nucleotide_dihedral_backbone

biotite.structure.nucleotide_dihedral_backbone(atom_array: AtomArray[N] | AtomArrayStack[M, N]) → tuple[ndarray[tuple[N], dtype[floating]] | ndarray[tuple[M, N], dtype[floating]], ndarray[tuple[N], dtype[floating]] | ndarray[tuple[M, N], dtype[floating]], ndarray[tuple[N], dtype[floating]] | ndarray[tuple[M, N], dtype[floating]], ndarray[tuple[N], dtype[floating]] | ndarray[tuple[M, N], dtype[floating]], ndarray[tuple[N], dtype[floating]] | ndarray[tuple[M, N], dtype[floating]], ndarray[tuple[N], dtype[floating]] | ndarray[tuple[M, N], dtype[floating]]]

Measure the six characteristic backbone dihedral angles of a nucleotide chain.

Parameters:

atom_arrayAtomArray or AtomArrayStack

The nucleic acid structure to measure the dihedral angles for. For missing backbone atoms the corresponding angles are NaN.

Returns:

alpha, beta, gamma, delta, epsilon, zetandarray, shape=(m,n) or shape=(n,), dtype=float

An array containing the six backbone dihedral angles for every nucleotide residue. \(\alpha\) is not defined at the 5’-terminus, \(\epsilon\) and \(\zeta\) are not defined at the 3’-terminus. In these places the arrays have NaN values. If an AtomArrayStack is given, the output angles are 2-dimensional, the first dimension corresponds to the model number.

Notes

The nucleotide backbone dihedral angles are defined as follows (indices refer to the residue position along the chain):

• \(\alpha\): O3’(i-1) - P(i) - O5’(i) - C5’(i)

• \(\beta\): P(i) - O5’(i) - C5’(i) - C4’(i)

• \(\gamma\): O5’(i) - C5’(i) - C4’(i) - C3’(i)

• \(\delta\): C5’(i) - C4’(i) - C3’(i) - O3’(i)

• \(\epsilon\): C4’(i) - C3’(i) - O3’(i) - P(i+1)

• \(\zeta\): C3’(i) - O3’(i) - P(i+1) - O5’(i+1)