# 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',)

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