// global variables double cv_fact double nc_fact // global functions float energy_of_alistruct ( const char** sequences, const char* structure, int n_seq, float* energy ) int get_alipf_arrays ( short*** S_p, short*** S5_p, short*** S3_p, unsigned short*** a2s_p, char*** Ss_p, FLT_OR_DBL** qb_p, FLT_OR_DBL** qm_p, FLT_OR_DBL** q1k_p, FLT_OR_DBL** qln_p, short** pscore ) void update_alifold_params (void) float** get_ribosum ( const char** Alseq, int n_seq, int length )
double cv_fact
Deprecated See vrna_md_t.cv_fact , and vrna_mfe() to avoid using global variables
Default is 1.
double nc_fact
Deprecated See vrna_md_t.nc_fact , and vrna_mfe() to avoid using global variables
Default is 1.
float energy_of_alistruct ( const char** sequences, const char* structure, int n_seq, float* energy )
Deprecated Usage of this function is discouraged! Use vrna_eval_structure() , and vrna_eval_covar_structure() instead!
Parameters:
sequences | The NULL terminated array of sequences |
structure | The consensus structure |
n_seq | The number of sequences in the alignment |
energy | A pointer to an array of at least two floats that will hold the free energies (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term) |
Returns:
free energy in kcal/mol
int get_alipf_arrays ( short*** S_p, short*** S5_p, short*** S3_p, unsigned short*** a2s_p, char*** Ss_p, FLT_OR_DBL** qb_p, FLT_OR_DBL** qm_p, FLT_OR_DBL** q1k_p, FLT_OR_DBL** qln_p, short** pscore )
Deprecated It is discouraged to use this function! The new vrna_fold_compound_t allows direct access to all necessary consensus structure prediction related variables!
Parameters:
S_p | A pointer to the ‘S’ array (integer representation of nucleotides) |
S5_p | A pointer to the ‘S5’ array |
S3_p | A pointer to the ‘S3’ array |
a2s_p | A pointer to the alignment-column to sequence position mapping array |
Ss_p | A pointer to the ‘Ss’ array |
qb_p | A pointer to the Q B matrix |
qm_p | A pointer to the Q M matrix |
q1k_p | A pointer to the 5’ slice of the Q matrix ( \(q1k(k) = Q(1, k)\) ) |
qln_p | A pointer to the 3’ slice of the Q matrix ( \(qln(l) = Q(l, n)\) ) |
pscore | A pointer to the start of a pscore list |
Returns:
Non Zero if everything went fine, 0 otherwise
Note
To obtain meaningful pointers, call alipf_fold first!
See also:
pf_alifold(), alipf_circ_fold()
vrna_fold_compound_t , vrna_fold_compound_comparative() , vrna_pf()
void update_alifold_params (void)
Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like temperature
Deprecated Usage of this function is discouraged! The new API uses vrna_fold_compound_t to lump all folding related necessities together, including the energy parameters. Use vrna_update_fold_params() to update the energy parameters within a vrna_fold_compound_t .
float** get_ribosum ( const char** Alseq, int n_seq, int length )