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/
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Bio.PDB.PSEA.
run_psea
(fname)¶ 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.
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Bio.PDB.PSEA.
psea
(pname)¶ Parse PSEA output file.
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Bio.PDB.PSEA.
psea2HEC
(pseq)¶ Translate PSEA secondary structure string into HEC.
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Bio.PDB.PSEA.
annotate
(m, ss_seq)¶ Apply secondary structure information to residues in model.