main main mp_intro 2Dfold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ 2Dfold_8h TwoDfold_vars * get_TwoDfold_variables group__kl__neighborhood__mfe.html gac9284f132cf0eaa0a2f43590eda05488 (const char *seq, const char *structure1, const char *structure2, int circ) void destroy_TwoDfold_variables group__kl__neighborhood__mfe.html ga05bf4f31d216b1b160fd2d3d68e9b487 (TwoDfold_vars *our_variables) TwoDfold_solution * TwoDfoldList group__kl__neighborhood__mfe.html ga47da790166020558d27323aef489703e (TwoDfold_vars *vars, int distance1, int distance2) char * TwoDfold_backtrack_f5 group__kl__neighborhood__mfe.html gaf4dc05bf8fc1ea53acd7aeb798ba80c2 (unsigned int j, int k, int l, TwoDfold_vars *vars) 2Dpfold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ 2Dpfold_8h TwoDpfold_vars * get_TwoDpfold_variables group__kl__neighborhood__pf.html ga1aca740e2a75ab2b2951538266e53d64 (const char *seq, const char *structure1, char *structure2, int circ) TwoDpfold_vars * get_TwoDpfold_variables_from_MFE group__kl__neighborhood__pf.html gacc2f66da7ee62096cab629fce7112216 (TwoDfold_vars *mfe_vars) void destroy_TwoDpfold_variables group__kl__neighborhood__pf.html gafe994291458ee2ac34d3eb825ef62a15 (TwoDpfold_vars *vars) TwoDpfold_solution * TwoDpfoldList group__kl__neighborhood__pf.html ga3e1cd3b24eb635c65181182cbb4ae3eb (TwoDpfold_vars *vars, int maxDistance1, int maxDistance2) char * TwoDpfold_pbacktrack group__kl__neighborhood__stochbt.html gae251288f50dd4ae7d315af0085775f71 (TwoDpfold_vars *vars, int d1, int d2) char * TwoDpfold_pbacktrack5 group__kl__neighborhood__stochbt.html ga13430ac6a7f90df426774f131647d2c7 (TwoDpfold_vars *vars, int d1, int d2, unsigned int length) alifold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ alifold_8h void update_alifold_params alifold_8h.html ac484c6bd429bafbd353b91044508d8e9 (void) float alifold group__consensus__mfe__fold.html ga4cf00f0659e5f0480335d69e797f05b1 (const char **strings, char *structure) float circalifold group__consensus__mfe__fold.html gadbd3b0b1c144cbfb4efe704b2b260f96 (const char **strings, char *structure) void free_alifold_arrays group__consensus__mfe__fold.html ga72095e4554b5d577250ea14c42acc49e (void) int get_mpi group__consensus__fold.html gaa2d600be90844094ec145ea14a314d2f (char *Alseq[], int n_seq, int length, int *mini) float ** readribosum group__consensus__fold.html ga5e125c9586fcd4e2e1559fe76f7289cc (char *name) float energy_of_alistruct group__consensus__fold.html ga1c48869c03b49a342bf4cbdd61900081 (const char **sequences, const char *structure, int n_seq, float *energy) void encode_ali_sequence group__consensus__fold.html gaa3e40277c837d6f7603afe319884c786 (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ) void alloc_sequence_arrays group__consensus__fold.html ga8a560930f7f2582cc3967723a86cfdfa (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ) void free_sequence_arrays group__consensus__fold.html ga298a420a8c879202e2617b3f724fde38 (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss) float alipf_fold_par group__consensus__pf__fold.html ga4d2ff54d8210fc7cceeeff389d4dbd1d (const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular) float alipf_fold group__consensus__pf__fold.html gad32ded7d753ccaf211ab35782d1f42a9 (const char **sequences, char *structure, plist **pl) float alipf_circ_fold group__consensus__pf__fold.html ga6b4dde1d43b79ab3753508c46cf50363 (const char **sequences, char *structure, plist **pl) FLT_OR_DBL * export_ali_bppm group__consensus__pf__fold.html ga11b6ab8bd9be1821fea352b190a01cab (void) char * alipbacktrack group__consensus__stochbt.html ga0df40248788f0fb17ebdc59d74116d1c (double *prob) int get_alipf_arrays group__consensus__fold.html ga5349960075b1847720a2e9df021e2675 (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore) double cv_fact group__consensus__fold.html gaf3cbac6ff5d706d6e414677841ddf94c double nc_fact group__consensus__fold.html ga502948a122a2af5b914355b1f3ea2f61 cofold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ cofold_8h float cofold group__mfe__cofold.html gabc8517f22cfe70595ee81fc837910d52 (const char *sequence, char *structure) float cofold_par group__mfe__cofold.html gafe430060533f14b11fc611f60b3f1f6f (const char *string, char *structure, paramT *parameters, int is_constrained) void free_co_arrays group__mfe__cofold.html gaafb33d7473eb9af9d1b168ca8761c41a (void) void update_cofold_params group__mfe__cofold.html ga4fcbf34e77b99bfbb2333d2ab0c41a57 (void) void export_cofold_arrays_gq group__mfe__cofold.html ga5f5bf4df35d0554f6ace9579f8744c48 (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p) void export_cofold_arrays group__mfe__cofold.html ga5cb6b59983f1f74ccc00b9b9c4e84482 (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p) SOLUTION * zukersubopt group__subopt__zuker.html ga0d5104e3ecf119d8eabd40aa5fe47f90 (const char *string) SOLUTION * zukersubopt_par group__subopt__zuker.html ga6d98a9450d1affadf144ac79f543da8c (const char *string, paramT *parameters) void get_monomere_mfes cofold_8h.html a4958b517c613e4d2afd5bce6c1060a79 (float *e1, float *e2) void initialize_cofold cofold_8h.html afee0c32208aa2ac97338b6e3fbad7fa5 (int length) convert_epars.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ convert__epars_8h #define VRNA_CONVERT_OUTPUT_ALL group__energy__parameters__convert.html ga8dc6aee5a806c49b71557152f9616bc4 #define VRNA_CONVERT_OUTPUT_HP group__energy__parameters__convert.html gaf66fe2cb11dfcfd32d791049c254a8a4 #define VRNA_CONVERT_OUTPUT_STACK group__energy__parameters__convert.html gad23522d63f8d4c50d5a5deee9bee3ef2 #define VRNA_CONVERT_OUTPUT_MM_HP group__energy__parameters__convert.html gaa892c7b4957459090f3e08da298cc347 #define VRNA_CONVERT_OUTPUT_MM_INT group__energy__parameters__convert.html ga4ff223fb1f9c62cd92d9ab811ad03d55 #define VRNA_CONVERT_OUTPUT_MM_INT_1N group__energy__parameters__convert.html gaf5d3743219f83c6348155cd81e755bbb #define VRNA_CONVERT_OUTPUT_MM_INT_23 group__energy__parameters__convert.html ga78382ec622ba99e0ac2262317bdd7316 #define VRNA_CONVERT_OUTPUT_MM_MULTI group__energy__parameters__convert.html gae67af9f1cdf7baf2865481282a5d1034 #define VRNA_CONVERT_OUTPUT_MM_EXT group__energy__parameters__convert.html gaf14ead7ef1fdbe725ade653750fc51e3 #define VRNA_CONVERT_OUTPUT_DANGLE5 group__energy__parameters__convert.html ga036ffd996d8c8a9acf631760dd1da24b #define VRNA_CONVERT_OUTPUT_DANGLE3 group__energy__parameters__convert.html ga34a8a5479ef885834ef32f3fb43d79bc #define VRNA_CONVERT_OUTPUT_INT_11 group__energy__parameters__convert.html ga079aafefd5f8ab57ee5120099a34bd25 #define VRNA_CONVERT_OUTPUT_INT_21 group__energy__parameters__convert.html gacf770881d9034431ebe741642342a1f9 #define VRNA_CONVERT_OUTPUT_INT_22 group__energy__parameters__convert.html gaa307671e2631cdacad9cbe4c6583b05f #define VRNA_CONVERT_OUTPUT_BULGE group__energy__parameters__convert.html ga7092fe0be4de6f02cc0bf08e81af726a #define VRNA_CONVERT_OUTPUT_INT group__energy__parameters__convert.html gac5c2289fdf8ff1b980976d1613ff943a #define VRNA_CONVERT_OUTPUT_ML group__energy__parameters__convert.html gaf2c8755d64eff3852aa45df9ac80a4fe #define VRNA_CONVERT_OUTPUT_MISC group__energy__parameters__convert.html ga46d5b1535ae86060b6317565b7c6b40b #define VRNA_CONVERT_OUTPUT_SPECIAL_HP group__energy__parameters__convert.html gaa1ff48a79642d69579d1766561ec6db6 #define VRNA_CONVERT_OUTPUT_VANILLA group__energy__parameters__convert.html ga0d4e8a836bb4864ab5129c085dbf592d #define VRNA_CONVERT_OUTPUT_NINIO group__energy__parameters__convert.html ga2eb0462f16939ddacdaf751a88d675ce #define VRNA_CONVERT_OUTPUT_DUMP group__energy__parameters__convert.html gac86976e9c2a55b3a6481ea60044f6098 void convert_parameter_file group__energy__parameters__convert.html gafbe538bc4eb2cf2a33326e1010005f8a (const char *iname, const char *oname, unsigned int options) data_structures.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ data__structures_8h plist cpair COORDINATE sect bondT bondTEn model_detailsT paramT pf_paramT PAIR INTERVAL SOLUTION cofoldF ConcEnt pairpro pair_info move_t intermediate_t path_t pu_contrib interact pu_out constrain duplexT folden snoopT dupVar TwoDfold_solution TwoDfold_vars TwoDpfold_solution TwoDpfold_vars #define MAXALPHA data__structures_8h.html a05a5ffe718aa431d97419a12fb082379 #define MAXDOS data__structures_8h.html a5ec740b80afb4906ba4311dbd8ddbd89 dist_vars.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ dist__vars_8h Postorder_list Tree swString int edit_backtrack dist__vars_8h.html aa03194c513af6b860e7b33e370b82bdb char * aligned_line dist__vars_8h.html ac1605fe3448ad0a0b809c4fb8f6a854a [4] int cost_matrix dist__vars_8h.html ab65d8ff14c6937612212526a60f59b3c duplex.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ duplex_8h edit_cost.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ edit__cost_8h energy_const.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ energy__const_8h #define GASCONST energy__const_8h.html ab1e4a8d82f24ed5db01dde5f25269cf1 #define K0 energy__const_8h.html a307c72605e3713972b4f4fb2d53ea20e #define INF energy__const_8h.html a12c2040f25d8e3a7b9e1c2024c618cb6 #define FORBIDDEN energy__const_8h.html a5064c29ab2d1e20c2304b3c67562774d #define BONUS energy__const_8h.html a96a9822fa134450197dd454b1478a193 #define NBPAIRS energy__const_8h.html a5e75221c779d618eab81e096f37e32ce #define TURN energy__const_8h.html ae646250fd59311356c7e5722a81c3a96 #define MAXLOOP energy__const_8h.html ad1bd6eabac419670ddd3c9ed82145988 findpath.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ findpath_8h int find_saddle findpath_8h.html ad0e14268e309af773ecd1fce6244ee50 (const char *seq, const char *struc1, const char *struc2, int max) path_t * get_path findpath_8h.html a0ff35d65c892a3403af937c00a867ef9 (const char *seq, const char *s1, const char *s2, int maxkeep) void free_path findpath_8h.html a326e6d1640bbfd035e3869f5f4c188f7 (path_t *path) fold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ fold_8h float fold_par group__mfe__fold.html gadb973133c241d57c04b253df35e4d34e (const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular) float fold group__mfe__fold.html gaadafcb0f140795ae62e5ca027e335a9b (const char *sequence, char *structure) float circfold group__mfe__fold.html ga4ac63ab3e8d9a80ced28b8052d94e423 (const char *sequence, char *structure) float energy_of_structure group__eval.html gaf93986cb3cb29770ec9cca69c9fab8cf (const char *string, const char *structure, int verbosity_level) float energy_of_struct_par group__eval.html gab5169ea4f72f250e43811463a33f4e40 (const char *string, const char *structure, paramT *parameters, int verbosity_level) float energy_of_circ_structure group__eval.html gaeb14f3664aec67fc03268ac75253f0f8 (const char *string, const char *structure, int verbosity_level) float energy_of_circ_struct_par group__eval.html ga75dc765ee4a1177832bc817c94cf88e5 (const char *string, const char *structure, paramT *parameters, int verbosity_level) int energy_of_structure_pt group__eval.html ga8831445966b761417e713360791299d8 (const char *string, short *ptable, short *s, short *s1, int verbosity_level) int energy_of_struct_pt_par group__eval.html gada4701dd7519b29da75ceac147601f4e (const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level) void free_arrays group__mfe__fold.html ga107fdfe5fd641868156bfd849f6866c7 (void) void parenthesis_structure fold_8h.html a87b7869bd1d8dc79c60775c74e009e9b (char *structure, bondT *bp, int length) void parenthesis_zuker fold_8h.html a325f3835c68f34fe833b2b7a5828857f (char *structure, bondT *bp, int length) void update_fold_params group__mfe__fold.html ga41bf8f6fa15b94471f7095cad9f0ccf3 (void) float energy_of_move fold_8h.html a539ecaed89730f7644c202f304d7529b (const char *string, const char *structure, int m1, int m2) int energy_of_move_pt fold_8h.html a49e0ee561be69faf0568213546f6a53f (short *pt, short *s, short *s1, int m1, int m2) int loop_energy fold_8h.html a507d4fd93f4b398d793ba2402731388d (short *ptable, short *s, short *s1, int i) void assign_plist_from_db fold_8h.html adaa59b81664e2e36cb9932e891558fae (plist **pl, const char *struc, float pr) int LoopEnergy fold_8h.html a2163034a25c6115d894b199e97e03f6c (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1) int HairpinE fold_8h.html ab327ce11972f5ac069d52c8dedfdb700 (int size, int type, int si1, int sj1, const char *string) void initialize_fold fold_8h.html ac3f0a28d9cb609d388b155445073fd20 (int length) float energy_of_struct fold_8h.html ac2b37fea2145c94d925a3f33378ef87b (const char *string, const char *structure) int energy_of_struct_pt fold_8h.html a27ce6f68512d43bf1fe14a06c9d76d5c (const char *string, short *ptable, short *s, short *s1) float energy_of_circ_struct fold_8h.html a657222e2758c46bf13b416ef3032e417 (const char *string, const char *structure) int logML fold_8h.html a80c3c5fd35e7479704cc91d2d0367743 int uniq_ML fold_8h.html a6c5655c8b272e3e6cab74dd0f540294f int cut_point fold_8h.html ab9b2c3a37a5516614c06d0ab54b97cda int eos_debug group__eval.html ga567530678f6260a1a649a5beca5da4c5 fold_vars.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ fold__vars_8h void set_model_details fold__vars_8h.html a4c3257186a796182462f18a5480ac8b3 (model_detailsT *md) int fold_constrained fold__vars_8h.html a0afc287c2464866d94858c39175154af int noLonelyPairs fold__vars_8h.html a097eccaabd6ae8b4fef83cccff85bb5d int dangles fold__vars_8h.html a72b511ed1201f7e23ec437e468790d74 int noGU fold__vars_8h.html abf380d09e4f1ab94fc6af57cf0ad5d32 int no_closingGU fold__vars_8h.html aa8d1c7b92489179e1eafa562b7bdd259 int tetra_loop fold__vars_8h.html a4f6265bdf0ead7ff4628a360adbfd77e int energy_set fold__vars_8h.html afb1ef1166da85092ae8a325e02dcae71 int circ fold__vars_8h.html af9202a1a09f5828dc731e2d9a10fa111 int csv fold__vars_8h.html af2763d55a74663a5e60652b8880baa5b int oldAliEn fold__vars_8h.html ac408868ba00671cbc7d1d535105af045 int ribo fold__vars_8h.html a0656afca1d2853f9ee6591172f5638de char * RibosumFile fold__vars_8h.html a5dbaa0cca2c8c82048a0f0e38e164944 char * nonstandards fold__vars_8h.html a2695d91cc535d09c2eae5c3884e2ec64 double temperature fold__vars_8h.html ab4b11c8d9c758430960896bc3fe82ead int james_rule fold__vars_8h.html af349001ad3b4d008d0051d935b1b6261 int logML fold__vars_8h.html a80c3c5fd35e7479704cc91d2d0367743 int cut_point fold__vars_8h.html ab9b2c3a37a5516614c06d0ab54b97cda bondT * base_pair fold__vars_8h.html a0244a629b5ab4f58b77590c3dfd130dc double * pr fold__vars_8h.html a0f5757427fd5f2f79d6fca0081cd5a52 int * iindx fold__vars_8h.html a92089ae3a51b5d75a14ce9cc29cc8317 double pf_scale fold__vars_8h.html ad3b22044065acc6dee0af68931b52cfd int do_backtrack fold__vars_8h.html ad512b5dd4dbec60faccfe137bb474489 char backtrack_type fold__vars_8h.html a83bdb43472a259c71e69fa9f70f420c3 int gquad fold__vars_8h.html a25f2bdcdf56e813d288845484a13d704 gquad.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ gquad_8h int * get_gquad_matrix gquad_8h.html a8b0784c14fa1208d0aebbebdc1318b7a (short *S, paramT *P) int parse_gquad gquad_8h.html ae41763215b9c64d2a7b67f0df8a28078 (const char *struc, int *L, int l[3]) PRIVATE int backtrack_GQuad_IntLoop gquad_8h.html a54475a8eb898fa1e8af8ab5f5375f3be (int c, int i, int j, int type, short *S, int *ggg, int *index, int *p, int *q, paramT *P) PRIVATE int backtrack_GQuad_IntLoop_L gquad_8h.html a118ec7289f1936bd810be7fe50b98212 (int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, paramT *P) inverse.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ inverse_8h float inverse_fold group__inverse__fold.html ga7af026de55d4babad879f2c92559cbbc (char *start, const char *target) float inverse_pf_fold group__inverse__fold.html gaeef52ecbf2a2450ad585a344f9826806 (char *start, const char *target) char * symbolset group__inverse__fold.html ga8f791e7740a5a28b9f6fafb4e60301d9 float final_cost group__inverse__fold.html ga7f17d3b169af048d32bb185039a9c09c int give_up group__inverse__fold.html ga7ec4ba51f86e1717a1e174264e4a75ce int inv_verbose group__inverse__fold.html gafcfc65fba01b9cca5946726ed9057a63 Lfold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ Lfold_8h float Lfold group__local__mfe__fold.html ga16e5a70e60835bb969eaecbe6482f1be (const char *string, char *structure, int maxdist) float Lfoldz group__local__mfe__fold.html gab6d79eecc180f586679f7b85cce5cbe9 (const char *string, char *structure, int maxdist, int zsc, double min_z) float aliLfold group__local__consensus__fold.html ga20a173a3cdb83f5d1778e36c1a6b1f2b (const char **strings, char *structure, int maxdist) loop_energies.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ loop__energies_8h PRIVATE int E_IntLoop loop__energies_8h.html a3e5ad89f451254b1fe366d77aa8ff7bd (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, paramT *P) PRIVATE int E_Hairpin loop__energies_8h.html aa362183cf6db89a10cdb0f5c4bd180c6 (int size, int type, int si1, int sj1, const char *string, paramT *P) PRIVATE int E_Stem loop__energies_8h.html af5a6594eba9b2622cb47076650c69819 (int type, int si1, int sj1, int extLoop, paramT *P) PRIVATE double exp_E_Stem loop__energies_8h.html a76cc24ec96199e04beddad13e7891e21 (int type, int si1, int sj1, int extLoop, pf_paramT *P) PRIVATE double exp_E_Hairpin loop__energies_8h.html a0e128184bb097dc2da33706f33b555a6 (int u, int type, short si1, short sj1, const char *string, pf_paramT *P) PRIVATE double exp_E_IntLoop loop__energies_8h.html aa5e98e524e2a41e290b942b09544bc9e (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, pf_paramT *P) LPfold.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ LPfold_8h void update_pf_paramsLP group__local__pf__fold.html ga5a019014d37fe6105131dfc2fc447880 (int length) plist * pfl_fold group__local__pf__fold.html gaa1ecd401617ebc748a0220026543c777 (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup) plist * pfl_fold_par group__local__pf__fold.html gab354507e8028f3e1c52ef96bb1eb9df8 (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters) void putoutpU_prob group__local__pf__fold.html ga0bcb751860bbf34e3dfee8c2fbdb3ef3 (double **pU, int length, int ulength, FILE *fp, int energies) void putoutpU_prob_bin group__local__pf__fold.html ga9acb00ee10e96b1ca4ea394cd8bcec75 (double **pU, int length, int ulength, FILE *fp, int energies) void init_pf_foldLP LPfold_8h.html ae85bf55053e9fb295208be322e0fa07a (int length) MEA.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ MEA_8h float MEA MEA_8h.html a396ec6144c6a74fcbab4cea6b42d76c3 (plist *p, char *structure, double gamma) mm.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ mm_8h naview.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ naview_8h params.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ params_8h paramT * scale_parameters group__energy__parameters.html ga527ef619cd8210b84d5d53be1e0e29b6 (void) paramT * get_scaled_parameters group__energy__parameters.html 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init_pf_fold part__func_8h.html a15176e23eceeff8c7d14eabcfec8a2af (int length) char * centroid part__func_8h.html ae89a63bd83e75a80b2ba36d20b31ce81 (int length, double *dist) double mean_bp_dist part__func_8h.html ae9556ba7ded44fe2321b6f67c3fc02a3 (int length) double expLoopEnergy part__func_8h.html a68ba6f3a48e08ca131ab54621ce3a2d7 (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1) double expHairpinEnergy part__func_8h.html a7b6ab474cc80accc48010ccfcc59f96b (int u, int type, short si1, short sj1, const char *string) int st_back group__subopt__stochbt.html gacd79b1a570e6ad9be24cb11fe8cae30a part_func_co.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ part__func__co_8h cofoldF co_pf_fold group__pf__cofold.html gaa86a5f998789ed71813d23d7307a791b (char *sequence, char *structure) cofoldF co_pf_fold_par group__pf__cofold.html gabd873b450832ab5f21101fc5ab354d21 (char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int 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group__pf__cofold.html gaff27888c4088cc1f60fd59cbd589474c double F_monomer group__pf__cofold.html gac2d1851a710a8561390861155ca988fe [2] part_func_up.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ part__func__up_8h pu_contrib * pf_unstru group__up__cofold.html ga5b4ee40e190d2f633cd01cf0d2fe93cf (char *sequence, int max_w) interact * pf_interact group__up__cofold.html ga1aa0aa02bc3a724f87360c03097afd00 (const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5) void free_interact group__up__cofold.html gadde308fd5f696dc271b1532aa96fd12f (interact *pin) void free_pu_contrib_struct group__up__cofold.html gac20bd61824981d45ce0dc9934aa56df8 (pu_contrib *pu) plot_layouts.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ plot__layouts_8h #define VRNA_PLOT_TYPE_SIMPLE plot__layouts_8h.html ae6d17b9f0a53cf5205a9181e0f8422e9 #define VRNA_PLOT_TYPE_NAVIEW plot__layouts_8h.html a94d4c863ecac2f220f76658afb92f964 #define VRNA_PLOT_TYPE_CIRCULAR plot__layouts_8h.html a8c9eac631348da92136c8363ecdd9fb9 int simple_xy_coordinates plot__layouts_8h.html af4b9173e7d3fd361c3c85e6def194123 (short *pair_table, float *X, float *Y) int simple_circplot_coordinates plot__layouts_8h.html ac4ea13d35308f09940178d2b05a248c2 (short *pair_table, float *x, float *y) int rna_plot_type plot__layouts_8h.html a5964c4581431b098b80027d6e14dcdd4 profiledist.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ profiledist_8h float profile_edit_distance profiledist_8h.html abe75e90e00a1e5dd8862944ed53dad5d (const float *T1, const float *T2) float * Make_bp_profile_bppm profiledist_8h.html a8822fd5268be115c6e6cdc92009436cc (double *bppm, int length) void print_bppm profiledist_8h.html a8e0b4fe3698b3502945116ecc0ba6160 (const float *T) void free_profile profiledist_8h.html a9b0b84a5a45761bf42d7c835dcdb3b85 (float *T) float * Make_bp_profile profiledist_8h.html a904c7eaf4a2413567c00ac4891749d18 (int length) PS_dot.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ PS__dot_8h int PS_rna_plot PS__dot_8h.html a0873c7cc4cd7a11c9a2cea19dde7e9c9 (char *string, char *structure, char *file) int PS_rna_plot_a PS__dot_8h.html a47856b2504b566588785597b6ebb8271 (char *string, char *structure, char *file, char *pre, char *post) int gmlRNA PS__dot_8h.html a70834bc8c0aad4fe6824ff76ccb8f329 (char *string, char *structure, char *ssfile, char option) int ssv_rna_plot PS__dot_8h.html add368528755f9a830727b680243541df (char *string, char *structure, char *ssfile) int svg_rna_plot PS__dot_8h.html ae7853539b5df98f294b4af434e979304 (char *string, char *structure, char *ssfile) int xrna_plot PS__dot_8h.html a2f6d5953e6a323df898896b8d6614483 (char *string, char *structure, char *ssfile) int PS_dot_plot_list PS__dot_8h.html a00ea223b5cf02eb2faae5ff29f0d5e12 (char *seq, char *filename, plist *pl, plist *mf, char *comment) int aliPS_color_aln PS__dot_8h.html aab48d4dac655d688abe921389ac2847c (const char *structure, const char *filename, const char *seqs[], const char *names[]) int PS_dot_plot PS__dot_8h.html a689a97a7e3b8a2df14728b8204d9d57b (char *string, char *file) read_epars.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ read__epars_8h void read_parameter_file group__energy__parameters__rw.html ga165a142a3c68fb6655c69ef4ab7cd749 (const char fname[]) void write_parameter_file group__energy__parameters__rw.html ga8a43459be386a7489feeab68dc2c6c76 (const char fname[]) RNAstruct.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ RNAstruct_8h char * b2HIT RNAstruct_8h.html a07b7e90e712559a1992fba3ac6d21bbd (const char *structure) char * b2C RNAstruct_8h.html a9c80d92391f2833549a8b6dac92233f0 (const char *structure) char * b2Shapiro RNAstruct_8h.html a5cd2feb367feeacad0c03cb7ddba5f10 (const char *structure) char * add_root RNAstruct_8h.html a880d33066dd95441e5fbb73c57ed1c3e (const char *structure) char * expand_Shapiro RNAstruct_8h.html abe3d815b420dc4553bfb23511198b4c6 (const char *coarse) char * expand_Full RNAstruct_8h.html a78d73cd54a068ef2812812771cdddc6f (const char *structure) char * unexpand_Full RNAstruct_8h.html a260c4b622093b76a883bf96628280de1 (const char *ffull) char * unweight RNAstruct_8h.html a09a80253ac7b6bae606871ba7c6e5136 (const char *wcoarse) void unexpand_aligned_F RNAstruct_8h.html a1054c4477d53b31d79d4cb132100e87a (char *align[2]) void parse_structure RNAstruct_8h.html a3c79042e6bf6f01706bf30ec9e69e8ac (const char *structure) int loop_size RNAstruct_8h.html a3f31e0e48125601bfa57b52f8b038e8e [STRUC] int helix_size RNAstruct_8h.html a8218c0d581a3fba2a1a56a196abe19a5 [STRUC] int loop_degree RNAstruct_8h.html aef14e2f8ab3f61e8e659ba6b9003b08a [STRUC] int loops RNAstruct_8h.html a439fcb9f8d4f9f4d2227fde5fbfecb30 int unpaired RNAstruct_8h.html add2f952597e02d66e1116a9d11d252d6 int pairs RNAstruct_8h.html a6341cbb704924824e0236c1dce791032 stringdist.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ stringdist_8h swString * Make_swString stringdist_8h.html a3125991b3a403b3f89230474deb3f22e (char *string) float string_edit_distance stringdist_8h.html a89e3c335ef17780576d7c0e713830db9 (swString *T1, swString *T2) subopt.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ subopt_8h SOLUTION * subopt group__subopt__wuchty.html ga700f662506a233e42dd7fda74fafd40e (char *seq, char *structure, int delta, FILE *fp) SOLUTION * subopt_par group__subopt__wuchty.html ga554dedfcdb249fdf151caade58666e4d (char *seq, char *structure, paramT *parameters, int delta, int is_constrained, int is_circular, FILE *fp) SOLUTION * subopt_circ group__subopt__wuchty.html ga8634516e4740e0b6c9a46d2bae940340 (char *seq, char *sequence, int delta, FILE *fp) int subopt_sorted group__subopt__wuchty.html ga873cf8ed69e0437f8efa8b1fec854a0e double print_energy group__subopt__wuchty.html ga5e57d914bcb5feeecdf520e25313fcfe int density_of_states group__dos.html ga937634a76b46a22530a74906f1957a9e [MAXDOS+1] treedist.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ treedist_8h Tree * make_tree treedist_8h.html a08fe4d5afd385dce593b86eaf010c6e3 (char *struc) float tree_edit_distance treedist_8h.html a3b21f1925f7071f46d93431a835217bb (Tree *T1, Tree *T2) void print_tree treedist_8h.html a21ad4de3ba4055aeef08b28c9ad48894 (Tree *t) void free_tree treedist_8h.html acbc1cb9bce582ea945e4a467c76a57aa (Tree *t) utils.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/ utils_8h #define VRNA_INPUT_ERROR utils_8h.html ad403c9ea58f1836689404c2931419c8c #define VRNA_INPUT_QUIT utils_8h.html a72f3c6ca5c83d2b9baed2922d19c403d #define VRNA_INPUT_MISC utils_8h.html a8e3241b321c9c1a78a69e59e2e019a71 #define VRNA_INPUT_FASTA_HEADER utils_8h.html a2f0d8069e93d3ac54d9320d6bdb8e7e7 #define VRNA_INPUT_SEQUENCE utils_8h.html a8566d6787972100e68b5a2a159b4cf45 #define VRNA_INPUT_CONSTRAINT utils_8h.html ac08a9df45b9721b97a47dbfe7a6e5f85 #define VRNA_INPUT_NO_TRUNCATION utils_8h.html a086742158293217a46ae2f71bb296937 #define VRNA_INPUT_NO_REST utils_8h.html a7a2e8c50a0c7ce82e60da1016e1367fd #define VRNA_INPUT_NO_SPAN utils_8h.html a0de536599b881c787b0943a2671da476 #define VRNA_INPUT_NOSKIP_BLANK_LINES utils_8h.html ab4db885222b3b69608310d7c7e63e286 #define VRNA_INPUT_BLANK_LINE utils_8h.html a305474b93ccb79ae4c7754016a8ddd84 #define VRNA_INPUT_NOSKIP_COMMENTS utils_8h.html a0f6311f11bed1842e3a527ab27b294c6 #define VRNA_INPUT_COMMENT utils_8h.html af2062e0eeefffd3ed639af460b3d4fab #define VRNA_CONSTRAINT_PIPE utils_8h.html a4e8d7120619b21df0309af425acbc9a2 #define VRNA_CONSTRAINT_DOT utils_8h.html a55e1d16fd693ae9ec8e987b0750da804 #define VRNA_CONSTRAINT_X utils_8h.html a077c56550c915d4516d84a5ed8d051f4 #define VRNA_CONSTRAINT_ANG_BRACK utils_8h.html a0512d790f738742cbdcf3f7c87b46f48 #define VRNA_CONSTRAINT_RND_BRACK utils_8h.html aa20bfca4bb2903c8548000a33d7bbb53 #define VRNA_CONSTRAINT_MULTILINE utils_8h.html a7d725ef525b29891abef3f1ed42599a4 #define VRNA_CONSTRAINT_NO_HEADER utils_8h.html a08d12a9a846ea593b7171d277c9f033f #define VRNA_CONSTRAINT_ALL utils_8h.html a0a697f77a6fbb10f34e16fa68ed9e655 #define VRNA_CONSTRAINT_G utils_8h.html a99dc6b23dc4080a76e2ed1a81c20e94d #define VRNA_OPTION_MULTILINE utils_8h.html abec89c09874528c6cb73140a4c3d86d7 #define MIN2 utils_8h.html ae0b9cd0ce090bd69b951aa73e8fa4f7d (A, B) #define MAX2 utils_8h.html a33297b3679c713b0c4d897cd0fe3b122 (A, B) #define MIN3 utils_8h.html a721b8d5f3abef17f10293f1f7f8c958e (A, B, C) #define MAX3 utils_8h.html a8d577123d2e66d2b7d0bf9af6e172b93 (A, B, C) #define XSTR utils_8h.html a03943706e48069237cd57f2d35ca987e (s) #define STR utils_8h.html a6388870e639eee9c0a69446876f1f8cc (s) #define FILENAME_MAX_LENGTH utils_8h.html afb228174279df9486a5cb56ac0bc79a3 #define FILENAME_ID_LENGTH utils_8h.html a33c3b1826b8e2739f09f111ec719ded5 void * space utils_8h.html ad7e1e137b3bf1f7108933d302a7f0177 (unsigned size) void * xrealloc utils_8h.html a9037ada838835b1b9db41581a021b0c8 (void *p, unsigned size) void nrerror utils_8h.html a127ce946e56b5a5773781cabe68e38c5 (const char message[]) void warn_user utils_8h.html af2355fa8746f2f30fbe71db65dea3d51 (const char message[]) void init_rand utils_8h.html a8aaa6d9be6f803f496d9b97375c371f3 (void) double urn utils_8h.html aaa328491c84996e445d027fde9800f2e (void) int int_urn utils_8h.html a68ff0849d44f62fe491800378a5ffcb4 (int from, int to) char * time_stamp utils_8h.html a7afeb906cb36e9d77379eabc6907ac46 (void) char * random_string utils_8h.html a1b95eac365a021572e1c37e5993a89be (int l, const char symbols[]) int hamming utils_8h.html ad9dc7bfc9aa664dc6698f17ce07fc7e7 (const char *s1, const char *s2) int hamming_bound utils_8h.html a96d3c36717d624514055ce201cab1542 (const char *s1, const char *s2, int n) char * get_line utils_8h.html abe51806d14cff0789a8c1df7dbc45b71 (FILE *fp) unsigned int get_input_line utils_8h.html a8ef1835eb83f542396f59f0b205965e5 (char **string, unsigned int options) unsigned int read_record utils_8h.html afd194a69af9d92b5b0412a7627ac1595 (char **header, char **sequence, char ***rest, unsigned int options) char * pack_structure utils_8h.html ac6dfa5e22928c087c6e09ff0054a7ced (const char *struc) char * unpack_structure utils_8h.html a071c6921efe1eb974f115ee6fefa3c39 (const char *packed) short * make_pair_table utils_8h.html a89c32307ee50a0026f4a3131fac0845a (const char *structure) short * copy_pair_table utils_8h.html afeaa6d68eef3a99d0a7aa08aa91c6601 (const short *pt) short * alimake_pair_table utils_8h.html a3c81b3967056c3888b8472b65fbb16f5 (const char *structure) short * make_pair_table_snoop utils_8h.html a9aa3bf3b4346bb7fb88efc154dd07a79 (const char *structure) int * make_loop_index_pt utils_8h.html a4358e89f64cc87a563b7ef3855f75bed (short *pt) void print_tty_input_seq utils_8h.html a6bf778117d31b7fd90db435323f4ef74 (void) void print_tty_input_seq_str utils_8h.html ae4ef89b662a3e9b5b5f0781d9757aba0 (const char *s) void print_tty_constraint_full utils_8h.html ae8ae8a34962b9959be3f6c40f0a80ac1 (void) void print_tty_constraint utils_8h.html a4d167deb70bb51723e44374dc981deb2 (unsigned int option) void str_DNA2RNA utils_8h.html ad3f18dd83f958f18b2f26ecb99305208 (char *sequence) void str_uppercase utils_8h.html a17b796b806f96b70382077fb5bc519bb (char *sequence) int * get_iindx utils_8h.html a55c0f6b3b07b6adf2ee235ba901fe397 (unsigned int length) int * get_indx utils_8h.html a4d9ee1572c1bfcd02d3d3f2db8a6530f (unsigned int length) void constrain_ptypes utils_8h.html a36c3a6c3218b041f992052767bc74549 (const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type) unsigned short xsubi utils_8h.html af9a866c8417afda7368bbac939ab3c47 [3] 1.8.4_epars.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/ 1_88_84__epars_8h 1.8.4_intloops.h /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/ 1_88_84__intloops_8h mp_parse mp_parse mp_utils mp_utils utils_struc utils_dot toc utils_misc utils_ss utils_seq utils_aln mp_example mp_example folding_routines group__folding__routines.html mfe_fold pf_fold subopt_fold cofold consensus_fold local_fold energy_parameters eval inverse_fold class_fold mfe_fold group__mfe__fold.html mfe_cofold consensus_mfe_fold local_mfe_fold kl_neighborhood_mfe float fold_par group__mfe__fold.html gadb973133c241d57c04b253df35e4d34e (const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular) float fold group__mfe__fold.html gaadafcb0f140795ae62e5ca027e335a9b (const char *sequence, char *structure) float circfold group__mfe__fold.html ga4ac63ab3e8d9a80ced28b8052d94e423 (const char *sequence, char *structure) void free_arrays group__mfe__fold.html ga107fdfe5fd641868156bfd849f6866c7 (void) void update_fold_params group__mfe__fold.html ga41bf8f6fa15b94471f7095cad9f0ccf3 (void) pf_fold group__pf__fold.html mea_fold centroid_fold pf_cofold up_cofold consensus_pf_fold local_pf_fold kl_neighborhood_pf float pf_fold_par group__pf__fold.html ga1839c61275760944b3a007c41d5c0823 (const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular) float pf_fold group__pf__fold.html gadc3db3d98742427e7001a7fd36ef28c2 (const char *sequence, char *structure) float pf_circ_fold group__pf__fold.html ga819ce5fca8984004ac81c4a3b04cb735 (const char *sequence, char *structure) void free_pf_arrays group__pf__fold.html gae73db3f49a94f0f72e067ecd12681dbd (void) void update_pf_params group__pf__fold.html ga384e927890f9c034ff09fa66da102d28 (int length) void update_pf_params_par group__pf__fold.html ga0733527a94de3b79eee3c3c03c99c1bc (int length, pf_paramT *parameters) double * export_bppm group__pf__fold.html ga6d463707d5f64bdc4d21515b7dd9b115 (void) void assign_plist_from_pr group__pf__fold.html ga03e15e831a31b1154855ab47edbdb019 (plist **pl, double *probs, int length, double cutoff) int get_pf_arrays group__pf__fold.html ga18607e79e106cad827f482eedd2f632e (short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p) double mean_bp_distance group__pf__fold.html ga79cbc375af65f11609feb6b055269e7d (int length) double mean_bp_distance_pr group__pf__fold.html ga72d84525f0afd3a9d60d830a2f501fa5 (int length, double *pr) mea_fold group__mea__fold.html centroid_fold group__centroid__fold.html char * get_centroid_struct_pl group__centroid__fold.html ga9aba0ba1433a6d259331e0fe9fc4a9a6 (int length, double *dist, plist *pl) char * get_centroid_struct_pr group__centroid__fold.html gacdabece4aa1e20c9eaa97acb4c4dcc38 (int length, double *dist, double *pr) subopt_fold group__subopt__fold.html subopt_zuker subopt_wuchty subopt_stochbt subopt_zuker group__subopt__zuker.html SOLUTION * zukersubopt group__subopt__zuker.html ga0d5104e3ecf119d8eabd40aa5fe47f90 (const char *string) SOLUTION * zukersubopt_par group__subopt__zuker.html ga6d98a9450d1affadf144ac79f543da8c (const char *string, paramT *parameters) subopt_wuchty group__subopt__wuchty.html SOLUTION * subopt group__subopt__wuchty.html ga700f662506a233e42dd7fda74fafd40e (char *seq, char *structure, int delta, FILE *fp) SOLUTION * subopt_par group__subopt__wuchty.html ga554dedfcdb249fdf151caade58666e4d (char *seq, char *structure, paramT *parameters, int delta, int is_constrained, int is_circular, FILE *fp) SOLUTION * subopt_circ group__subopt__wuchty.html ga8634516e4740e0b6c9a46d2bae940340 (char *seq, char *sequence, int delta, FILE *fp) int subopt_sorted group__subopt__wuchty.html ga873cf8ed69e0437f8efa8b1fec854a0e double print_energy group__subopt__wuchty.html ga5e57d914bcb5feeecdf520e25313fcfe subopt_stochbt group__subopt__stochbt.html consensus_stochbt kl_neighborhood_stochbt char * pbacktrack group__subopt__stochbt.html gac03ca6db186bb3bf0a2a326d7fb3ba03 (char *sequence) char * pbacktrack_circ group__subopt__stochbt.html ga00474051204ac9ad576b3e45174d03ff (char *sequence) int st_back group__subopt__stochbt.html gacd79b1a570e6ad9be24cb11fe8cae30a cofold group__cofold.html mfe_cofold pf_cofold up_cofold mfe_cofold group__mfe__cofold.html cofold.h float cofold group__mfe__cofold.html gabc8517f22cfe70595ee81fc837910d52 (const char *sequence, char *structure) float cofold_par group__mfe__cofold.html gafe430060533f14b11fc611f60b3f1f6f (const char *string, char *structure, paramT *parameters, int is_constrained) void free_co_arrays group__mfe__cofold.html gaafb33d7473eb9af9d1b168ca8761c41a (void) void update_cofold_params group__mfe__cofold.html ga4fcbf34e77b99bfbb2333d2ab0c41a57 (void) void export_cofold_arrays_gq group__mfe__cofold.html ga5f5bf4df35d0554f6ace9579f8744c48 (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p) void export_cofold_arrays group__mfe__cofold.html ga5cb6b59983f1f74ccc00b9b9c4e84482 (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p) pf_cofold group__pf__cofold.html part_func_co.h cofoldF co_pf_fold group__pf__cofold.html gaa86a5f998789ed71813d23d7307a791b (char *sequence, char *structure) cofoldF co_pf_fold_par group__pf__cofold.html gabd873b450832ab5f21101fc5ab354d21 (char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained) double * export_co_bppm group__pf__cofold.html ga11f0252c1d2c4697253ff4b5bd392d3c (void) void free_co_pf_arrays group__pf__cofold.html gade3ce34ae8214811374b1d28a40dc247 (void) void update_co_pf_params group__pf__cofold.html ga6e0f36c1f9b7d9dd4bfbad914c1119e5 (int length) void update_co_pf_params_par group__pf__cofold.html ga117d880df45bef444d5e2785ffa40a53 (int length, pf_paramT *parameters) void compute_probabilities group__pf__cofold.html ga15ae04ac5ab84e876dcf0093120cb617 (double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength) ConcEnt * get_concentrations group__pf__cofold.html ga5545cb936ac4ff93c7d699d46e72e8c7 (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc) int mirnatog group__pf__cofold.html gaff27888c4088cc1f60fd59cbd589474c double F_monomer group__pf__cofold.html gac2d1851a710a8561390861155ca988fe [2] up_cofold group__up__cofold.html part_func_up.h pu_contrib * pf_unstru group__up__cofold.html ga5b4ee40e190d2f633cd01cf0d2fe93cf (char *sequence, int max_w) interact * pf_interact group__up__cofold.html ga1aa0aa02bc3a724f87360c03097afd00 (const char *s1, const char *s2, pu_contrib *p_c, pu_contrib *p_c2, int max_w, char *cstruc, int incr3, int incr5) void free_interact group__up__cofold.html gadde308fd5f696dc271b1532aa96fd12f (interact *pin) void free_pu_contrib_struct group__up__cofold.html gac20bd61824981d45ce0dc9934aa56df8 (pu_contrib *pu) consensus_fold group__consensus__fold.html consensus_mfe_fold consensus_pf_fold consensus_stochbt local_consensus_fold int get_mpi group__consensus__fold.html gaa2d600be90844094ec145ea14a314d2f (char *Alseq[], int n_seq, int length, int *mini) float ** readribosum group__consensus__fold.html ga5e125c9586fcd4e2e1559fe76f7289cc (char *name) float energy_of_alistruct group__consensus__fold.html ga1c48869c03b49a342bf4cbdd61900081 (const char **sequences, const char *structure, int n_seq, float *energy) void encode_ali_sequence group__consensus__fold.html gaa3e40277c837d6f7603afe319884c786 (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ) void alloc_sequence_arrays group__consensus__fold.html ga8a560930f7f2582cc3967723a86cfdfa (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ) void free_sequence_arrays group__consensus__fold.html ga298a420a8c879202e2617b3f724fde38 (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss) int get_alipf_arrays group__consensus__fold.html ga5349960075b1847720a2e9df021e2675 (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore) double cv_fact group__consensus__fold.html gaf3cbac6ff5d706d6e414677841ddf94c double nc_fact group__consensus__fold.html ga502948a122a2af5b914355b1f3ea2f61 consensus_mfe_fold group__consensus__mfe__fold.html float alifold group__consensus__mfe__fold.html ga4cf00f0659e5f0480335d69e797f05b1 (const char **strings, char *structure) float circalifold group__consensus__mfe__fold.html gadbd3b0b1c144cbfb4efe704b2b260f96 (const char **strings, char *structure) void free_alifold_arrays group__consensus__mfe__fold.html ga72095e4554b5d577250ea14c42acc49e (void) consensus_pf_fold group__consensus__pf__fold.html float alipf_fold_par group__consensus__pf__fold.html ga4d2ff54d8210fc7cceeeff389d4dbd1d (const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular) float alipf_fold group__consensus__pf__fold.html gad32ded7d753ccaf211ab35782d1f42a9 (const char **sequences, char *structure, plist **pl) float alipf_circ_fold group__consensus__pf__fold.html ga6b4dde1d43b79ab3753508c46cf50363 (const char **sequences, char *structure, plist **pl) FLT_OR_DBL * export_ali_bppm group__consensus__pf__fold.html ga11b6ab8bd9be1821fea352b190a01cab (void) consensus_stochbt group__consensus__stochbt.html char * alipbacktrack group__consensus__stochbt.html ga0df40248788f0fb17ebdc59d74116d1c (double *prob) local_fold group__local__fold.html local_mfe_fold local_pf_fold local_consensus_fold local_mfe_fold group__local__mfe__fold.html float Lfold group__local__mfe__fold.html ga16e5a70e60835bb969eaecbe6482f1be (const char *string, char *structure, int maxdist) float Lfoldz group__local__mfe__fold.html gab6d79eecc180f586679f7b85cce5cbe9 (const char *string, char *structure, int maxdist, int zsc, double min_z) local_pf_fold group__local__pf__fold.html void update_pf_paramsLP group__local__pf__fold.html ga5a019014d37fe6105131dfc2fc447880 (int length) plist * pfl_fold group__local__pf__fold.html gaa1ecd401617ebc748a0220026543c777 (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup) plist * pfl_fold_par group__local__pf__fold.html gab354507e8028f3e1c52ef96bb1eb9df8 (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters) void putoutpU_prob group__local__pf__fold.html ga0bcb751860bbf34e3dfee8c2fbdb3ef3 (double **pU, int length, int ulength, FILE *fp, int energies) void putoutpU_prob_bin group__local__pf__fold.html ga9acb00ee10e96b1ca4ea394cd8bcec75 (double **pU, int length, int ulength, FILE *fp, int energies) local_consensus_fold group__local__consensus__fold.html float aliLfold 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get_boltzmann_factors_ali group__energy__parameters.html gaf0c74574b40f2778556535bf9d382828 (unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale) energy_parameters_rw group__energy__parameters__rw.html energy_parameters_convert read_epars.h void read_parameter_file group__energy__parameters__rw.html ga165a142a3c68fb6655c69ef4ab7cd749 (const char fname[]) void write_parameter_file group__energy__parameters__rw.html ga8a43459be386a7489feeab68dc2c6c76 (const char fname[]) energy_parameters_convert group__energy__parameters__convert.html convert_epars.h #define VRNA_CONVERT_OUTPUT_ALL group__energy__parameters__convert.html ga8dc6aee5a806c49b71557152f9616bc4 #define VRNA_CONVERT_OUTPUT_HP group__energy__parameters__convert.html gaf66fe2cb11dfcfd32d791049c254a8a4 #define VRNA_CONVERT_OUTPUT_STACK group__energy__parameters__convert.html gad23522d63f8d4c50d5a5deee9bee3ef2 #define VRNA_CONVERT_OUTPUT_MM_HP group__energy__parameters__convert.html gaa892c7b4957459090f3e08da298cc347 #define VRNA_CONVERT_OUTPUT_MM_INT group__energy__parameters__convert.html ga4ff223fb1f9c62cd92d9ab811ad03d55 #define VRNA_CONVERT_OUTPUT_MM_INT_1N group__energy__parameters__convert.html gaf5d3743219f83c6348155cd81e755bbb #define VRNA_CONVERT_OUTPUT_MM_INT_23 group__energy__parameters__convert.html ga78382ec622ba99e0ac2262317bdd7316 #define VRNA_CONVERT_OUTPUT_MM_MULTI group__energy__parameters__convert.html gae67af9f1cdf7baf2865481282a5d1034 #define VRNA_CONVERT_OUTPUT_MM_EXT group__energy__parameters__convert.html gaf14ead7ef1fdbe725ade653750fc51e3 #define VRNA_CONVERT_OUTPUT_DANGLE5 group__energy__parameters__convert.html ga036ffd996d8c8a9acf631760dd1da24b #define VRNA_CONVERT_OUTPUT_DANGLE3 group__energy__parameters__convert.html ga34a8a5479ef885834ef32f3fb43d79bc #define VRNA_CONVERT_OUTPUT_INT_11 group__energy__parameters__convert.html ga079aafefd5f8ab57ee5120099a34bd25 #define VRNA_CONVERT_OUTPUT_INT_21 group__energy__parameters__convert.html gacf770881d9034431ebe741642342a1f9 #define VRNA_CONVERT_OUTPUT_INT_22 group__energy__parameters__convert.html gaa307671e2631cdacad9cbe4c6583b05f #define VRNA_CONVERT_OUTPUT_BULGE group__energy__parameters__convert.html ga7092fe0be4de6f02cc0bf08e81af726a #define VRNA_CONVERT_OUTPUT_INT group__energy__parameters__convert.html gac5c2289fdf8ff1b980976d1613ff943a #define VRNA_CONVERT_OUTPUT_ML group__energy__parameters__convert.html gaf2c8755d64eff3852aa45df9ac80a4fe #define VRNA_CONVERT_OUTPUT_MISC group__energy__parameters__convert.html ga46d5b1535ae86060b6317565b7c6b40b #define VRNA_CONVERT_OUTPUT_SPECIAL_HP group__energy__parameters__convert.html gaa1ff48a79642d69579d1766561ec6db6 #define VRNA_CONVERT_OUTPUT_VANILLA group__energy__parameters__convert.html ga0d4e8a836bb4864ab5129c085dbf592d #define VRNA_CONVERT_OUTPUT_NINIO group__energy__parameters__convert.html ga2eb0462f16939ddacdaf751a88d675ce #define VRNA_CONVERT_OUTPUT_DUMP group__energy__parameters__convert.html gac86976e9c2a55b3a6481ea60044f6098 void convert_parameter_file group__energy__parameters__convert.html gafbe538bc4eb2cf2a33326e1010005f8a (const char *iname, const char *oname, unsigned int options) eval group__eval.html float energy_of_structure group__eval.html gaf93986cb3cb29770ec9cca69c9fab8cf (const char *string, const char *structure, int verbosity_level) float energy_of_struct_par group__eval.html gab5169ea4f72f250e43811463a33f4e40 (const char *string, const char *structure, paramT *parameters, int verbosity_level) float energy_of_circ_structure group__eval.html gaeb14f3664aec67fc03268ac75253f0f8 (const char *string, const char *structure, int verbosity_level) float energy_of_circ_struct_par group__eval.html ga75dc765ee4a1177832bc817c94cf88e5 (const char *string, const char *structure, paramT *parameters, int verbosity_level) int energy_of_structure_pt group__eval.html ga8831445966b761417e713360791299d8 (const char *string, short *ptable, short *s, short *s1, int verbosity_level) int energy_of_struct_pt_par group__eval.html gada4701dd7519b29da75ceac147601f4e (const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level) int eos_debug group__eval.html ga567530678f6260a1a649a5beca5da4c5 inverse_fold group__inverse__fold.html inverse.h float inverse_fold group__inverse__fold.html ga7af026de55d4babad879f2c92559cbbc (char *start, const char *target) float inverse_pf_fold group__inverse__fold.html gaeef52ecbf2a2450ad585a344f9826806 (char *start, const char *target) char * symbolset group__inverse__fold.html ga8f791e7740a5a28b9f6fafb4e60301d9 float final_cost group__inverse__fold.html ga7f17d3b169af048d32bb185039a9c09c int give_up group__inverse__fold.html ga7ec4ba51f86e1717a1e174264e4a75ce int inv_verbose group__inverse__fold.html gafcfc65fba01b9cca5946726ed9057a63 class_fold group__class__fold.html kl_neighborhood dos kl_neighborhood group__kl__neighborhood.html kl_neighborhood_mfe kl_neighborhood_pf kl_neighborhood_stochbt kl_neighborhood_mfe group__kl__neighborhood__mfe.html 2Dfold.h TwoDfold_vars * get_TwoDfold_variables group__kl__neighborhood__mfe.html gac9284f132cf0eaa0a2f43590eda05488 (const char *seq, const char *structure1, const char *structure2, int circ) void destroy_TwoDfold_variables group__kl__neighborhood__mfe.html ga05bf4f31d216b1b160fd2d3d68e9b487 (TwoDfold_vars *our_variables) TwoDfold_solution * TwoDfoldList group__kl__neighborhood__mfe.html ga47da790166020558d27323aef489703e (TwoDfold_vars *vars, int distance1, int distance2) char * TwoDfold_backtrack_f5 group__kl__neighborhood__mfe.html gaf4dc05bf8fc1ea53acd7aeb798ba80c2 (unsigned int j, int k, int l, TwoDfold_vars *vars) kl_neighborhood_pf group__kl__neighborhood__pf.html 2Dpfold.h TwoDpfold_vars * get_TwoDpfold_variables group__kl__neighborhood__pf.html ga1aca740e2a75ab2b2951538266e53d64 (const char *seq, const char *structure1, char *structure2, int circ) TwoDpfold_vars * get_TwoDpfold_variables_from_MFE 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