RNAlib-2.1.9h
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#include "data_structures.h"
5
6#ifdef __GNUC__
7#define DEPRECATED(func) func __attribute__ ((deprecated))
8#else
9#define DEPRECATED(func) func
10#endif
11
55extern int mirnatog;
56
60extern double F_monomer[2];
61
80cofoldF co_pf_fold( char *sequence,
81 char *structure);
82
100cofoldF co_pf_fold_par( char *sequence,
101 char *structure,
102 pf_paramT *parameters,
103 int calculate_bppm,
104 int is_constrained);
105
115FLT_OR_DBL *export_co_bppm(void);
116
121
136void update_co_pf_params(int length);
137
158 pf_paramT *parameters);
159
177void compute_probabilities(double FAB,
178 double FEA,
179 double FEB,
180 struct plist *prAB,
181 struct plist *prA,
182 struct plist *prB,
183 int Alength);
184
204 double FEAA,
205 double FEBB,
206 double FEA,
207 double FEB,
208 double *startconc);
209
210
215/*
216#################################################
217# DEPRECATED FUNCTIONS #
218#################################################
219*/
220
226DEPRECATED(plist *get_plist( struct plist *pl,
227 int length,
228 double cut_off));
233DEPRECATED(void init_co_pf_fold(int length));
234
235#endif
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
void update_co_pf_params_par(int length, pf_paramT *parameters)
Recalculate energy parameters.
void compute_probabilities(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
double * export_co_bppm(void)
Get a pointer to the base pair probability array.
void update_co_pf_params(int length)
Recalculate energy parameters.
cofoldF co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
cofoldF co_pf_fold_par(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
double F_monomer[2]
Free energies of the two monomers.
ConcEnt * 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()
int mirnatog
Toggles no intrabp in 2nd mol.
void init_co_pf_fold(int length)
plist * get_plist(struct plist *pl, int length, double cut_off)
Definition data_structures.h:344
Definition data_structures.h:332
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition data_structures.h:203
this datastructure is used as input parameter in functions of PS_dot.h and others
Definition data_structures.h:48