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# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# 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.
"""Unit test for Residues"""
import unittest
from Bio.SCOP.Residues import *
import sys
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
return test_suite()
class ResiduesTests(unittest.TestCase):
res = (
( "-", () ),
( "A:", (("A", "", ""),) ),
( "1:", (("1", "", ""),) ),
( "1-100", (("", "1", "100"),) ),
( "B:1-101", (("B", "1" ,"101"),) ),
( "1:1a-100a", (("1", "1a", "100a"),) ),
( "a:-100a--1a", (("a", "-100a", "-1a"),) ),
( "-1-100", (("", "-1", "100"),) ),
( "-1-100", (("", "-1", "100"),) ),
( "A:12-19,A:23-25", (("A","12","19"),("A","23","25")) ),
( "12-19,1:23-25", (("","12","19"),("1","23","25")) ),
( "0-1,1:-1a-25a,T:", (("","0","1"),("1","-1a","25a"),("T","","")) ),
)
def testParse(self):
for loc in self.res :
r = Residues(loc[0])
assert r.fragments == loc[1], str(r.locations)
def testStr(self):
for loc in self.res :
r = Residues(loc[0])
assert str(r) == loc[0], str(r)+" is not "+loc[0]
def testAstralParse(self) :
"""Astral encloses residue subsets in brackets. Lets make sure we
can parse those too.
"""
for loc in self.res :
r = Residues("("+loc[0]+")")
assert r.fragments == loc[1], str(r.locations)
def testPdbId(self):
pdbid ="1ddf"
for loc in self.res :
r = Residues("\t 1ddf \t"+loc[0]+"\t\n\n\n")
assert r.pdbid == pdbid
assert str(r) == pdbid+" "+loc[0]
r = Residues(pdbid+" "+loc[0])
assert r.pdbid == pdbid
assert str(r) == pdbid+" "+loc[0]
r = Residues("104l A:112-113")
assert r.pdbid == "104l"
assert r.fragments == (('A', '112', '113'),)
def testJustPdbId(self) :
r = Residues("1sds")
assert r.pdbid == "1sds"
assert not r.fragments
def testParseError(self) :
try:
r = Residues("09324923423hh./;,.389")
assert 0, "Should never get here: "+str(r)
except ValueError, e :
pass
def test_suite():
return unittest.makeSuite(ResiduesTests)
if __name__ == '__main__':
unittest.main()
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