# 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)
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)
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