RNAlib-2.2.0RC0
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This module contains all functions and variables related to energy evaluation of sequence/structure pairs. More...
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 | |
This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
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.
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
P | A data structure containing the prescaled energy contributions and the model details (may be NULL). |
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.
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
P | A data structure containing the prescaled energy contributions and the model details (may be NULL). |
file | A file handle where this function should print to (may be NULL). |
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.
string | RNA sequence in uppercase letters |
pt | Secondary structure as pair_table |
P | A data structure containing the prescaled energy contributions and the model details (may be NULL). |
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.
string | RNA sequence in uppercase letters |
pt | Secondary structure as pair_table |
P | A data structure containing the prescaled energy contributions and the model details (may be NULL). |
file | A file handle where this function should print to (may be NULL). |
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.
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
P | A data structure containing the prescaled energy contributions and the model details (may be NULL). |
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.
pt | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
P | A data structure containing the prescaled energy contributions and the model details (may be NULL). |
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
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
verbosity_level | a flag to turn verbose output on/off |
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
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
parameters | A data structure containing the prescaled energy contributions and the model details. |
verbosity_level | A flag to turn verbose output on/off |
float energy_of_circ_structure | ( | const char * | string, |
const char * | structure, | ||
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
string | RNA sequence |
structure | Secondary structure in dot-bracket notation |
verbosity_level | A flag to turn verbose output on/off |
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
string | RNA sequence |
structure | Secondary structure in dot-bracket notation |
parameters | A data structure containing the prescaled energy contributions and the model details. |
verbosity_level | A flag to turn verbose output on/off |
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
string | RNA sequence |
ptable | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
verbosity_level | a flag to turn verbose output on/off |
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
string | RNA sequence in uppercase letters |
ptable | The pair table of the secondary structure |
s | Encoded RNA sequence |
s1 | Encoded RNA sequence |
parameters | A data structure containing the prescaled energy contributions and the model details. |
verbosity_level | A flag to turn verbose output on/off |