Secondary structure annotation

Although biotite.structure offers the function annotate_sse() to assign secondary structure elements based on the P-SEA algorithm, DSSP can also be used via the biotite.application.dssp subpackage. Let us demonstrate this on the example of the good old miniprotein TC5b.

from tempfile import gettempdir
import biotite.database.rcsb as rcsb
import biotite.application.dssp as dssp
import biotite.structure.io.pdbx as pdbx

pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("1l2y", "bcif", gettempdir()))
atom_array = pdbx.get_structure(pdbx_file, model=1)
app = dssp.DsspApp(atom_array)
app.start()
app.join()
sse = app.get_sse()
print("".join(sse))

CHHHHHHHTTGGGGTCCCCC

Similar to the MSA examples, DsspApp has the convenience method DsspApp.annotate_sse() as shortcut.