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comparison corebio/resource/stride.py @ 4:4d47ab2b7bcc

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author davidmurphy
date Fri, 13 Jan 2012 07:18:19 -0500
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3:09d2dac9ef73 4:4d47ab2b7bcc
1
2 # Copyright (c) 2003 Gavin E. Crooks
3 # Copyright (c) 2005 David D. Ding <dding@berkeley.edu>
4 #
5 # This software is distributed under the MIT Open Source License.
6 # <http://www.opensource.org/licenses/mit-license.html>
7 #
8 # Permission is hereby granted, free of charge, to any person obtaining a
9 # copy of this software and associated documentation files (the "Software"),
10 # to deal in the Software without restriction, including without limitation
11 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
12 # and/or sell copies of the Software, and to permit persons to whom the
13 # Software is furnished to do so, subject to the following conditions:
14 #
15 # The above copyright notice and this permission notice shall be included
16 # in all copies or substantial portions of the Software.
17 #
18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
21 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
23 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
24 # THE SOFTWARE.
25
26 """STRIDE: Protein secondary structure assignment from atomic coordinates.
27
28 This module provides an interface to STRIDE, a c program used to recognize
29 secondary structural elements in proteins from their atomic coordinates.
30
31 """
32
33 from corebio.seq import Seq, protein_alphabet, Alphabet
34 from corebio.resource.astral import to_one_letter_code
35
36 # alphabet for stride secondary structure
37 stride_alphabet = Alphabet("HGIEBC12345678@&T")
38
39 # Dictionary for conversion between names and alphabet
40 stride_alphabet_names = (
41 "H", "AlphaHelix",
42 "G", "310Helix",
43 "I", "PiHelix",
44 "E", "Strand",
45 "b", "Bridge",
46 "B", "Bridge",
47 "C", "Coil",
48 "1", "TurnI",
49 "2", "TurnI'",
50 "3", "TurnII",
51 "4", "TurnII'",
52 "5", "TurnVIa",
53 "6", "TurnVIb",
54 "7", "TurnVIII",
55 "8", "TurnIV",
56 "@", "GammaClassic",
57 "&", "GammaInv",
58 "T", "Turn"
59 )
60
61
62 class Stride(object) :
63 def __init__(self, stride_file) :
64 """ Read and parse a STRIDE output file.
65
66 args:
67 - stride_file : An open file handle
68 attributes :
69 - pdbid : The PDB id.
70 - res : A list of Res objects, one per PDB resiude
71 """
72 res =[]
73 f=stride_file
74 self.pdbid = f.readline()[75:79]
75 for l in f:
76 if l[0:3] =="ASG":
77 res.append(Res(l))
78
79 self.res = res # A list of Res objects
80
81 self._res_dict = None
82
83 def total_area(self) :
84 """ Return the solvent accessible area """
85 area = 0
86 for i in self.res :
87 area += i.solvent_acc_area
88 return area
89
90 def primary(self):
91 """ Return the protein primary sequence as a Seq object."""
92 return Seq(''.join([r.primary_seq for r in self.res]), protein_alphabet)
93
94 def secondary(self):
95 """Return the secondary structure of the protien as a Seq object"""
96 return Seq(''.join([r.secondary_str for r in self.res]), stride_alphabet)
97
98
99 def get_res(self, chainid, resid) :
100 """ Return the given resiude """
101 if not self._res_dict :
102 d = {}
103 for r in self.res :
104 d[ (r.chainid, r.resid)] = r
105 self._res_dict =d
106
107 return self._res_dict[(chainid, resid)]
108
109
110
111 class Res(object):
112 """ Structural information of a single resiude. An ASG line from a stride
113 output file.
114
115 Attributes :
116 - chainid
117 - resid
118 - primary_seq
119 - secondary_str
120 - solvent_acc_area
121 - phi
122 - psi
123 """
124
125 def __init__(self, res_line) :
126 """ Eats a single 'ASG' line from a stride file, splits it up
127 into parts and return a Res object."""
128
129 if (len(res_line)<70):
130 raise ValueError("Line not long enough")
131 try:
132 self.chainid = res_line[9:10]
133 # STRIDE converts blank chain ids into dashes. Undo.
134 if self.chainid=="-" : self.chainid = " "
135
136 # In rare cases STRIDE columns can be misaligned. Grab extra
137 # white space to compensate.
138 self.resid = res_line[10:15].strip()
139 self.primary_seq = to_one_letter_code[res_line[5:8].capitalize()]
140 self.secondary_str = res_line[24:25]
141 self.solvent_acc_area = float(res_line[64:71])
142 self.phi = float(res_line[42:49].strip())
143 self.psi = float(res_line[52:59].strip())
144 except FloatingPointError:
145 raise FloatingPointError("Can't float phi, psi, or area")
146 except KeyError:
147 raise KeyError("Can't find three letter code in dictionary")
148 except LookupError:
149 raise LookupError("One of the values is out of index of res_line")
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