RNAlib-2.3.1
part_func_co.h
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1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
3 
4 #ifdef DEPRECATION_WARNINGS
5 # ifdef __GNUC__
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
7 # else
8 # define DEPRECATED(func) func
9 # endif
10 #else
11 # define DEPRECATED(func) func
12 #endif
13 
14 /* make this interface backward compatible with RNAlib < 2.2.0 */
15 #define VRNA_BACKWARD_COMPAT
16 
64 
67 
68 
69 #ifdef VRNA_BACKWARD_COMPAT
70 
74 typedef struct vrna_dimer_pf_s cofoldF;
75 
79 typedef struct vrna_dimer_conc_s ConcEnt;
80 
81 #endif
82 
84 #include <ViennaRNA/params.h>
85 
89 extern int mirnatog;
90 
94 extern double F_monomer[2];
95 
100  /* free energies for: */
101  double F0AB;
102  double FAB;
103  double FcAB;
104  double FA;
105  double FB;
106 };
107 
112  double A0;
113  double B0;
114  double ABc;
115  double AAc;
116  double BBc;
117  double Ac;
118  double Bc;
119 };
120 
136  char *structure);
137 
156 void vrna_pf_dimer_probs(double FAB,
157  double FA,
158  double FB,
159  vrna_plist_t *prAB,
160  const vrna_plist_t *prA,
161  const vrna_plist_t *prB,
162  int Alength,
163  const vrna_exp_param_t *exp_params);
164 
185  double FcAA,
186  double FcBB,
187  double FEA,
188  double FEB,
189  const double *startconc,
190  const vrna_exp_param_t *exp_params);
191 
196 /*
197 #################################################
198 # DEPRECATED FUNCTIONS #
199 #################################################
200 */
201 
220 DEPRECATED(vrna_dimer_pf_t co_pf_fold( char *sequence, char *structure));
221 
241 DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));
242 
248 DEPRECATED(vrna_plist_t *get_plist( vrna_plist_t *pl,
249  int length,
250  double cut_off));
251 
271 DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength));
272 
293 DEPRECATED(vrna_dimer_conc_t *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));
294 
299 DEPRECATED(void init_co_pf_fold(int length));
300 
314 DEPRECATED(FLT_OR_DBL *export_co_bppm(void));
315 
323 DEPRECATED(void free_co_pf_arrays(void));
324 
335 DEPRECATED(void update_co_pf_params(int length));
336 
356 DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));
357 
358 #endif
double A0
start concentration A
Definition: part_func_co.h:112
void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
double B0
start concentration B
Definition: part_func_co.h:113
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:454
double ABc
End concentration AB.
Definition: part_func_co.h:114
void update_co_pf_params(int length)
Recalculate energy parameters.
FLT_OR_DBL * export_co_bppm(void)
Get a pointer to the base pair probability array.
double F0AB
Null model without DuplexInit.
Definition: part_func_co.h:101
double FA
monomer A
Definition: part_func_co.h:104
Data structure for concentration dependency computations.
Definition: part_func_co.h:111
int mirnatog
Toggles no intrabp in 2nd mol.
vrna_plist_t * get_plist(vrna_plist_t *pl, int length, double cut_off)
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:99
vrna_dimer_pf_t vrna_pf_dimer(vrna_fold_compound_t *vc, char *structure)
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers...
void init_co_pf_fold(int length)
double FB
monomer B
Definition: part_func_co.h:105
vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:182
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
void vrna_pf_dimer_probs(double FAB, double FA, double FB, vrna_plist_t *prAB, const vrna_plist_t *prA, const vrna_plist_t *prB, int Alength, const vrna_exp_param_t *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
vrna_dimer_conc_t * vrna_pf_dimer_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
vrna_dimer_conc_t * get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
double FcAB
true hybrid states only
Definition: part_func_co.h:103
Data structure returned by vrna_pf_dimer()
Definition: part_func_co.h:99
double F_monomer[2]
Free energies of the two monomers.
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
double FAB
all states with DuplexInit correction
Definition: part_func_co.h:102