1 import string
2 import re
3 import fssp_rec
4 from Bio.Align import Generic
5 from Bio import Alphabet
6 fff_rec = fssp_rec.fff_rec
7 """
8 A module to handle FSSP files. For now it parses only the header, summary and alignment
9 sections.
10
11 functions: read_fssp(file_handle): reads an fssp file into the records. Returns a
12 tuple of two instances.
13 mult_align: returns a Biopyton alignment object
14 """
15 header_records = {
16 'database' : re.compile('^DATABASE'),
17 'pdbid': re.compile('^PDBID'),
18 'header': re.compile('^HEADER'),
19 'compnd': re.compile('^COMPND'),
20 'author': re.compile('^AUTHOR'),
21 'source': re.compile('^SOURCE'),
22 'seqlength': re.compile('^SEQLENGTH'),
23 'nalign': re.compile('^NALIGN')
24 }
25
26 summary_title = re.compile('## +SUMMARY')
27 summary_rec = re.compile(' *[0-9]+: +[1-9][0-9a-z]{3,3}')
28 alignments_title= re.compile('## +ALIGNMENTS')
29 alignments_rec = re.compile(' *[0-9]+ +-{0,1}[0-9]+')
30 equiv_title = re.compile('## +EQUIVALENCES')
31
34 self.database = None
35 self.pdbid = ''
36 self.header = ''
37 self.compnd = ''
38 self.source = ''
39 self.author = []
40 self.seqlength = 0
41 self.nalign = 0
43 for i in header_records.keys():
44 if header_records[i].match(inline):
45 if i == 'database' or i == 'seqlength' or i == 'nalign':
46 setattr(self,i,int(string.split(inline)[1]))
47 elif i == 'compnd' or i == 'author':
48 setattr(self,i,string.split(inline)[1:])
49 elif i == 'source' or i == 'header':
50 attr = inline[inline.find(' ')+1:].strip()
51 setattr(self,i,attr)
52 else:
53 setattr(self,i,string.split(inline)[1])
54
57 inStr = string.strip(inStr)
58 if len(inStr) <> 1 and len(inStr)<> 2:
59 raise ValueError, 'PosAlign: length not 2 chars' + inStr
60 if inStr == '..':
61 self.aa = '-'
62 self.gap = 1
63 else:
64 self.gap = 0
65 self.aa = inStr[0]
66 if self.aa == string.lower(self.aa):
67 self.aa = 'C'
68 if len(inStr) == 2:
69 self.ss = string.upper(inStr[1])
70 else:
71 self.ss = '0'
72
74 if self.gap:
75 outstring = '..'
76 else:
77 outstring = self.aa+string.lower(self.ss)
78 return outstring
79
80 __str__ = __repr__
81
82
83
84
86 """ Contains info from an FSSP summary record"""
88 self.raw = in_str
89 in_rec = string.split(string.strip(in_str))
90
91 self.nr = string.atoi(in_rec[0][:-1])
92 self.pdb1 = in_rec[1][:4]
93 if len(in_rec[1]) == 4:
94 self.chain1='0'
95 elif len(in_rec[1]) == 5:
96 self.chain1=in_rec[1][4]
97 else:
98 raise ValueError, 'Bad PDB ID 1'
99 self.pdb2 = in_rec[2][:4]
100 if len(in_rec[2]) == 4:
101 self.chain2='0'
102 elif len(in_rec[2]) == 5:
103 self.chain2=in_rec[2][4]
104 else:
105 raise ValueError, 'Bad PDB ID 2'
106 self.zscore = string.atof(in_rec[3])
107 self.rmsd = string.atof(in_rec[4])
108 self.lali = string.atof(in_rec[5])
109 self.lseq2 = string.atof(in_rec[6])
110 self.pID = string.atof(in_rec[7])
111 self.revers = string.atoi(in_rec[8])
112 self.permut = string.atoi(in_rec[9])
113 self.nfrag = string.atoi(in_rec[10])
114 self.topo = in_rec[11]
115 self.doc = ''
116 for i in in_rec[12:]:
117 self.doc = self.doc + i + ' '
118 self.doc = string.rstrip(self.doc) + '\n'
119
122 __str__ = __repr__
123
145 j = 1
146 for i in self.PosAlignList:
147 self.pos_align_dict[j] = i
148 j = j + 1
149
150
153
154
155
156 self.pdb_res_dict = {}
157 self.abs_res_dict = {}
158 self.data = {}
163
164
166 return self[self.abs_res_dict[num]]
167
168
170 return self[self.pdb_res_dict[num]]
171
172
174 s = ''
175 sorted_pos_nums = self.abs_res_dict.keys()
176 sorted_pos_nums.sort()
177 for i in sorted_pos_nums:
178 s += self.abs(i).pos_align_dict[num].aa
179 return s
180
182 mult_align_dict = {}
183 for j in self.abs(1).pos_align_dict.keys():
184 mult_align_dict[j] = ''
185 for fssp_rec in self.values():
186 for j in fssp_rec.pos_align_dict.keys():
187 mult_align_dict[j] += fssp_rec.pos_align_dict[j].aa
188 seq_order = mult_align_dict.keys()
189 seq_order.sort()
190 out_str = ''
191 for i in seq_order:
192 out_str += '> %d\n' % i
193 k = 0
194 for j in mult_align_dict[i]:
195 k += 1
196 if k % 72 == 0:
197 out_str += '\n'
198 out_str += j
199 out_str += '\n'
200 return out_str
201
204
205
206
207
208
264