RNAlib-2.4.4

Partition function for two RNA sequences. More...

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Functions

vrna_dimer_pf_t vrna_pf_co_fold (const char *seq, char *structure, vrna_ep_t **pl)
 Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More...
 
vrna_dimer_pf_t co_pf_fold (char *sequence, char *structure)
 Calculate partition function and base pair probabilities. More...
 
vrna_dimer_pf_t co_pf_fold_par (char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained)
 Calculate partition function and base pair probabilities. More...
 
vrna_ep_tget_plist (vrna_ep_t *pl, int length, double cut_off)
 
void compute_probabilities (double FAB, double FEA, double FEB, vrna_ep_t *prAB, vrna_ep_t *prA, vrna_ep_t *prB, int Alength)
 Compute Boltzmann probabilities of dimerization without homodimers. More...
 
void init_co_pf_fold (int length)
 
FLT_OR_DBLexport_co_bppm (void)
 Get a pointer to the base pair probability array. More...
 
void free_co_pf_arrays (void)
 Free the memory occupied by co_pf_fold() More...
 
void update_co_pf_params (int length)
 Recalculate energy parameters. More...
 
void update_co_pf_params_par (int length, vrna_exp_param_t *parameters)
 Recalculate energy parameters. More...
 

Variables

int mirnatog
 Toggles no intrabp in 2nd mol.
 
double F_monomer [2]
 Free energies of the two monomers.
 

Detailed Description

Partition function for two RNA sequences.

Function Documentation

◆ co_pf_fold()

vrna_dimer_pf_t co_pf_fold ( char *  sequence,
char *  structure 
)

Calculate partition function and base pair probabilities.

This is the cofold partition function folding. The second molecule starts at the cut_point nucleotide.

Note
OpenMP: Since this function relies on the global parameters do_backtrack, dangles, temperature and pf_scale it is not threadsafe according to concurrent changes in these variables! Use co_pf_fold_par() instead to circumvent this issue.
Deprecated:
{Use vrna_pf_dimer() instead!}
Parameters
sequenceConcatenated RNA sequences
structureWill hold the structure or constraints
Returns
vrna_dimer_pf_t structure containing a set of energies needed for concentration computations.

◆ co_pf_fold_par()

vrna_dimer_pf_t co_pf_fold_par ( char *  sequence,
char *  structure,
vrna_exp_param_t parameters,
int  calculate_bppm,
int  is_constrained 
)

Calculate partition function and base pair probabilities.

This is the cofold partition function folding. The second molecule starts at the cut_point nucleotide.

Deprecated:
Use vrna_pf_dimer() instead!
See also
get_boltzmann_factors(), co_pf_fold()
Parameters
sequenceConcatenated RNA sequences
structurePointer to the structure constraint
parametersData structure containing the precalculated Boltzmann factors
calculate_bppmSwitch to turn Base pair probability calculations on/off (0==off)
is_constrainedSwitch to indicate that a structure contraint is passed via the structure argument (0==off)
Returns
vrna_dimer_pf_t structure containing a set of energies needed for concentration computations.

◆ get_plist()

vrna_ep_t* get_plist ( vrna_ep_t pl,
int  length,
double  cut_off 
)

DO NOT USE THIS FUNCTION ANYMORE

Deprecated:
{ This function is deprecated and will be removed soon!} use assign_plist_from_pr() instead!

◆ compute_probabilities()

void compute_probabilities ( double  FAB,
double  FEA,
double  FEB,
vrna_ep_t prAB,
vrna_ep_t prA,
vrna_ep_t prB,
int  Alength 
)

Compute Boltzmann probabilities of dimerization without homodimers.

Given the pair probabilities and free energies (in the null model) for a dimer AB and the two constituent monomers A and B, compute the conditional pair probabilities given that a dimer AB actually forms. Null model pair probabilities are given as a list as produced by assign_plist_from_pr(), the dimer probabilities 'prAB' are modified in place.

Deprecated:
{ Use vrna_pf_dimer_probs() instead!}
Parameters
FABfree energy of dimer AB
FEAfree energy of monomer A
FEBfree energy of monomer B
prABpair probabilities for dimer
prApair probabilities monomer
prBpair probabilities monomer
AlengthLength of molecule A

◆ init_co_pf_fold()

void init_co_pf_fold ( int  length)

DO NOT USE THIS FUNCTION ANYMORE

Deprecated:
{ This function is deprecated and will be removed soon!}

◆ export_co_bppm()

FLT_OR_DBL* export_co_bppm ( void  )

Get a pointer to the base pair probability array.

Accessing the base pair probabilities for a pair (i,j) is achieved by

FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; 
Deprecated:
This function is deprecated and will be removed soon! The base pair probability array is available through the vrna_fold_compound_t data structure, and its associated vrna_mx_pf_t member.
See also
vrna_idx_row_wise()
Returns
A pointer to the base pair probability array

◆ free_co_pf_arrays()

void free_co_pf_arrays ( void  )

Free the memory occupied by co_pf_fold()

Deprecated:
This function will be removed for the new API soon! See vrna_pf_dimer(), vrna_fold_compound(), and vrna_fold_compound_free() for an alternative

◆ update_co_pf_params()

void update_co_pf_params ( int  length)

Recalculate energy parameters.

This function recalculates all energy parameters given the current model settings.

Deprecated:
Use vrna_exp_params_subst() instead!
Parameters
lengthLength of the current RNA sequence

◆ update_co_pf_params_par()

void update_co_pf_params_par ( int  length,
vrna_exp_param_t parameters 
)

Recalculate energy parameters.

This function recalculates all energy parameters given the current model settings. It's second argument can either be NULL or a data structure containing the precomputed Boltzmann factors. In the first scenario, the necessary data structure will be created automatically according to the current global model settings, i.e. this mode might not be threadsafe. However, if the provided data structure is not NULL, threadsafety for the model parameters dangles, pf_scale and temperature is regained, since their values are taken from this data structure during subsequent calculations.

Deprecated:
Use vrna_exp_params_subst() instead!
Parameters
lengthLength of the current RNA sequence
parametersdata structure containing the precomputed Boltzmann factors