def test08highestOccupancyLevel(self):
rawAtom = "ATOM 661 CA AMET A 101 16.070 45.718 27.607 0.20 7.83 C "
anAtom = Atom(rawAtom)
pdbFileName = "../../pdbs/multipleLocations.pdb"
pdb = PDB(pdbFileName)
pdb.load_atoms_hetams()
assert 'A' == anAtom.alternateLocation()
print "%c" % (pdb.getHighestOccupancyLocation(anAtom),)
assert 'B' == pdb.getHighestOccupancyLocation(anAtom)
def setUp(self):
self.atom = Atom(AtomTestCase.rawAtom)
self.atom2 = Atom(AtomTestCase.rawAtom2)
self.atom3 = Atom(AtomTestCase.rawAtom3)
self.atom4 = Atom(AtomTestCase.rawAtom4)
self.atom5 = Atom(AtomTestCase.rawAtom5)
self.atom6 = Atom(AtomTestCase.rawAtom6)
self.atom7 = Atom(AtomTestCase.rawAtom7)
def testinInsertionsSegment(self):
rawStartAtom = "ATOM 1 N ALA L 1T 95.966 23.494 131.088 1.00 78.27 N "
rawInResidueAtom = "ATOM 21 C GLU L 1Q 90.085 26.425 128.760 1.00 63.99 C "
rawMiddleAtom = "ATOM 158 N CYS L 1 81.822 27.897 122.945 1.00 35.25 N "
rawEndAtom = "ATOM 271 N LYS L 14A 86.041 46.599 116.234 1.00 45.79 N "
rawoutOfsegmentAtom = "ATOM 378 O GLY L 14N 92.287 43.790 140.820 1.00101.24 O "
rawoutOfsegmentAtom2 = "ATOM 378 O GLY L 15N 92.287 43.790 140.820 1.00101.24 O "
startAtom = Atom(rawStartAtom)
inResidueAtom = Atom(rawInResidueAtom)
middleAtom = Atom(rawMiddleAtom)
endAtom = Atom(rawEndAtom)
outOfsegmentAtom = Atom(rawoutOfsegmentAtom)
outOfsegmentAtom2 = Atom(rawoutOfsegmentAtom2)
start = 1
stop = 14
startInsertion = "T"
stopInsertion = "M"
startOrder = False
stopOrder = True
assert startAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
assert (
inResidueAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
)
assert middleAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
assert endAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
assert (
outOfsegmentAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
== False
)
assert (
outOfsegmentAtom2.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
== False
)
class AtomTestCase(unittest.TestCase):
rawAtom = "ATOM 1 N SER A 4 12.140 45.657 29.217 1.00 40.81 N "
rawAtom2 = "ATOM 1162 CG2 VAL B 147X 10.793 0.886 28.197 1.00 11.51 C2+"
rawAtom3 = "ATOM 48 N PRO C 8 -2.513 -13.594 63.478 1.00 2.00 N"
rawAtom4 = "ATOM 49 CA PRO D 8 -1.194 -14.125 63.727 1.00 2.00 C"
rawAtom5 = "ATOM 50 C PRO E 8 -0.065 -13.490 62.933 1.00 6.90 C"
rawAtom6 = "ATOM 51 O PRO F 8 -0.289 -12.746 61.987 1.00 16.83 O"
rawAtom7 = "ATOM 52 CB PRO G 8 -1.402 -15.549 63.449 1.00 2.00 C"
def setUp(self):
self.atom = Atom(AtomTestCase.rawAtom)
self.atom2 = Atom(AtomTestCase.rawAtom2)
self.atom3 = Atom(AtomTestCase.rawAtom3)
self.atom4 = Atom(AtomTestCase.rawAtom4)
self.atom5 = Atom(AtomTestCase.rawAtom5)
self.atom6 = Atom(AtomTestCase.rawAtom6)
self.atom7 = Atom(AtomTestCase.rawAtom7)
def tearDown(self):
self.atom = None
self.atom2 = None
def test1ToString(self):
assert AtomTestCase.rawAtom == self.atom.toString()
assert AtomTestCase.rawAtom2 == self.atom2.toString()
def test2Shift(self):
shift = matrix([0.01, 0.01, 0.01]).T
self.atom.shift(shift)
assert (
"ATOM 1 N SER A 4 12.150 45.667 29.227 1.00 40.81 N " == self.atom.toString()
)
def test3Center(self):
center = matrix([0.00, 0.00, 0.00]).T
self.atom.center(center)
assert AtomTestCase.rawAtom == self.atom.toString()
def test4inBackbone(self):
assert self.atom.inBackbone() == True
assert self.atom3.inBackbone() == True
assert self.atom4.inBackbone() == True
assert self.atom6.inBackbone() == True
assert self.atom7.inBackbone() == True
assert self.atom2.inBackbone() == False
assert self.atom5.inBackbone() == False
def test5InChain(self):
assert self.atom.inChain(" A ")
assert self.atom2.inChain(" A ") == False
def test6InSegment(self):
assert self.atom.inSegment(4, 5)
assert self.atom2.inSegment(148, 150) == False
assert self.atom2.inSegment(147, 150) == True
def test7atomWeight(self):
assert self.atom.atomicWeight() == 14.0067
def testinInsertionsSegment(self):
rawStartAtom = "ATOM 1 N ALA L 1T 95.966 23.494 131.088 1.00 78.27 N "
rawInResidueAtom = "ATOM 21 C GLU L 1Q 90.085 26.425 128.760 1.00 63.99 C "
rawMiddleAtom = "ATOM 158 N CYS L 1 81.822 27.897 122.945 1.00 35.25 N "
rawEndAtom = "ATOM 271 N LYS L 14A 86.041 46.599 116.234 1.00 45.79 N "
rawoutOfsegmentAtom = "ATOM 378 O GLY L 14N 92.287 43.790 140.820 1.00101.24 O "
rawoutOfsegmentAtom2 = "ATOM 378 O GLY L 15N 92.287 43.790 140.820 1.00101.24 O "
startAtom = Atom(rawStartAtom)
inResidueAtom = Atom(rawInResidueAtom)
middleAtom = Atom(rawMiddleAtom)
endAtom = Atom(rawEndAtom)
outOfsegmentAtom = Atom(rawoutOfsegmentAtom)
outOfsegmentAtom2 = Atom(rawoutOfsegmentAtom2)
start = 1
stop = 14
startInsertion = "T"
stopInsertion = "M"
startOrder = False
stopOrder = True
assert startAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
assert (
inResidueAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
)
assert middleAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
assert endAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder) == True
assert (
outOfsegmentAtom.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
== False
)
assert (
outOfsegmentAtom2.inInsertionsSegment(start, stop, startInsertion, stopInsertion, startOrder, stopOrder)
== False
)
def testgetResidue(self):
assert self.atom.getResidue() == (4, " ")
assert self.atom2.getResidue() == (147, "X")
