywordtype}{int} type,} 199\DoxyCodeLine{00723 \textcolor{keywordtype}{short} si1,} 200\DoxyCodeLine{00724 \textcolor{keywordtype}{short} sj1,} 201\DoxyCodeLine{00725 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string}),} 202\DoxyCodeLine{\Hypertarget{part__func_8h_source_l00726}\mbox{\hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{00726}} \textcolor{stringliteral}{"{}"{}});} 203\DoxyCodeLine{00727 } 204\DoxyCodeLine{00728 \textcolor{comment}{/* this doesn't work if free\_pf\_arrays() is called before */}} 205\DoxyCodeLine{00729 DEPRECATED(\textcolor{keywordtype}{void} assign\_plist\_gquad\_from\_pr(\mbox{\hyperlink{group__struct__utils__plist_structvrna__elem__prob__s}{vrna\_ep\_t}} **pl,} 206\DoxyCodeLine{00730 \textcolor{keywordtype}{int} length,} 207\DoxyCodeLine{00731 \textcolor{keywordtype}{double} cut\_off),} 208\DoxyCodeLine{00732 \textcolor{stringliteral}{"{}Use vrna\_plist\_from\_probs() instead"{}});} 209\DoxyCodeLine{00733 } 210\DoxyCodeLine{00734 \textcolor{preprocessor}{\#endif}} 211\DoxyCodeLine{00735 } 212\DoxyCodeLine{00736 \textcolor{preprocessor}{\#endif}} 213 214\end{DoxyCode} 215