# H/subopt.h File Reference

RNAsubopt and density of states declarations. More...

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## Functions

SOLUTION * | subopt (char *seq, char *sequence, int delta, FILE *fp)
| Returns list of subopt structures or writes to fp.
SOLUTION * | subopt_circ (char *seq, char *sequence, int delta, FILE *fp)
| Returns list of circular subopt structures or writes to fp.

## Variables

int | subopt_sorted
| Sort output by energy.
double | print_energy
| printing threshold for use with logML

## Detailed Description

RNAsubopt and density of states declarations.

## Function Documentation

SOLUTION* subopt | ( | char * | seq,
|  | char * | sequence,
|  | int | delta,
|  | FILE * | fp |
| ) |  |  |

Returns list of subopt structures or writes to fp.

This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a SOLUTION * list terminated by an entry were the 'structure' pointer is NULL.

Parameters:

  seq

  Parameters:

    sequence

    Parameters:

      delta

      Parameters:

        fp

        Returns:

SOLUTION* subopt_circ | ( | char * | seq,
|  | char * | sequence,
|  | int | delta,
|  | FILE * | fp |
| ) |  |  |

Returns list of circular subopt structures or writes to fp.

This function is similar to subopt() but calculates secondary structures assuming the RNA sequence to be circular instead of linear

Parameters:

  seq

  Parameters:

    sequence

    Parameters:

      delta

      Parameters:

        fp

        Returns: