biotite.structure.base_pairs_glycosidic_bond

biotite.structure.base_pairs_glycosidic_bond(atom_array, base_pairs)[source]

Calculate the glycosidic bond orientation for given base pairs in an AtomArray according to the Leontis-Westhof nomenclature. 1

Parameters
atom_arrayAtomArray

The AtomArray containing the bases.

base_pairsndarray, dtype=int, shape=(n,2)

Each row is equivalent to one base pair and contains the first indices of the residues corresponding to each base. The structure of the ndarray is the same as the output of base_pairs().

Returns
resultsndarray, dtype=edge, shape=(n,)

The ndarray has the same dimensions as base_pairs. Each cell corresponds to the interacting edge of the referenced base in base_pairs. Each row is equivalent to the respective base pair. The glycosidic bond orientation is stored as integer that is interpreted as member of the the GlycosidicBond class.

See also

base_pairs
base_pairs_edge
GlycosidicBond

Notes

The orientation is found using the geometric centers of the bases and the glycosidic bonds as described in 2.

References

1

N. B. Leontis, E. Westhof, “Geometric nomenclature and classification of RNA base pairs.,” RNA, vol. 7, pp. 499–512, April 2001. doi: 10.1017/s1355838201002515

2

H. Yang, F. Jossinet, N. Leontis, L. Chen, J. Westbrook, H. Berman, E. Westhof, “Tools for the automatic identification and classification of RNA base pairs,” Nucleic Acids Research, vol. 31, pp. 3450–3460, July 2003. doi: 10.1093/nar/gkg529

Examples

Compute the glycosidic bond orientations for the dna helix with the PDB ID 1QXB:

>>> from os.path import join
>>> dna_helix = load_structure(
...     join(path_to_structures, "base_pairs", "1qxb.cif")
... )
>>> basepairs = base_pairs(dna_helix)
>>> orientations = base_pairs_glycosidic_bond(dna_helix, basepairs)
>>> print(orientations)
[1 1 1 1 1 1 1 1 1 1 1 1]

The resulting integers can be interpreted as GlycosidicBond Enum:

>>> for orientation in orientations:
...     print(GlycosidicBond(orientation))
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS
GlycosidicBond.CIS