RNAlib-2.1.9h
cofold.h
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1#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__
2#define __VIENNA_RNA_PACKAGE_COFOLD_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
65float cofold( const char *sequence,
66 char *structure);
67
72float cofold_par( const char *string,
73 char *structure,
74 paramT *parameters,
75 int is_constrained);
76
80void free_co_arrays(void);
81
86
87void update_cofold_params_par(paramT *parameters);
88
89
105void export_cofold_arrays_gq( int **f5_p,
106 int **c_p,
107 int **fML_p,
108 int **fM1_p,
109 int **fc_p,
110 int **ggg_p,
111 int **indx_p,
112 char **ptype_p);
113
128void export_cofold_arrays(int **f5_p,
129 int **c_p,
130 int **fML_p,
131 int **fM1_p,
132 int **fc_p,
133 int **indx_p,
134 char **ptype_p);
135
136
153SOLUTION *zukersubopt(const char *string);
154
161SOLUTION *zukersubopt_par( const char *string,
162 paramT *parameters);
163
172void get_monomere_mfes( float *e1,
173 float *e2);
174
175
180DEPRECATED(void initialize_cofold(int length));
181
182#endif
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
void initialize_cofold(int length)
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
void update_cofold_params(void)
Recalculate parameters.
void export_cofold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)
Export the arrays of partition function cofold.
void export_cofold_arrays_gq(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)
Export the arrays of partition function cofold (with gquadruplex support)
void free_co_arrays(void)
Free memory occupied by cofold()
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
float cofold_par(const char *string, char *structure, paramT *parameters, int is_constrained)
Compute the minimum free energy of two interacting RNA molecules.
SOLUTION * zukersubopt(const char *string)
Compute Zuker type suboptimal structures.
SOLUTION * zukersubopt_par(const char *string, paramT *parameters)
Compute Zuker type suboptimal structures.
Solution element from subopt.c.
Definition data_structures.h:318
The datastructure that contains temperature scaled energy parameters.
Definition data_structures.h:122