Bio.PDB.PSEA module

Wrappers for PSEA, a program for secondary structure assignment.

See this citation for P-SEA, PMID: 9183534

Labesse G, Colloc’h N, Pothier J, Mornon J-P: P-SEA: a new efficient assignment of secondary structure from C_alpha. Comput Appl Biosci 1997 , 13:291-295


Run PSEA and return output filename.

Note that this assumes the P-SEA binary is called “psea” and that it is on the path.

Note that P-SEA will write an output file in the current directory using the input filename with extension “.sea”.

Note that P-SEA will write output to the terminal while run.


Parse PSEA output file.


Translate PSEA secondary structure string into HEC.

Bio.PDB.PSEA.annotate(m, ss_seq)

Apply secondary structure information to residues in model.

class Bio.PDB.PSEA.PSEA(model, filename)

Bases: object

Define PSEA class.

PSEA object is a wrapper to PSEA program for secondary structure assignment.

__init__(self, model, filename)

Initialize the class.


Return secondary structure string.