RNAlib-2.2.0-RC3
LPfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2 #define VIENNA_RNA_PACKAGE_LPFOLD_H
3 
5 #include <ViennaRNA/params.h>
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
30 void update_pf_paramsLP(int length);
31 
38 void update_pf_paramsLP_par(int length, vrna_exp_param_t *parameters);
39 
77 plist *pfl_fold(char *sequence,
78  int winSize,
79  int pairSize,
80  float cutoffb,
81  double **pU,
82  struct plist **dpp2,
83  FILE *pUfp,
84  FILE *spup);
85 
92 plist *pfl_fold_par(char *sequence,
93  int winSize,
94  int pairSize,
95  float cutoffb,
96  double **pU,
97  struct plist **dpp2,
98  FILE *pUfp,
99  FILE *spup,
100  vrna_exp_param_t *parameters);
101 
102 
103 void putoutpU_prob_par( double **pU,
104  int length,
105  int ulength,
106  FILE *fp,
107  int energies,
108  vrna_exp_param_t *parameters);
109 
110 
125 void putoutpU_prob(double **pU,
126  int length,
127  int ulength,
128  FILE *fp,
129  int energies);
130 
131 void putoutpU_prob_bin_par( double **pU,
132  int length,
133  int ulength,
134  FILE *fp,
135  int energies,
136  vrna_exp_param_t *parameters);
137 
152 void putoutpU_prob_bin(double **pU,
153  int length,
154  int ulength,
155  FILE *fp,
156  int energies);
157 
163 DEPRECATED(void init_pf_foldLP(int length));
164 
165 #endif
void putoutpU_prob_bin(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a binary file.
plist * pfl_fold_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters)
Compute partition functions for locally stable secondary structures.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
void init_pf_foldLP(int length)
void update_pf_paramsLP(int length)
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
plist * pfl_fold(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup)
Compute partition functions for locally stable secondary structures.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86