RNAlib-2.2.9

- Main Page
- Related Pages
- Modules
- Data Structures
- Files

- File List
- Globals

LPfold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2 #define VIENNA_RNA_PACKAGE_LPFOLD_H
3
4 #include <ViennaRNA/data_structures.h>
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
putoutpU_prob_bin
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.
pfl_fold
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.
data_structures.h
init_pf_foldLP
void init_pf_foldLP(int length)
params.h
vrna_exp_param_s
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
update_pf_paramsLP
void update_pf_paramsLP(int length)
putoutpU_prob
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
vrna_plist_s
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
pfl_fold_par
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.