RNAlib-2.2.0RC0

This module contains all functions and variables related to energy evaluation of sequence/structure pairs. More...

+ Collaboration diagram for Energy evaluation:

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...
 
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...
 

Variables

int eos_debug
 verbose info from energy_of_struct
 

Detailed Description

This module contains all functions and variables related to energy evaluation of sequence/structure pairs.

Function Documentation

float vrna_eval_structure ( const char *  string,
const char *  structure,
paramT P 
)

Calculate the free energy of an already folded RNA.

This function allows for energy evaluation of a given sequence/structure pair. If the optional parameter 'P' is not NULL, the scoring model as determined by 'P' will be used for energy evaluation. Otherwise, default parameters are used.

See also
vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(), vrna_get_energy_contributions()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
Returns
The free energy of the input structure given the input sequence in kcal/mol
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.

This function allows for detailed energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout. If the optional parameter 'P' is not NULL, the scoring model as determined by 'P' will be used for energy evaluation. Otherwise, default parameters are used.

See also
vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(), vrna_get_energy_contributions()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the input structure given the input sequence in kcal/mol
int vrna_eval_structure_pt ( const char *  string,
const short *  pt,
paramT P 
)

Calculate the free energy of an already folded RNA.

This function allows for energy evaluation of a given sequence/structure pair. If the optional parameter 'P' is not NULL, the scoring model as determined by 'P' will be used for energy evaluation. Otherwise, default parameters are used.

See also
vrna_pt_get(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(), vrna_get_energy_contributions()
Parameters
stringRNA sequence in uppercase letters
ptSecondary structure as pair_table
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
Returns
The free energy of the input structure given the input sequence in 10cal/mol
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.

This function allows for energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout. If the optional parameter 'P' is not NULL, the scoring model as determined by 'P' will be used for energy evaluation. Otherwise, default parameters are used.

See also
vrna_pt_get(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(), vrna_get_energy_contributions()
Parameters
stringRNA sequence in uppercase letters
ptSecondary structure as pair_table
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the input structure given the input sequence in 10cal/mol
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)

If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening). If the optional parameter 'P' is not NULL, the scoring model as determined by 'P' will be used for energy evaluation. Otherwise, default parameters are used.

See also
vrna_eval_move_pt(), vrna_get_energy_contributions()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
m1first coordinate of base pair
m2second coordinate of base pair
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
Returns
energy change of the move in kcal/mol
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)

If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening). If the optional parameter 'P' is not NULL, the scoring model as determined by 'P' will be used for energy evaluation. Otherwise, default parameters are used.

See also
vrna_eval_move(), vrna_get_energy_contributions()
Parameters
ptthe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
m1first coordinate of base pair
m2second coordinate of base pair
PA data structure containing the prescaled energy contributions and the model details (may be NULL).
Returns
energy change of the move in 10cal/mol
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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe implementation.
Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
verbosity_levela flag to turn verbose output on/off
Returns
the free energy of the input structure given the input sequence in kcal/mol
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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
parametersA data structure containing the prescaled energy contributions and the model details.
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in kcal/mol
float energy_of_circ_structure ( const char *  string,
const char *  structure,
int  verbosity_level 
)

Calculate the free energy of an already folded circular RNA.

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe implementation.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence
structureSecondary structure in dot-bracket notation
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in kcal/mol
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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence
structureSecondary structure in dot-bracket notation
parametersA data structure containing the prescaled energy contributions and the model details.
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in kcal/mol
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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe implementation.
Deprecated:
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
See also
vrna_eval_structure_pt()
Parameters
stringRNA sequence
ptablethe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
verbosity_levela flag to turn verbose output on/off
Returns
the free energy of the input structure given the input sequence in 10kcal/mol
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.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Deprecated:
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
See also
vrna_eval_structure_pt()
Parameters
stringRNA sequence in uppercase letters
ptableThe pair table of the secondary structure
sEncoded RNA sequence
s1Encoded RNA sequence
parametersA data structure containing the prescaled energy contributions and the model details.
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in 10kcal/mol