`DsspApp`#

class biotite.application_v2.dssp.DsspApp(path: PathLike[str] | str = 'mkdssp')[source]#

Bases: LocalApp

A handle to the DSSP software.

DSSP differentiates between 8 different types of secondary structure elements:

C: loop, coil or irregular

H: \({\alpha}\)-helix

B: \({\beta}\)-bridge

E: extended strand, participation in \({\beta}\)-ladder

G: 3 ₁₀-helix

I: \({\pi}\)-helix

T: hydrogen bonded turn

S: bend

Parameters:

pathstr, optional: Path of the DSSP binary.

Examples

>>> sse = DsspApp().run(atom_array).result()
>>> print(sse)
['C' 'H' 'H' 'H' 'H' 'H' 'H' 'H' 'T' 'T' 'G' 'G' 'G' 'G' 'T' 'C' 'P' 'P'
 'P' 'C']

run(atom_array: AtomArray) → CommandSetup[ndarray[tuple[K], dtype[str_]]]#

Assign the secondary structure of the given atom array.

Parameters:

atom_arrayAtomArray: The atom array to be annotated.

Returns:

futureFuture of ndarray, shape=(k,), dtype=”U1”: A handle to the running assignment. Call Future.result() to obtain the array of DSSP secondary structure symbols, one per residue in the input atom array.

DsspApp#

`DsspApp`#