RNAlib-2.4.18
pk_plex.h
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1 #ifndef VIENNA_RNA_PACKAGE_PK_PLEX_H
2 #define VIENNA_RNA_PACKAGE_PK_PLEX_H
3 
45 typedef int (vrna_callback_pk_plex_score)(const short *pt,
46  int start_5,
47  int end_5,
48  int start_3,
49  int end_3,
50  void *data);
51 
58 typedef struct vrna_pk_plex_option_s *vrna_pk_plex_opt_t;
59 
66 
68 
75  char *structure;
76  double energy;
77  double dGpk;
78  double dGint;
79  double dG1;
80  double dG2;
81  unsigned int start_5;
82  unsigned int end_5;
83  unsigned int start_3;
84  unsigned int end_3;
85 };
86 
118  const int **accessibility,
119  vrna_pk_plex_opt_t options);
120 
121 
132 int **
133 vrna_pk_plex_accessibility(const char *sequence,
134  unsigned int unpaired,
135  double cutoff);
136 
137 
147 
148 
160 vrna_pk_plex_opt(unsigned int delta,
161  unsigned int max_interaction_length,
162  int pk_penalty);
163 
164 
177 vrna_pk_plex_opt_fun(unsigned int delta,
178  unsigned int max_interaction_length,
179  vrna_callback_pk_plex_score *scoring_function,
180  void *scoring_data);
181 
182 
187 #endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
double energy
Net free energy in kcal/mol.
Definition: pk_plex.h:76
char * structure
Secondary Structure in dot-bracket notation.
Definition: pk_plex.h:75
unsigned int start_3
Start coordinate of the 3' interaction site.
Definition: pk_plex.h:83
double dG2
Opening energy for the 3' interaction site used in the heuristic.
Definition: pk_plex.h:80
unsigned int end_3
End coordinate of the 3' interaction site.
Definition: pk_plex.h:84
double dGint
Free energy of PK forming duplex interaction.
Definition: pk_plex.h:78
double dGpk
Free energy of PK loop in kcal/mol.
Definition: pk_plex.h:77
double dG1
Opening energy for the 5' interaction site used in the heuristic.
Definition: pk_plex.h:79
unsigned int end_5
End coordinate of the 5' interaction site.
Definition: pk_plex.h:82
unsigned int start_5
Start coordinate of the 5' interaction site.
Definition: pk_plex.h:81
vrna_pk_plex_t * vrna_pk_plex(vrna_fold_compound_t *fc, const int **accessibility, vrna_pk_plex_opt_t options)
Predict Pseudoknot interactions in terms of a two-step folding process.
vrna_pk_plex_opt_t vrna_pk_plex_opt_fun(unsigned int delta, unsigned int max_interaction_length, vrna_callback_pk_plex_score *scoring_function, void *scoring_data)
Simple options for PKplex algorithm.
int() vrna_callback_pk_plex_score(const short *pt, int start_5, int end_5, int start_3, int end_3, void *data)
Pseudoknot loop scoring function prototype.
Definition: pk_plex.h:45
vrna_pk_plex_opt_t vrna_pk_plex_opt(unsigned int delta, unsigned int max_interaction_length, int pk_penalty)
Simple options for PKplex algorithm.
vrna_pk_plex_opt_t vrna_pk_plex_opt_defaults(void)
Default options for PKplex algorithm.
struct vrna_pk_plex_option_s * vrna_pk_plex_opt_t
RNA PKplex options object.
Definition: pk_plex.h:58
int ** vrna_pk_plex_accessibility(const char *sequence, unsigned int unpaired, double cutoff)
Obtain a list of opening energies suitable for PKplex computations.
A result of the RNA PKplex interaction prediction.
Definition: pk_plex.h:74
int unpaired
contains the number of unpaired bases.