Package Bio :: Package PDB :: Module PSEA
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Module PSEA

source code

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/

Classes [hide private]
  PSEA
Functions [hide private]
 
run_psea(fname)
Run PSEA and return output filename.
source code
 
psea(pname)
Parse PSEA output file.
source code
 
psea2HEC(pseq)
Translate PSEA secondary structure string into HEC.
source code
 
annotate(m, ss_seq)
Apply seconardary structure information to residues in model.
source code
Variables [hide private]
  __package__ = 'Bio.PDB'
Function Details [hide private]

run_psea(fname)

source code 
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.