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.
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 not write output to the terminal while run unless
verbose is set to True.
- 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.
- __firstlineno__ = 101
- __static_attributes__ = ('ss_seq',)