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 
65 float cofold( const char *sequence,
66  char *structure);
67 
72 float cofold_par( const char *string,
73  char *structure,
74  paramT *parameters,
75  int is_constrained);
76 
80 void free_co_arrays(void);
81 
85 void update_cofold_params(void);
86 
87 void update_cofold_params_par(paramT *parameters);
88 
89 
105 void 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 
128 void 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 
153 SOLUTION *zukersubopt(const char *string);
154 
161 SOLUTION *zukersubopt_par( const char *string,
162  paramT *parameters);
163 
172 void get_monomere_mfes( float *e1,
173  float *e2);
174 
175 
180 DEPRECATED(void initialize_cofold(int length));
181 
182 #endif
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.
The datastructure that contains temperature scaled energy parameters.
Definition: data_structures.h:122
void get_monomere_mfes(float *e1, float *e2)
get_monomer_free_energies
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)
Solution element from subopt.c.
Definition: data_structures.h:318
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
void free_co_arrays(void)
Free memory occupied by cofold()
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.
float cofold(const char *sequence, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
SOLUTION * zukersubopt_par(const char *string, paramT *parameters)
Compute Zuker type suboptimal structures.
void initialize_cofold(int length)