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

ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/

Bio.PDB.PSEA.run_psea(fname, verbose=False)

Run PSEA and return output filename.

Bio.PDB.PSEA.psea(pname)

Parse PSEA output file.

Bio.PDB.PSEA.psea2HEC(pseq)

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__(model, filename)

Initialize the class.

get_seq()

Return secondary structure string.