1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
|
# Copyright (C) 2006, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# 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 os
from Bio.PDB.Polypeptide import is_aa
def 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.
"""
os.system("psea "+fname)
last=fname.split("/")[-1]
base=last.split(".")[0]
return base+".sea"
def psea(pname):
"""Parse PSEA output file."""
fname=run_psea(pname)
start=0
ss=""
with open(fname, 'r') as fp:
for l in fp.readlines():
if l[0:6]==">p-sea":
start=1
continue
if not start:
continue
if l[0]=="\n":
break
ss=ss+l[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 seconardary 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]
#os.system("rm "+fname)
class PSEA(object):
def __init__(self, model, filename):
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
if __name__=="__main__":
import sys
from Bio.PDB import PDBParser
# Parse PDB file
p=PDBParser()
s=p.get_structure('X', sys.argv[1])
# Annotate structure with PSEA sceondary structure info
PSEA(s[0], sys.argv[1])
|
