Deprecated Interface for Local (Sliding Window) Partition Function Computation
Functions
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void update_pf_paramsLP(int length)
- #include <ViennaRNA/LPfold.h>
- Parameters:
length –
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void update_pf_paramsLP_par(int length, vrna_exp_param_t *parameters)
- #include <ViennaRNA/LPfold.h>
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vrna_ep_t *pfl_fold(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup)
- #include <ViennaRNA/LPfold.h>
Compute partition functions for locally stable secondary structures.
pfl_fold computes partition functions for every window of size ‘winSize’ possible in a RNA molecule, allowing only pairs with a span smaller than ‘pairSize’. It returns the mean pair probabilities averaged over all windows containing the pair in ‘pl’. ‘winSize’ should always be >= ‘pairSize’. Note that in contrast to Lfold(), bases outside of the window do not influence the structure at all. Only probabilities higher than ‘cutoffb’ are kept.
If ‘pU’ is supplied (i.e is not the NULL pointer), pfl_fold() will also compute the mean probability that regions of length ‘u’ and smaller are unpaired. The parameter ‘u’ is supplied in ‘pup[0][0]’. On return the ‘pup’ array will contain these probabilities, with the entry on ‘pup[x][y]’ containing the mean probability that x and the y-1 preceding bases are unpaired. The ‘pU’ array needs to be large enough to hold n+1 float* entries, where n is the sequence length.
If an array dpp2 is supplied, the probability of base pair (i,j) given that there already exists a base pair (i+1,j-1) is also computed and saved in this array. If pUfp is given (i.e. not NULL), pU is not saved but put out imediately. If spup is given (i.e. is not NULL), the pair probabilities in pl are not saved but put out imediately.
- Parameters:
sequence – RNA sequence
winSize – size of the window
pairSize – maximum size of base pair
cutoffb – cutoffb for base pairs
pU – array holding all unpaired probabilities
dpp2 – array of dependent pair probabilities
pUfp – file pointer for pU
spup – file pointer for pair probabilities
- Returns:
list of pair probabilities
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vrna_ep_t *pfl_fold_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters)
- #include <ViennaRNA/LPfold.h>
Compute partition functions for locally stable secondary structures.
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void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
- #include <ViennaRNA/LPfold.h>
Writes the unpaired probabilities (pU) or opening energies into a file.
Can write either the unpaired probabilities (accessibilities) pU or the opening energies -log(pU)kT into a file
- Parameters:
pU – pair probabilities
length – length of RNA sequence
ulength – maximum length of unpaired stretch
fp – file pointer of destination file
energies – switch to put out as opening energies
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void putoutpU_prob_bin(double **pU, int length, int ulength, FILE *fp, int energies)
- #include <ViennaRNA/LPfold.h>
Writes the unpaired probabilities (pU) or opening energies into a binary file.
Can write either the unpaired probabilities (accessibilities) pU or the opening energies -log(pU)kT into a file
- Parameters:
pU – pair probabilities
length – length of RNA sequence
ulength – maximum length of unpaired stretch
fp – file pointer of destination file
energies – switch to put out as opening energies
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void update_pf_paramsLP(int length)