# H/loop_energies.h File Reference

Energy evaluation for MFE and partition function calculations. More...

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## Functions
PRIVATE int | E_IntLoop (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, paramT *P)
PRIVATE int | E_Hairpin (int size, int type, int si1, int sj1, const char *string, paramT *P)
PRIVATE int | E_Stem (int type, int si1, int sj1, int extLoop, paramT *P)
PRIVATE double | exp_E_Stem (int type, int si1, int sj1, int extLoop, pf_paramT *P)
PRIVATE double | exp_E_Hairpin (int u, int type, short si1, short sj1, const char *string, pf_paramT *P)
PRIVATE double | exp_E_IntLoop (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, pf_paramT *P)

## Detailed Description

Energy evaluation for MFE and partition function calculations.

This file contains functions for the calculation of the free energy of a hairpin- [ E_Hairpin() ] or interior-loop [ E_IntLoop()] .
The unit of the free energy returned is

In case of computing the partition function, this file also supplies functions which return the Boltzmann weights for a hairpin- [ exp_E_Hairpin() ] or interior-loop [ exp_E_IntLoop() ].

## Function Documentation

PRIVATE int E_IntLoop | ( | int | n1,
|  | int | n2,
|  | int | type,
|  | int | type_2,
|  | int | si1,
|  | int | sj1,
|  | int | sp1,
|  | int | sq1,
|  | paramT * | P |
| ) |  |  |

## Compute the Energy of an interior-loop

This function computes the free energy of an interior-loop with the following structure:

            3'  5'
            |   |
            U - V
        a_n       b_1
         .        .
         .        .
         .        .
        a_1       b_m
            X - Y
            |   |
            5'  3'

This general structure depicts an interior-loop that is closed by the base pair (X,Y). The enclosed base pair is (V,U) which leaves the unpaired bases a_1-a_n and b_1-b_n that constitute the loop. In this example, the length of the interior-loop is where n or m may be 0 resulting in a bulge-loop or base pair stack. The mismatching nucleotides for the closing pair (X,Y) are:
5'-mismatch: a_1
3'-mismatch: b_m
and for the enclosed base pair (V,U):
5'-mismatch: b_1
3'-mismatch: a_n

Note:
  Base pairs are always denoted in 5'->3' direction. Thus the enclosed base pair must be 'turned arround' when evaluating the free energy of the interior-loop

See also:
  scale_parameters()
  paramT

Note:
  This function is threadsafe

Parameters:

    | n1 | The size of the 'left'-loop (number of unpaired nucleotides) Parameters:
      | n2 | The size of the 'right'-loop (number of unpaired nucleotides) Parameters:
        | type | The pair type of the base pair closing the interior loop Parameters:
          | type_2 | The pair type of the enclosed base pair Parameters:
            | si1 | The 5'-mismatching nucleotide of the closing pair Parameters:
              | sj1 | The 3'-mismatching nucleotide of the closing pair Parameters:
                | sp1 | The 3'-mismatching nucleotide of the enclosed pair Parameters:
                  | sq1 | The 5'-mismatching nucleotide of the enclosed pair Parameters:
                  | P | The datastructure containing scaled energy parameters Returns: The Free energy of the Interior-loop in dcal/mol

PRIVATE int E_Hairpin | ( | int | size,
|  | int | type,
|  | int | si1,
|  | int | sj1,
|  | const char * | string,
|  | paramT * | P |
| ) |  |  |

## Compute the Energy of a hairpin-loop

To evaluate the free energy of a hairpin-loop, several parameters have to be known. A general hairpin-loop has this structure:

            a3 a4
          a2     a5
          a1     a6
            X - Y
            |   |
            5'  3'

where X-Y marks the closing pair [e.g. a (G,C) pair]. The length of this loop is 6 as there are six unpaired nucleotides (a1-a6) enclosed by (X,Y). The 5' mismatching nucleotide is a1 while the 3' mismatch is a6. The nucleotide sequence of this loop is "a1.a2.a3.a4.a5.a6"

Note:
  The parameter sequence should contain the sequence of the loop in capital letters of the nucleic acid alphabet if the loop size is below 7. This is useful for unusually stable tri-, tetra- and hexa-loops which are treated differently (based on experimental data) if they are tabulated.

See also:
  scale_parameters()
  paramT

Warning:
  Not (really) thread safe! A threadsafe implementation will replace this function in a future release!
  Energy evaluation may change due to updates in global variable "tetra_loop"

Parameters:

    | size | The size of the loop (number of unpaired nucleotides) Parameters:
      | type | The pair type of the base pair closing the hairpin Parameters:
        | si1 | The 5'-mismatching nucleotide Parameters:
          | sj1 | The 3'-mismatching nucleotide Parameters:
            | string | The sequence of the loop Parameters:
            | P | The datastructure containing scaled energy parameters Returns: The Free energy of the Hairpin-loop in dcal/mol

PRIVATE int E_Stem | ( | int | type,
|  | int | si1,
|  | int | sj1,
|  | int | extLoop,
|  | paramT * | P |
| ) |  |  |

## Compute the energy contribution of a stem branching off a loop-region

This function computes the energy contribution of a stem that branches off a loop region. This can be the case in multiloops, when a stem branching off increases the degree of the loop but also immediately interior base pairs of an exterior loop contribute free energy. To switch the bahavior of the function according to the evaluation of a multiloop- or exterior-loop-stem, you pass the flag 'extLoop'. The returned energy contribution consists of a TerminalAU penalty if the pair type is greater than 2, dangling end contributions of mismatching nucleotides adjacent to the stem if only one of the si1, sj1 parameters is greater than 0 and mismatch energies if both mismatching nucleotides are positive values. Thus, to avoid incooperating dangling end or mismatch energies just pass a negative number, e.g. -1 to the mismatch argument.

This is an illustration of how the energy contribution is assembled:

            3'  5'
            |   |
            X - Y
      5'-si1     sj1-3'

Here, (X,Y) is the base pair that closes the stem that branches off a loop region. The nucleotides si1 and sj1 are the 5'- and 3'- mismatches, respectively. If the base pair type of (X,Y) is greater than 2 (i.e. an A-U or G-U pair, the TerminalAU penalty will be included in the energy contribution returned. If si1 and sj1 are both nonnegative numbers, mismatch energies will also be included. If one of sij or sj1 is a negtive value, only 5' or 3' dangling end contributions are taken into account. To prohibit any of these mismatch contributions to be incoorporated, just pass a negative number to both, si1 and sj1. In case the argument extLoop is 0, the returned energy contribution also includes the internal-loop-penalty of a multiloop stem with closing pair type.

See also:
  E_MLstem()
  E_ExtLoop()

Note:
  This function is threadsafe

Parameters:

    | type | The pair type of the first base pair un the stem Parameters:
      | si1 | The 5'-mismatching nucleotide Parameters:
        | sj1 | The 3'-mismatching nucleotide Parameters:
          | extLoop | A flag that indicates whether the contribution reflects the one of an exterior loop or not Parameters:
          | P | The datastructure containing scaled energy parameters Returns: The Free energy of the branch off the loop in dcal/mol

PRIVATE double exp_E_Stem | ( | int | type,
|  | int | si1,
|  | int | sj1,
|  | int | extLoop,
|  | pf_paramT * | P |
| ) |  |  |

## Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region

This is the partition function variant of E_Stem()

See also:
  E_Stem()

Note:
  This function is threadsafe

Returns:
  The Boltzmann weighted energy contribution of the branch off the loop

PRIVATE double exp_E_Hairpin | ( | int | u,
|  | int | type,
|  | short | si1,
|  | short | sj1,
|  | const char * | string,
|  | pf_paramT * | P |
| ) |  |  |

## Compute Boltzmann weight of a hairpin loop

multiply by scale[u+2]

See also:
  get_scaled_pf_parameters()
  pf_paramT
  E_Hairpin()

Warning:
  Not (really) thread safe! A threadsafe implementation will replace this function in a future release!
  Energy evaluation may change due to updates in global variable "tetra_loop"

Parameters:

    | u | The size of the loop (number of unpaired nucleotides) Parameters:
      | type | The pair type of the base pair closing the hairpin Parameters:
        | si1 | The 5'-mismatching nucleotide Parameters:
          | sj1 | The 3'-mismatching nucleotide Parameters:
            | string | The sequence of the loop Parameters:
            | P | The datastructure containing scaled Boltzmann weights of the energy parameters Returns: The Boltzmann weight of the Hairpin-loop

PRIVATE double exp_E_IntLoop | ( | int | u1,
|  | int | u2,
|  | int | type,
|  | int | type2,
|  | short | si1,
|  | short | sj1,
|  | short | sp1,
|  | short | sq1,
|  | pf_paramT * | P |
| ) |  |  |

## Compute Boltzmann weight of interior loop

multiply by scale[u1+u2+2] for scaling

See also:
  get_scaled_pf_parameters()
  pf_paramT
  E_IntLoop()

Note:
  This function is threadsafe

Parameters:

    | u1 | The size of the 'left'-loop (number of unpaired nucleotides) Parameters:
      | u2 | The size of the 'right'-loop (number of unpaired nucleotides) Parameters:
        | type | The pair type of the base pair closing the interior loop Parameters:
          | type2 | The pair type of the enclosed base pair Parameters:
            | si1 | The 5'-mismatching nucleotide of the closing pair Parameters:
              | sj1 | The 3'-mismatching nucleotide of the closing pair Parameters:
                | sp1 | The 3'-mismatching nucleotide of the enclosed pair Parameters:
                  | sq1 | The 5'-mismatching nucleotide of the enclosed pair Parameters:
                  | P | The datastructure containing scaled Boltzmann weights of the energy parameters Returns: The Boltzmann weight of the Interior-loop