CofoldedAlignment

class biotite.application_v2.viennarna.CofoldedAlignment(alignments: list[Alignment], dot_bracket: str, free_energy: float | None = None, covariance_energy: float | None = None, spans: list[tuple[int, int]] | None = None)

Bases: object

The predicted consensus secondary structure of a complex of multiple ribonucleic acid alignments.

Attributes:

alignmentslist of Alignment

The alignments the complex is composed of.

dot_bracketstr

The consensus secondary structure in dot-bracket notation with strands separated by &, indexed by alignment column.

free_energyfloat, optional

The free energy (kcal/mol) of the complex.

covariance_energyfloat, optional

The energy (kcal/mol) of the covariance term, if reported separately by the software.

spanslist of tuple (int, int), optional

If the dot_bracket describes only local parts of the alignments, the (start, stop) range (0-based, exclusive stop) of alignment columns each segment occupies. None means each segment spans all columns.

base_pairs() → ndarray[tuple[N, C4], dtype[integer]]

Get the consensus base pairs in alignment-column coordinates.

Returns:

base_pairsndarray, shape=(n,4), dtype=int

Each row is (strand_i, col_i, strand_j, col_j) with the columns referring to the respective alignment.

base_pairs_of(sequence_index: int) → ndarray[tuple[N, C4], dtype[integer]]

Get the consensus base pairs projected onto one sequence of each alignment.

The same sequence_index is applied to every alignment. Base pairs where either column is a gap in the selected sequence are omitted.

Parameters:

sequence_indexint

The index of the sequence, applied to every alignment.

Returns:

base_pairsndarray, shape=(n,4), dtype=int

Each row is (strand_i, pos_i, strand_j, pos_j) with the positions given in the ungapped numbering of the selected sequence of each alignment.

classmethod from_single(single: FoldedAlignment) → CofoldedAlignment

Create a CofoldedAlignment from a single-alignment FoldedAlignment.

Parameters:

singleFoldedAlignment

The single-alignment structure.

Returns:

cofoldedCofoldedAlignment

The equivalent complex containing a single alignment.