- biotite.structure.annotate_sse(atom_array, chain_id=None)[source]¶
Calculate the secondary structure elements (SSEs) of a peptide chain based on the P-SEA algorithm. 
The annotation is based CA coordinates only, specifically distances and dihedral angles. Discontinuities between chains are detected by residue ID.
The atom array to annotate for. Non-peptide residues are also allowed and obtain a
- chain_idstr, optional
The peptide atoms belonging to this chain are filtered and annotated. DEPRECATED: By now multiple chains can be annotated at once. To annotate only a certain chain, filter the atom_array before giving it as input to this function.
An array containing the secondary structure elements, where the index corresponds to a residue of atom_array (see e.g.
''indicates that a residue is not an amino acid or it comprises no
Although this function is based on the original P-SEA algorithm, there are deviations compared to the official P-SEA software in some cases. Do not rely on getting the exact same results.
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']
Four ways to get the secondary structure of a protein