H/LPfold.h File Reference

Function declarations of partition function variants of the Lfold algorithm. More...

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Functions

void update_pf_paramsLP (int length)
plistpfl_fold (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup)
 Compute partition functions for locally stable secondary structures (berni! update me)
void putoutpU_prob (double **pU, int length, int ulength, FILE *fp, int energies)
 Writes the unpaired probabilities (pU) or opening energies into a file.
void putoutpU_prob_bin (double **pU, int length, int ulength, FILE *fp, int energies)
 Writes the unpaired probabilities (pU) or opening energies into a binary file.
void init_pf_foldLP (int length)
 Dunno if this function was ever used by external programs linking to RNAlib, but it was declared PUBLIC before.

Detailed Description

Function declarations of partition function variants of the Lfold algorithm.


Function Documentation

void update_pf_paramsLP ( int  length  ) 
Parameters:
length 
plist* pfl_fold ( char *  sequence,
int  winSize,
int  pairSize,
float  cutoffb,
double **  pU,
struct plist **  dpp2,
FILE *  pUfp,
FILE *  spup 
)

Compute partition functions for locally stable secondary structures (berni! update me)

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
Parameters:
winSize size of the window
Parameters:
pairSize maximum size of base pair
Parameters:
cutoffb cutoffb for base pairs
Parameters:
pU array holding all unpaired probabilities
Parameters:
dpp2 array of dependent pair probabilities
Parameters:
pUfp file pointer for pU
Parameters:
spup file pointer for pair probabilities
Returns:
list of pair probabilities
void putoutpU_prob ( double **  pU,
int  length,
int  ulength,
FILE *  fp,
int  energies 
)

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
Parameters:
length length of RNA sequence
Parameters:
ulength maximum length of unpaired stretch
Parameters:
fp file pointer of destination file
Parameters:
energies switch to put out as opening energies
void putoutpU_prob_bin ( double **  pU,
int  length,
int  ulength,
FILE *  fp,
int  energies 
)

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
Parameters:
length length of RNA sequence
Parameters:
ulength maximum length of unpaired stretch
Parameters:
fp file pointer of destination file
Parameters:
energies switch to put out as opening energies
void init_pf_foldLP ( int  length  ) 

Dunno if this function was ever used by external programs linking to RNAlib, but it was declared PUBLIC before.

Anyway, never use this function as it will be removed soon and does nothing at all

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