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# Copyright (C) 2006, Thomas Hamelryck ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""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/
"""
import subprocess
import os
from Bio.PDB.Polypeptide import is_aa
def 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.
"""
last = fname.split("/")[-1]
base = last.split(".")[0]
cmd = ["psea", fname]
p = subprocess.run(cmd, capture_output=True, universal_newlines=True)
if verbose:
print(p.stdout)
if not p.stderr.strip() and os.path.exists(base + ".sea"):
return base + ".sea"
else:
raise RuntimeError(f"Error running p-sea: {p.stderr}")
def psea(pname):
"""Parse PSEA output file."""
fname = run_psea(pname)
start = 0
ss = ""
with open(fname) as fp:
for line in fp:
if line[0:6] == ">p-sea":
start = 1
continue
if not start:
continue
if line[0] == "\n":
break
ss = ss + line[0:-1]
return ss
def psea2HEC(pseq):
"""Translate PSEA secondary structure string into HEC."""
seq = []
for ss in pseq:
if ss == "a":
n = "H"
elif ss == "b":
n = "E"
elif ss == "c":
n = "C"
seq.append(n)
return seq
def annotate(m, ss_seq):
"""Apply secondary structure information to residues in model."""
c = m.get_list()[0]
all = c.get_list()
residues = []
# Now remove HOH etc.
for res in all:
if is_aa(res):
residues.append(res)
L = len(residues)
if not L == len(ss_seq):
raise ValueError("Length mismatch %i %i" % (L, len(ss_seq)))
for i in range(0, L):
residues[i].xtra["SS_PSEA"] = ss_seq[i]
# subprocess.call(["rm", fname])
class PSEA:
"""Define PSEA class.
PSEA object is a wrapper to PSEA program for secondary structure assignment.
"""
def __init__(self, model, filename):
"""Initialize the class."""
ss_seq = psea(filename)
ss_seq = psea2HEC(ss_seq)
annotate(model, ss_seq)
self.ss_seq = ss_seq
def get_seq(self):
"""Return secondary structure string."""
return self.ss_seq
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