RNAlib-2.3.1
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Partition function for two RNA sequences. More...
Go to the source code of this file.
Data Structures | |
struct | vrna_dimer_pf_s |
Data structure returned by vrna_pf_dimer() More... | |
struct | vrna_dimer_conc_s |
Data structure for concentration dependency computations. More... | |
Typedefs | |
typedef struct vrna_dimer_pf_s | vrna_dimer_pf_t |
Typename for the data structure that stores the dimer partition functions, vrna_dimer_pf_s, as returned by vrna_pf_dimer() | |
typedef struct vrna_dimer_conc_s | vrna_dimer_conc_t |
Typename for the data structure that stores the dimer concentrations, vrna_dimer_conc_s, as required by vrna_pf_dimer_concentration() | |
typedef struct vrna_dimer_pf_s | cofoldF |
Backward compatibility typedef for vrna_dimer_pf_s. | |
typedef struct vrna_dimer_conc_s | ConcEnt |
Backward compatibility typedef for vrna_dimer_conc_s. | |
Functions | |
vrna_dimer_pf_t | vrna_pf_dimer (vrna_fold_compound_t *vc, char *structure) |
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More... | |
void | vrna_pf_dimer_probs (double FAB, double FA, double FB, vrna_plist_t *prAB, const vrna_plist_t *prA, const vrna_plist_t *prB, int Alength, const vrna_exp_param_t *exp_params) |
Compute Boltzmann probabilities of dimerization without homodimers. More... | |
vrna_dimer_conc_t * | vrna_pf_dimer_concentrations (double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params) |
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. 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_plist_t * | get_plist (vrna_plist_t *pl, int length, double cut_off) |
void | compute_probabilities (double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength) |
Compute Boltzmann probabilities of dimerization without homodimers. More... | |
vrna_dimer_conc_t * | get_concentrations (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc) |
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. More... | |
void | init_co_pf_fold (int length) |
FLT_OR_DBL * | export_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. | |
Partition function for two RNA sequences.
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.
sequence | Concatenated RNA sequences |
structure | Will hold the structure or constraints |
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.
sequence | Concatenated RNA sequences |
structure | Pointer to the structure constraint |
parameters | Data structure containing the precalculated Boltzmann factors |
calculate_bppm | Switch to turn Base pair probability calculations on/off (0==off) |
is_constrained | Switch to indicate that a structure contraint is passed via the structure argument (0==off) |
vrna_plist_t* get_plist | ( | vrna_plist_t * | pl, |
int | length, | ||
double | cut_off | ||
) |
DO NOT USE THIS FUNCTION ANYMORE
void compute_probabilities | ( | double | FAB, |
double | FEA, | ||
double | FEB, | ||
vrna_plist_t * | prAB, | ||
vrna_plist_t * | prA, | ||
vrna_plist_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.
FAB | free energy of dimer AB |
FEA | free energy of monomer A |
FEB | free energy of monomer B |
prAB | pair probabilities for dimer |
prA | pair probabilities monomer |
prB | pair probabilities monomer |
Alength | Length of molecule A |
vrna_dimer_conc_t* get_concentrations | ( | double | FEAB, |
double | FEAA, | ||
double | FEBB, | ||
double | FEA, | ||
double | FEB, | ||
double * | startconc | ||
) |
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers.
This function takes an array 'startconc' of input concentrations with alternating entries for the initial concentrations of molecules A and B (terminated by two zeroes), then computes the resulting equilibrium concentrations from the free energies for the dimers. Dimer free energies should be the dimer-only free energies, i.e. the FcAB entries from the vrna_dimer_pf_t struct.
FEAB | Free energy of AB dimer (FcAB entry) |
FEAA | Free energy of AA dimer (FcAB entry) |
FEBB | Free energy of BB dimer (FcAB entry) |
FEA | Free energy of monomer A |
FEB | Free energy of monomer B |
startconc | List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0] |
void init_co_pf_fold | ( | int | length | ) |
DO NOT USE THIS FUNCTION ANYMORE
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];
void free_co_pf_arrays | ( | void | ) |
Free the memory occupied by co_pf_fold()
void update_co_pf_params | ( | int | length | ) |
Recalculate energy parameters.
This function recalculates all energy parameters given the current model settings.
length | Length of the current RNA sequence |
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.
length | Length of the current RNA sequence |
parameters | data structure containing the precomputed Boltzmann factors |