def testAppend(self):
# should raise if appending an atom with atom._residue (already part of another residue)
self.assertRaises(structure.InvalidOperation,
self.residue.atoms.append, self.chain[2]['CA'])
# should not raise InvalidOperation (same residue)
self.assertRaises(structure.DuplicateAtomIDError,
self.residue.atoms.append, self.residue['CA'])
atom = structure.Atom(999999, 'Cx', structure.ChemElements.C,
numpy.array([1, 1, 1]))
self.residue.atoms.append(atom)
self.assertTrue(atom.name in self.residue)
self.assertEqual(atom.residue, self.residue)
# test alternate handling
atom2 = structure.Atom(999999,
'Cx',
structure.ChemElements.C,
numpy.array([2, 2, 2]),
alternate=True)
self.residue.atoms.append(atom2)
self.assertTrue(
isinstance(self.residue['Cx'], structure.DisorderedAtom))
self.assertEqual(self.residue['Cx'].length, 2)
atom3 = structure.Atom(999999, 'Cx', structure.ChemElements.C,
numpy.array([3, 3, 3]))
self.residue.atoms.append(atom3)
self.assertEqual(self.residue['Cx'].length, 3)
def testApplyTransformation(self):
"""
@see: [CSB 0000030]
"""
r = numpy.eye(3)
t = numpy.array([1, 1, 1])
residue = self.chain.residues[1]
atom1 = structure.Atom(99999,
'Cx',
structure.ChemElements.C,
numpy.array([2, 2, 2]),
alternate=True)
atom1.occupancy = 0.2
atom2 = structure.Atom(99999,
'Cx',
structure.ChemElements.C,
numpy.array([2, 2, 2]),
alternate=True)
atom2.occupancy = 0.8
residue.atoms.append(atom1)
residue.atoms.append(atom2)
self.chain.transform(r, t)
disatom = residue.atoms['Cx']
self.assertTrue(isinstance(disatom, structure.DisorderedAtom))
self.assertEqual(disatom.vector.tolist(), [3, 3, 3])
# now the regression itself
for altatom in disatom:
self.assertEqual(altatom.vector.tolist(), [3, 3, 3])
def testAppendAtom(self):
"""
@see: [CSB 0000122]
"""
r = structure.ProteinResidue(1, sequence.ProteinAlphabet.ALA)
a1 = structure.Atom(1,
'CA',
structure.ChemElements.C, [1, 1, 1],
alternate='A')
a2 = structure.Atom(1,
'CA',
structure.ChemElements.C, [1, 1, 1],
alternate='B')
r.atoms.append(a1)
r.atoms.append(a2)
self.assertEqual(a1.residue, r)
self.assertEqual(a2.residue, r)
def testAppend(self):
self.assertEqual(self.residue.atoms['CA'].serial_number, 2)
alt = structure.Atom(1000,
'CA',
structure.ChemElements.C,
self.atom.vector.copy(),
alternate='C')
alt.occupancy = 1.0
self.residue.atoms.append(alt)
self.assertEqual(self.residue.atoms['CA'].serial_number, 1000)
self.assertTrue(
isinstance(self.residue.atoms['CA'], structure.DisorderedAtom))
def make_chain(coordinates, sequence=None, chainid='A'):
"""Creates a Chain instance from a coordinate array assuming that these are
the positions of CA atoms.
"""
if sequence is None: sequence = ['ALA'] * len(coordinates)
residues = []
for i in range(len(sequence)):
residue = structure.ProteinResidue(i+1, sequence[i],
sequence_number=i+1)
atom = structure.Atom(i+1, 'CA', 'C', coordinates[i])
atom.occupancy = 1.0
residue.atoms.append(atom)
residues.append(residue)
return structure.Chain(chainid, residues=residues)
def setUp(self):
super(TestDisorderedAtom, self).setUp()
self.structure = self.config.getPickle('1nz9.model1.pickle')
self.chain = self.structure['A']
self.residue = self.chain[0]
self.atom = self.residue['CA']
self.alt = structure.Atom(999,
'CA',
structure.ChemElements.C,
self.atom.vector.copy(),
alternate='B')
self.atom.occupancy = 0.9
self.alt.occupancy = 0.1
self.residue.atoms.append(self.alt)
self.disatom = self.residue['CA']