# Command Files

The RNAlib and many programs of the ViennaRNA Package can parse and apply data from so-called command files. These commands may refer to structure constraints or even extensions of the RNA folding grammar (such as grammar:unstructured domains).

Commands are given as a line of whitespace delimited data fields. The syntax we use extends the constraint definitions used in the mfold or UNAfold software, where each line begins with a command character followed by a set of positions.

However, we introduce several new commands, and allow for an optional loop type context specifier in form of a sequence of characters, and an orientation flag that enables one to force a nucleotide to pair upstream, or downstream.

## Constraint commands

The following set of commands is recognized:

- `F` … Force

- `P` … Prohibit

- `C` … Conflicts/Context dependency

- `A` … Allow (for non-canonical pairs)

- `E` … Soft constraints for unpaired position(s), or base pair(s)

## RNA folding grammar exensions

- `UD` … Add ligand binding using the grammar:unstructured domains feature

## Specification of the loop type context

The optional loop type context specifier `[LOOP]` may be a combination of the following:

- `E` … Exterior loop

- `H` … Hairpin loop

- `I` … Internal/Interior loop

- `M` … Multibranch loop

- `A` … All loops

For structure constraints, we additionally allow one to address base pairs enclosed by a particular kind of loop, which results in the specifier `[WHERE]` which consists of `[LOOP]` plus the following character:

- `i` … enclosed pair of an Interior loop

- `m` … enclosed pair of a Multibranch loop

If no `[LOOP]` or `[WHERE]` flags are set, all contexts are considered (equivalent to `A` ).

## Controlling the orientation of base pairing

For particular nucleotides that are forced to pair, the following `[ORIENTATION]` flags may be used:

- `U` … Upstream

- `D` … Downstream

If no `[ORIENTATION]` flag is set, both directions are considered.

## Sequence coordinates

Sequence positions of nucleotides/base pairs are 1-based and consist of three positions \(i\), \(j\), and \(k\). Alternativly, four positions may be provided as a pair of two position ranges \([i:j]\), and \([k:l]\) using the `-` sign as delimiter within each range, i.e. `i-j`, and `k-l`.

## Valid constraint commands

Below are resulting general cases that are considered valid constraints:

- “Forcing a range of nucleotide positions to be paired”:

      F i 0 k [WHERE] [ORIENTATION]

  Description:

  Enforces the set of \(k\) consecutive nucleotides starting at position \(i\) to be paired. The optional loop type specifier `[WHERE]` allows to force them to appear as closing/enclosed pairs of certain types of loops.

- “Forcing a set of consecutive base pairs to form”::

      F i j k [WHERE]

  Description:

  Enforces the base pairs \((i,j), \ldots, (i+(k-1), j-(k-1))\) to form. The optional loop type specifier `[WHERE]` allows to specify in which loop context the base pair must appear.

- “Prohibiting a range of nucleotide positions to be paired”:

      P i 0 k [WHERE]

  Description:

  Prohibit a set of \(k\) consecutive nucleotides to participate in base pairing, i.e. make these positions unpaired. The optional loop type specifier `[WHERE]` allows to force the nucleotides to appear within the loop of specific types.

- “Probibiting a set of consecutive base pairs to form”:

      P i j k [WHERE]

  Description:

  Probibit the base pairs \((i,j), \ldots, (i+(k-1), j-(k-1))\) to form. The optional loop type specifier `[WHERE]` allows to specify the type of loop they are disallowed to be the closing or an enclosed pair of.

- “Prohibiting two ranges of nucleotides to pair with each other”:

      P i-j k-l [WHERE]

  Description:

  Prohibit any nucleotide \(p \in [i:j]\) to pair with any other nucleotide \(q \in [k:l]\). The optional loop type specifier `[WHERE]` allows to specify the type of loop they are disallowed to be the closing or an enclosed pair of.

- “Enforce a loop context for a range of nucleotide positions”:

      C i 0 k [WHERE]

  Description:

  This command enforces nucleotides to be unpaired similar to prohibiting nucleotides to be paired, as described above. It too marks the corresponding nucleotides to be unpaired, however, the `[WHERE]` flag can be used to enforce specfic loop types the nucleotides must appear in.

- “Remove pairs that conflict with a set of consecutive base pairs”:

      C i j k

  Description:

  Remove all base pairs that conflict with a set of consecutive base pairs \((i,j), \ldots, (i+(k-1), j-(k-1))\). Two base pairs \((i,j)\) and \((p,q)\) conflict with each other if \(i < p < j < q\), or \(p < i < q < j\).

- “Allow a set of consecutive (non-canonical) base pairs to form”:

      A i j k [WHERE]

  Description:

  This command enables the formation of the consecutive base pairs \((i,j), \ldots, (i+(k-1), j-(k-1))\), no matter if they are canonical, or non-canonical. In contrast to the above `F` and `W` commands, which remove conflicting base pairs, the `A` command does not. Therefore, it may be used to allow non-canoncial base pair interactions. Since the RNAlib does not contain free energy contributions \(E_{ij}\) for non-canonical base pairs \((i,j)\), they are scored as the maximum of similar, known contributions. In terms of a Nussinov like scoring function the free energy of non-canonical base pairs is therefore estimated as

  \[E_{ij} = \min \left[ \max_{(i,k) \in \{GC, CG, AU, UA, GU, UG\}} E_{ik}, \max_{(k,j) \in \{GC, CG, AU, UA, GU, UG\}} E_{kj} \right].\]

  The optional loop type specifier `[WHERE]` allows to specify in which loop context the base pair may appear.

- “Apply pseudo free energy to a range of unpaired nucleotide positions”:

      E i 0 k e

  Description:

  Use this command to apply a pseudo free energy of \(e\) to the set of \(k\) consecutive nucleotides, starting at position \(i\). The pseudo free energy is applied only if these nucleotides are considered unpaired in the recursions, or evaluations, and is expected to be given in units of \(\text{kcal} \cdot \text{mol}^{-1}\).

- “Apply pseudo free energy to a set of consecutive base pairs”:

      E i j k e

  Description:

  Use this command to apply a pseudo free energy of \(e\) to the set of base pairs \((i,j), \ldots, (i+(k-1), j-(k-1))\). Energies are expected to be given in units of \(\text{kcal} \cdot \text{mol}^{-1}\).

## Valid domain extensions commands

- “Add ligand binding to unpaired motif (a.k.a. unstructured domains)”:

      UD m e [LOOP]

  Description:

  Add ligand binding to unpaired sequence motif \(m\) (given in IUPAC format, capital letters) with binding energy \(e\) in particular loop type(s).

  Example:

      UD  AAA   -5.0    A

  The above example applies a binding free energy of \(-5\,\text{kcal} \cdot \text{mol}^{-1}\) for a motif `AAA` that may be present in all loop types.