예제 #1
0
    def setUp(self):

        self.crystal = Crystal({'a': 'T T G A C T C T C T T A A',
                                'b': Chain('G A G A G T C A'),
                                'c': 'T T G A C T C T C T T A A',
                                'd': Chain('G A G A G T C A')
                                })
예제 #2
0
    def setUp(self):

        self.crystal = Crystal({"a": "T T G A C T C T C T T A A",
                                "b": Chain("G A G A G T C A"),
                                "c": "T T G A C T C T C T T A A",
                                "d": Chain("G A G A G T C A")
                                })
예제 #3
0
class CrystalTestCase(unittest.TestCase):

    def setUp(self):

        self.crystal = Crystal({ 'a' : 'T T G A C T C T C T T A A',
                             'b' : Chain('G A G A G T C A'),
                             'c' : 'T T G A C T C T C T T A A',
                             'd' : Chain('G A G A G T C A')
                            })

    def testLen(self):
        self.assertEqual(len(self.crystal), len(self.crystal.data))

    def testGetItem(self):
        self.assertEqual(self.crystal[ 'a' ], self.crystal.data[ 'a' ])

    def testSetItem(self):
        target = copy.deepcopy(self.crystal)
        e = 'MET ALA LEU THR ASN ALA GLN ILE LEU ALA VAL ILE ASP SER'
        f = 'LEU GLY GLY GLY LEU GLN GLY THR LEU HIS CYS TYR GLU ILE PRO LEU'
        target[ 'e' ] = e
        target[ 'f' ] = Chain(f)
        self.assertEqual(Chain(e), target[ 'e' ])
        self.assertEqual(Chain(f), target[ 'f' ])

    def testDelItem(self):
        target = copy.deepcopy(self.crystal)
        del target[ 'b' ]
        self.assertFalse('b' in target.data)
        self.assertTrue('a' in target.data)
        self.assertTrue('c' in target.data)

    def testClear(self):
        target = copy.deepcopy(self.crystal)
        target.clear()
        self.assertEqual(len(target.data), 0)

    def testKeys(self):
        self.assertEqual(list(self.crystal.keys()),
                         list(self.crystal.data.keys()))

    def testValues(self):
        self.assertEqual(list(self.crystal.values()),
                         list(self.crystal.data.values()))

    def testItems(self):
        self.assertEqual(list(self.crystal.items()),
                         list(self.crystal.data.items()))

    def testKeys(self):
        self.assertEqual(list(self.crystal.keys()),
                         list(self.crystal.data.keys()))

    def testHasKey(self):
        self.assertTrue('b' in self.crystal)
        self.assertTrue('c' in self.crystal)
        self.assertFalse('z' in self.crystal)
예제 #4
0
class CrystalTestCase(unittest.TestCase):

    def setUp(self):

        self.crystal = Crystal({'a': 'T T G A C T C T C T T A A',
                                'b': Chain('G A G A G T C A'),
                                'c': 'T T G A C T C T C T T A A',
                                'd': Chain('G A G A G T C A')
                                })

    def testLen(self):
        self.assertEqual(len(self.crystal), len(self.crystal.data))

    def testGetItem(self):
        self.assertEqual(self.crystal['a'], self.crystal.data['a'])

    def testSetItem(self):
        target = copy.deepcopy(self.crystal)
        e = 'MET ALA LEU THR ASN ALA GLN ILE LEU ALA VAL ILE ASP SER'
        f = 'LEU GLY GLY GLY LEU GLN GLY THR LEU HIS CYS TYR GLU ILE PRO LEU'
        target['e'] = e
        target['f'] = Chain(f)
        self.assertEqual(Chain(e), target['e'])
        self.assertEqual(Chain(f), target['f'])

    def testDelItem(self):
        target = copy.deepcopy(self.crystal)
        del target['b']
        self.assertFalse('b' in target.data)
        self.assertTrue('a' in target.data)
        self.assertTrue('c' in target.data)

    def testClear(self):
        target = copy.deepcopy(self.crystal)
        target.clear()
        self.assertEqual(len(target.data), 0)

    def testKeys(self):
        self.assertEqual(list(self.crystal.keys()),
                         list(self.crystal.data.keys()))

    def testValues(self):
        self.assertEqual(list(self.crystal.values()),
                         list(self.crystal.data.values()))

    def testItems(self):
        self.assertEqual(list(self.crystal.items()),
                         list(self.crystal.data.items()))

    def testKeys(self):
        self.assertEqual(list(self.crystal.keys()),
                         list(self.crystal.data.keys()))

    def testHasKey(self):
        self.assertTrue('b' in self.crystal)
        self.assertTrue('c' in self.crystal)
        self.assertFalse('z' in self.crystal)
예제 #5
0
class CrystalTestCase(unittest.TestCase):
    def setUp(self):

        self.crystal = Crystal({
            "a": "T T G A C T C T C T T A A",
            "b": Chain("G A G A G T C A"),
            "c": "T T G A C T C T C T T A A",
            "d": Chain("G A G A G T C A")
        })

    def testLen(self):
        self.assertEqual(len(self.crystal), len(self.crystal.data))

    def testGetItem(self):
        self.assertEqual(self.crystal["a"], self.crystal.data["a"])

    def testSetItem(self):
        target = copy.deepcopy(self.crystal)
        e = "MET ALA LEU THR ASN ALA GLN ILE LEU ALA VAL ILE ASP SER"
        f = "LEU GLY GLY GLY LEU GLN GLY THR LEU HIS CYS TYR GLU ILE PRO LEU"
        target["e"] = e
        target["f"] = Chain(f)
        self.assertEqual(Chain(e), target["e"])
        self.assertEqual(Chain(f), target["f"])

    def testDelItem(self):
        target = copy.deepcopy(self.crystal)
        del target["b"]
        self.assertFalse("b" in target.data)
        self.assertIn("a", target.data)
        self.assertIn("c", target.data)

    def testClear(self):
        target = copy.deepcopy(self.crystal)
        target.clear()
        self.assertEqual(len(target.data), 0)

    def testKeys(self):
        self.assertEqual(list(self.crystal.keys()),
                         list(self.crystal.data.keys()))

    def testValues(self):
        self.assertEqual(list(self.crystal.values()),
                         list(self.crystal.data.values()))

    def testItems(self):
        self.assertEqual(list(self.crystal.items()),
                         list(self.crystal.data.items()))

    def testHasKey(self):
        self.assertIn("b", self.crystal)
        self.assertIn("c", self.crystal)
        self.assertFalse("z" in self.crystal)
예제 #6
0
    def setUp(self):

        self.crystal = Crystal({ 'a' : 'T T G A C T C T C T T A A',
                             'b' : Chain('G A G A G T C A'),
                             'c' : 'T T G A C T C T C T T A A',
                             'd' : Chain('G A G A G T C A')
                            })
예제 #7
0
 def __init__(self):
     self['Id'] = ''
     self['Features'] = ''
     self['Name'] = ''
     self['Sequence'] = Crystal({})
     self['Citation'] = Reference()
     self['Space Group'] = ''
     self['Cell Constants'] = {}
     self['Crystallization Conditions'] = []
     self['Refinement'] = ''
     self['Coordinates'] = ''