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
|
# Copyright 2018 by Francesco Gastaldello. All rights reserved.
#
# Converted by Francesco Gastaldello from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# 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.
"""Unit tests for the Bio.PDB.ResidueDepth module."""
import unittest
import warnings
from Bio.PDB import PDBParser, ResidueDepth
from Bio import MissingExternalDependencyError
from Bio.PDB.PDBExceptions import PDBConstructionWarning
msms_exe = None
from Bio._py3k import getoutput
try:
output = getoutput("msms -h")
if output.startswith("Usage : msms parameters"):
msms_exe = "msms"
except OSError:
pass
if not msms_exe:
raise MissingExternalDependencyError(
"Install MSMS if you want to use it in Biopython.")
class ResidueDepthTests(unittest.TestCase):
"""Test ResidueDepth module."""
def check_msms(self, prot_file, first_100_residues):
p = PDBParser()
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
s = p.get_structure("X", prot_file)
model = s[0]
rd = ResidueDepth(model)
res_chain = ''
for item in rd.property_list[:100]:
res_chain = res_chain + item[0].get_resname()
self.assertEqual(res_chain, first_100_residues)
def test_ResidueDepth_2XHE(self):
self.check_msms('PDB/2XHE.pdb', 'HISMETSERLEULYSSERALAVALLYSTHRVALLEUTH'
'RASNSERLEUARGSERVALALAASPGLYGLYASPTRPL'
'YSVALLEUVALVALASPLYSPROALALEUARGMETILE'
'SERGLUCYSALAARGMETSERGLUILELEUASPLEUGL'
'YVALTHRVALVALGLUASPVALSERLYSGLNARGLYSV'
'ALLEUPROGLNPHEHISGLYVALTYRPHEILEGLUPRO'
'THRGLUGLUASNLEUASPTYRVALILEARGASPPHEAL'
'AASPARGTHRPROTHRTYRGLUALAALAHISLEU')
def test_ResidueDepth_2BEG(self):
self.check_msms('PDB/2BEG.pdb', 'LEUVALPHEPHEALAGLUASPVALGLYSERASNLYSGL'
'YALAILEILEGLYLEUMETVALGLYGLYVALVALILEA'
'LALEUVALPHEPHEALAGLUASPVALGLYSERASNLYS'
'GLYALAILEILEGLYLEUMETVALGLYGLYVALVALIL'
'EALALEUVALPHEPHEALAGLUASPVALGLYSERASNL'
'YSGLYALAILEILEGLYLEUMETVALGLYGLYVALVAL'
'ILEALALEUVALPHEPHEALAGLUASPVALGLYSERAS'
'NLYSGLYALAILEILEGLYLEUMETVALGLYGLY')
def test_ResidueDepth_1LCD(self):
self.check_msms('PDB/1LCD.pdb', 'METLYSPROVALTHRLEUTYRASPVALALAGLUTYRAL'
'AGLYVALSERTYRGLNTHRVALSERARGVALVALASNG'
'LNALASERHISVALSERALALYSTHRARGGLULYSVAL'
'GLUALAALAMETALAGLULEUASNTYRILEPROASNAR'
'G')
def test_ResidueDepth_1A8O(self):
self.check_msms('PDB/1A8O.pdb', 'MSEASPILEARGGLNGLYPROLYSGLUPROPHEARGAS'
'PTYRVALASPARGPHETYRLYSTHRLEUARGALAGLUG'
'LNALASERGLNGLUVALLYSASNTRPMSETHRGLUTHR'
'LEULEUVALGLNASNALAASNPROASPCYSLYSTHRIL'
'ELEULYSALALEUGLYPROGLYALATHRLEUGLUGLUM'
'SEMSETHRALACYSGLNGLY')
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
