RNAlib-2.2.7
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 DEPRECATION_WARNINGS
8 # ifdef __GNUC__
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
10 # else
11 # define DEPRECATED(func) func
12 # endif
13 #else
14 # define DEPRECATED(func) func
15 #endif
16 
34 void update_pf_paramsLP(int length);
35 
42 void update_pf_paramsLP_par(int length, vrna_exp_param_t *parameters);
43 
81 plist *pfl_fold(char *sequence,
82  int winSize,
83  int pairSize,
84  float cutoffb,
85  double **pU,
86  plist **dpp2,
87  FILE *pUfp,
88  FILE *spup);
89 
96 plist *pfl_fold_par(char *sequence,
97  int winSize,
98  int pairSize,
99  float cutoffb,
100  double **pU,
101  plist **dpp2,
102  FILE *pUfp,
103  FILE *spup,
104  vrna_exp_param_t *parameters);
105 
106 
107 void putoutpU_prob_par( double **pU,
108  int length,
109  int ulength,
110  FILE *fp,
111  int energies,
112  vrna_exp_param_t *parameters);
113 
114 
129 void putoutpU_prob(double **pU,
130  int length,
131  int ulength,
132  FILE *fp,
133  int energies);
134 
135 void putoutpU_prob_bin_par( double **pU,
136  int length,
137  int ulength,
138  FILE *fp,
139  int energies,
140  vrna_exp_param_t *parameters);
141 
156 void putoutpU_prob_bin(double **pU,
157  int length,
158  int ulength,
159  FILE *fp,
160  int energies);
161 
167 DEPRECATED(void init_pf_foldLP(int length));
168 
169 #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(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, plist **dpp2, FILE *pUfp, FILE *spup)
Compute partition functions for locally stable secondary structures.
void init_pf_foldLP(int length)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
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.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
plist * pfl_fold_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, plist **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters)
Compute partition functions for locally stable secondary structures.