to_protein_blocks

biotite.structure.alphabet.to_protein_blocks(atoms: AtomArray[N]) → tuple[list[ProteinBlocksSequence], ndarray[tuple[K], dtype[integer]]]

Encode each chain in the given structure to the Protein Blocks structural alphabet. [1]

Parameters:

atomsAtomArray

The atom array to encode. May contain multiple chains.

Returns:

sequenceslist of ProteinBlocksSequence, length=n

The encoded Protein Blocks sequence for each peptide chain in the structure.

chain_start_indicesndarray, shape=(n,), dtype=int

The atom index where each chain starts.

References

[1]

A. G. de Brevern, C. Etchebest, S. Hazout, “Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks,” Proteins: Structure, Function, and Bioinformatics, vol. 41, pp. 271–287, 2000. doi: 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z

Examples

>>> sequences, chain_starts = to_protein_blocks(atom_array)
>>> print(sequences[0])
zzmmmmmnopjmnopacdzz

Gallery

Multiple Structural alignment of orthologous proteins

Multiple Structural alignment of orthologous proteins