RNAlib-2.1.9h
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
29void update_pf_paramsLP(int length);
30
37void update_pf_paramsLP_par(int length, pf_paramT *parameters);
38
76plist *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
91plist *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
102void putoutpU_prob_par( double **pU,
103 int length,
104 int ulength,
105 FILE *fp,
106 int energies,
107 pf_paramT *parameters);
108
109
124void putoutpU_prob(double **pU,
125 int length,
126 int ulength,
127 FILE *fp,
128 int energies);
129
130void putoutpU_prob_bin_par( double **pU,
131 int length,
132 int ulength,
133 FILE *fp,
134 int energies,
135 pf_paramT *parameters);
136
151void putoutpU_prob_bin(double **pU,
152 int length,
153 int ulength,
154 FILE *fp,
155 int energies);
156
162DEPRECATED(void init_pf_foldLP(int length));
163
164#endif
void init_pf_foldLP(int length)
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
void update_pf_paramsLP(int length)
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.
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, 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 data_structures.h:203
this datastructure is used as input parameter in functions of PS_dot.h and others
Definition data_structures.h:48