1
2
3
4
5
6 """Wrappers for PSEA, a program for secondary structure assignment.
7
8 See this citation for P-SEA, PMID: 9183534
9
10 Labesse G, Colloc'h N, Pothier J, Mornon J-P: P-SEA: a new efficient
11 assignment of secondary structure from C_alpha.
12 Comput Appl Biosci 1997 , 13:291-295
13
14 ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/
15 """
16
17 import os
18
19 from Bio.PDB.Polypeptide import is_aa
20
21
23 """Run PSEA and return output filename.
24
25 Note that this assumes the P-SEA binary is called "psea" and that it is
26 on the path.
27
28 Note that P-SEA will write an output file in the current directory using
29 the input filename with extension ".sea".
30
31 Note that P-SEA will write output to the terminal while run.
32 """
33 os.system("psea "+fname)
34 last=fname.split("/")[-1]
35 base=last.split(".")[0]
36 return base+".sea"
37
39 """Parse PSEA output file."""
40 fname=run_psea(pname)
41 start=0
42 ss=""
43 fp=open(fname, 'r')
44 for l in fp.readlines():
45 if l[0:6]==">p-sea":
46 start=1
47 continue
48 if not start:
49 continue
50 if l[0]=="\n":
51 break
52 ss=ss+l[0:-1]
53 fp.close()
54 return ss
55
57 """Translate PSEA secondary structure string into HEC."""
58 seq=[]
59 for ss in pseq:
60 if ss=="a":
61 n="H"
62 elif ss=="b":
63 n="E"
64 elif ss=="c":
65 n="C"
66 seq.append(n)
67 return seq
68
70 """Apply seconardary structure information to residues in model."""
71 c=m.get_list()[0]
72 all=c.get_list()
73 residues=[]
74
75 for res in all:
76 if is_aa(res):
77 residues.append(res)
78 L=len(residues)
79 if not (L==len(ss_seq)):
80 raise ValueError("Length mismatch %i %i" % (L, len(ss_seq)))
81 for i in range(0, L):
82 residues[i].xtra["SS_PSEA"]=ss_seq[i]
83
84
87 ss_seq=psea(filename)
88 ss_seq=psea2HEC(ss_seq)
89 annotate(model, ss_seq)
90 self.ss_seq=ss_seq
91
93 """
94 Return secondary structure string.
95 """
96 return self.ss_seq
97
98
99 if __name__=="__main__":
100
101 import sys
102 from Bio.PDB import PDBParser
103
104
105 p=PDBParser()
106 s=p.get_structure('X', sys.argv[1])
107
108
109 PSEA(s[0], sys.argv[1])
110