biotite.structure.annotate_sse

biotite.structure.annotate_sse(atom_array, chain_id)[source]

Calculate the secondary structure elements (SSE) of a peptide chain based on the P-SEA algorithm. [1]

The annotation is based CA coordinates only, specifically distances and dihedral angles.

Parameters
atom_arrayAtomArray

The atom array to annotate for.

chain_idstr

The chain ID to annotate for.

Returns
ssendarray

An array containing the secondary structure elements, where the index corresponds to the index of the CA-filtered atom_array. ‘a’ means \({\alpha}\)-helix, ‘b’ means \({\beta}\)-strand/sheet, ‘c’ means coil.

Notes

Although this function is based on the original P-SEA algorithm, there are deviatons compared to the official P-SEA software in some cases. Do not rely on getting the exact same results.

References

1

G Labesse, N Colloch, J Pothier, JP Mornon “P-SEA: a new efficient assignment of secondary structure from CA trace of protein.” Comput Appl Biosci, 13, 291-295 (1997).

Examples

SSE of PDB 1L2Y:

>>> sse = annotate_sse(atom_array, "A")
>>> print(sse)
['c' 'a' 'a' 'a' 'a' 'a' 'a' 'a' 'a' 'c' 'c' 'c' 'c' 'c' 'c' 'c' 'c' 'c'
 'c' 'c']