RNAlib-2.2.0RC0
eval.h File Reference

Functions and variables related to energy evaluation of sequence/structure pairs. More...

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Functions

float vrna_eval_structure (const char *string, const char *structure, paramT *P)
 Calculate the free energy of an already folded RNA. More...
 
float vrna_eval_structure_verbose (const char *string, const char *structure, paramT *P, FILE *file)
 Calculate the free energy of an already folded RNA and print contributions per loop. More...
 
int vrna_eval_structure_pt (const char *string, const short *pt, paramT *P)
 Calculate the free energy of an already folded RNA. More...
 
int vrna_eval_structure_pt_verbose (const char *string, const short *pt, paramT *P, FILE *file)
 Calculate the free energy of an already folded RNA. More...
 
int vrna_eval_loop_pt (const short *pt, const short *s, const short *s1, int i, paramT *P)
 Calculate energy of a loop. More...
 
float vrna_eval_move (const char *string, const char *structure, int m1, int m2, paramT *P)
 Calculate energy of a move (closing or opening of a base pair) More...
 
int vrna_eval_move_pt (short *pt, const short *s, const short *s1, int m1, int m2, paramT *P)
 Calculate energy of a move (closing or opening of a base pair) More...
 
float energy_of_structure (const char *string, const char *structure, int verbosity_level)
 Calculate the free energy of an already folded RNA using global model detail settings. More...
 
float energy_of_struct_par (const char *string, const char *structure, paramT *parameters, int verbosity_level)
 Calculate the free energy of an already folded RNA. More...
 
float energy_of_circ_structure (const char *string, const char *structure, int verbosity_level)
 Calculate the free energy of an already folded circular RNA. More...
 
float energy_of_circ_struct_par (const char *string, const char *structure, paramT *parameters, int verbosity_level)
 Calculate the free energy of an already folded circular RNA. More...
 
int energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level)
 Calculate the free energy of an already folded RNA. More...
 
int energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level)
 Calculate the free energy of an already folded RNA. More...
 
float energy_of_move (const char *string, const char *structure, int m1, int m2)
 Calculate energy of a move (closing or opening of a base pair) More...
 
int energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2)
 Calculate energy of a move (closing or opening of a base pair) More...
 
int loop_energy (short *ptable, short *s, short *s1, int i)
 Calculate energy of a loop. More...
 
float energy_of_struct (const char *string, const char *structure)
 
int energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1)
 
float energy_of_circ_struct (const char *string, const char *structure)
 

Variables

int cut_point
 set to first pos of second seq for cofolding
 
int eos_debug
 verbose info from energy_of_struct
 

Detailed Description

Functions and variables related to energy evaluation of sequence/structure pairs.

Function Documentation

int vrna_eval_loop_pt ( const short *  pt,
const short *  s,
const short *  s1,
int  i,
paramT P 
)

Calculate energy of a loop.

Parameters
ptthe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
iposition of covering base pair
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
Returns
free energy of the loop in 10cal/mol
float energy_of_move ( const char *  string,
const char *  structure,
int  m1,
int  m2 
)

Calculate energy of a move (closing or opening of a base pair)

If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).

Deprecated:
Use vrna_eval_move() instead!
See also
vrna_eval_move()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
m1first coordinate of base pair
m2second coordinate of base pair
Returns
energy change of the move in kcal/mol
int energy_of_move_pt ( short *  pt,
short *  s,
short *  s1,
int  m1,
int  m2 
)

Calculate energy of a move (closing or opening of a base pair)

If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).

Deprecated:
Use vrna_eval_move_pt() instead!
See also
vrna_eval_move_pt()
Parameters
ptthe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
m1first coordinate of base pair
m2second coordinate of base pair
Returns
energy change of the move in 10cal/mol
int loop_energy ( short *  ptable,
short *  s,
short *  s1,
int  i 
)

Calculate energy of a loop.

Deprecated:
Use vrna_eval_loop_pt() instead!
See also
vrna_eval_loop_pt()
Parameters
ptablethe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
iposition of covering base pair
Returns
free energy of the loop in 10cal/mol
float energy_of_struct ( const char *  string,
const char *  structure 
)

Calculate the free energy of an already folded RNA

Note
This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
Deprecated:
This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!
See also
energy_of_structure, energy_of_circ_struct(), energy_of_struct_pt()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
Returns
the free energy of the input structure given the input sequence in kcal/mol
int energy_of_struct_pt ( const char *  string,
short *  ptable,
short *  s,
short *  s1 
)

Calculate the free energy of an already folded RNA

Note
This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
Deprecated:
This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!
See also
make_pair_table(), energy_of_structure()
Parameters
stringRNA sequence
ptablethe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
Returns
the free energy of the input structure given the input sequence in 10kcal/mol
float energy_of_circ_struct ( const char *  string,
const char *  structure 
)

Calculate the free energy of an already folded circular RNA

Note
This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
Deprecated:
This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!
See also
energy_of_circ_structure(), energy_of_struct(), energy_of_struct_pt()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
Returns
the free energy of the input structure given the input sequence in kcal/mol