RNAlib-2.1.7
LPfold.h
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1 #ifndef __VIENNA_RNA_PACKAGE_LPFOLD_H__
2 #define __VIENNA_RNA_PACKAGE_LPFOLD_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 
29 void update_pf_paramsLP(int length);
30 
37 void update_pf_paramsLP_par(int length, pf_paramT *parameters);
38 
76 plist *pfl_fold(char *sequence,
77  int winSize,
78  int pairSize,
79  float cutoffb,
80  double **pU,
81  struct plist **dpp2,
82  FILE *pUfp,
83  FILE *spup);
84 
91 plist *pfl_fold_par(char *sequence,
92  int winSize,
93  int pairSize,
94  float cutoffb,
95  double **pU,
96  struct plist **dpp2,
97  FILE *pUfp,
98  FILE *spup,
99  pf_paramT *parameters);
100 
101 
102 void putoutpU_prob_par( double **pU,
103  int length,
104  int ulength,
105  FILE *fp,
106  int energies,
107  pf_paramT *parameters);
108 
109 
124 void putoutpU_prob(double **pU,
125  int length,
126  int ulength,
127  FILE *fp,
128  int energies);
129 
130 void putoutpU_prob_bin_par( double **pU,
131  int length,
132  int ulength,
133  FILE *fp,
134  int energies,
135  pf_paramT *parameters);
136 
151 void putoutpU_prob_bin(double **pU,
152  int length,
153  int ulength,
154  FILE *fp,
155  int energies);
156 
162 DEPRECATED(void init_pf_foldLP(int length));
163 
164 #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.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:171
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:52
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_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters)
Compute partition functions for locally stable secondary structures.
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.