def _test_frame_property(self, obj_type, obj_id, getter):
# Test frame property works correctly
molid = VMD.molecule.load('psf', data('water.psf'), 'pdb',
data('water.pdb'))
VMD.molecule.read(molid, 'dcd', data('water.1.dcd'), waitfor=-1)
mol = Molecule(molid)
# To check frame works correctly, check the 'x' coordinate of the object's first atom.
# Create residue linked to the molecule frame
obj = obj_type(obj_id)
self.assertEqual(obj.frame, NOW)
self.assertAlmostEqual(getter(obj), -1.3421925)
# Change the molecule frame, the object will follow
mol.frame = 0
self.assertEqual(obj.frame, NOW)
self.assertAlmostEqual(getter(obj), -1.493)
mol.frame = 4
self.assertEqual(obj.frame, NOW)
self.assertAlmostEqual(getter(obj), -1.4773947)
# Define the object's frame
obj.frame = 9
self.assertEqual(obj.frame, 9)
self.assertAlmostEqual(getter(obj), -1.4120502)
# Change the molecule frame, the object keeps its frame
mol.frame = 11
self.assertEqual(obj.frame, 9)
self.assertAlmostEqual(getter(obj), -1.4120502)
# Set the object's frame back to the molecule's frame
obj.frame = NOW
self.assertEqual(obj.frame, NOW)
self.assertAlmostEqual(getter(obj), -1.3674825)
def test_molecule_properties(self):
# Test basic properties of Molecule
mol = Molecule(self.molid)
# Check frame property
mol.frame = 3
self.assertEqual(VMD.molecule.get_frame(self.molid), 3)
self.assertEqual(mol.frame, 3)
mol.frame = 8
self.assertEqual(VMD.molecule.get_frame(self.molid), 8)
self.assertEqual(mol.frame, 8)
# Check name property
mol.name = 'My precious'
self.assertEqual(mol.name, 'My precious')
self.assertEqual(VMD.molecule.name(self.molid), 'My precious')
mol.name = 'The Ring'
self.assertEqual(mol.name, 'The Ring')
self.assertEqual(VMD.molecule.name(self.molid), 'The Ring')
# Check molecule property
self.assertIsInstance(mol.molecule, _Molecule)
# Check error if molecule does not exists
self.assertRaises(ValueError, Molecule, 66000)
def test_selection_updates(self):
# Test selection updates if frame is changed
molid = VMD.molecule.load('psf', data('water.psf'), 'pdb',
data('water.pdb'))
VMD.molecule.read(molid, 'dcd', data('water.1.dcd'), waitfor=-1)
mol = Molecule(molid)
# Create selection linked to the molecule frame
sel = Selection('x < -1.4')
self.assertEqual(list(sel), [Atom(9), Atom(18), Atom(19), Atom(20)])
# Change the molecule frame, the selection should follow
mol.frame = 0
self.assertEqual(list(sel), [
Atom(0),
Atom(1),
Atom(9),
Atom(10),
Atom(18),
Atom(19),
Atom(20)
])
mol.frame = 4
self.assertEqual(
list(sel),
[Atom(0), Atom(1),
Atom(9), Atom(18),
Atom(19), Atom(20)])
# Define the selection's frame
result = [
Atom(0, frame=9),
Atom(1, frame=9),
Atom(9, frame=9),
Atom(18, frame=9),
Atom(19, frame=9),
Atom(20, frame=9)
]
sel.frame = 9
self.assertEqual(list(sel), result)
# Change the molecule frame, the selection keeps its frame
mol.frame = 11
self.assertEqual(list(sel), result)
# Set the selection's frame back to the molecule's frame
sel.frame = NOW
self.assertEqual(list(sel), [Atom(9), Atom(18), Atom(19), Atom(20)])
def test_frames(self):
# Test frames wrapper
# Utility to get x coordinate through the trajectory to check results
sel = VMD.atomsel.atomsel('index 0', molid=self.molid)
def _get_x_coord():
# Utility to get x coordinate through trajectory
values = []
for frame in xrange(VMD.molecule.numframes(self.molid)):
sel.frame = frame
values.append(sel.get('x')[0])
return values
# Check number of frames and iterator
mol = Molecule(self.molid)
self.assertEqual(len(mol.frames), 13)
self.assertEqual(list(mol.frames), range(13))
# Test frame duplication - duplicate focused frame
mol.frame = 3
mol.frames.copy()
# Check there is one more frame
self.assertEqual(len(mol.frames), 14)
coords = [-1.493, -1.4911567, -1.4851371, -1.4858487, -1.4773947, -1.4746015, -1.4673382, -1.4535547,
-1.4307435, -1.4120502, -1.3853478, -1.3674825, -1.3421925, -1.4858487]
self.assertAlmostEqualSeqs(_get_x_coord(), coords)
# Check molecule is focused to the new frame
self.assertEqual(mol.frame, 13)
# Test frame duplication - duplicate defined frame
mol.frames.copy(4)
# Check there is one more frame
self.assertEqual(len(mol.frames), 15)
coords = [-1.493, -1.4911567, -1.4851371, -1.4858487, -1.4773947, -1.4746015, -1.4673382, -1.4535547,
-1.4307435, -1.4120502, -1.3853478, -1.3674825, -1.3421925, -1.4858487, -1.4773947]
self.assertAlmostEqualSeqs(_get_x_coord(), coords)
# Molecule is focused to the new frame
self.assertEqual(mol.frame, 14)
# Test frame deletion - positive index
del mol.frames[14]
self.assertEqual(len(mol.frames), 14)
coords = [-1.493, -1.4911567, -1.4851371, -1.4858487, -1.4773947, -1.4746015, -1.4673382, -1.4535547,
-1.4307435, -1.4120502, -1.3853478, -1.3674825, -1.3421925, -1.4858487]
self.assertAlmostEqualSeqs(_get_x_coord(), coords)
# Test frame deletion - negative index
del mol.frames[-2]
self.assertEqual(len(mol.frames), 13)
coords = [-1.493, -1.4911567, -1.4851371, -1.4858487, -1.4773947, -1.4746015, -1.4673382, -1.4535547,
-1.4307435, -1.4120502, -1.3853478, -1.3674825, -1.4858487]
self.assertAlmostEqualSeqs(_get_x_coord(), coords)
# Check deletion of frame slice
del mol.frames[2:11:3]
self.assertEqual(len(mol.frames), 10)
coords = [-1.493, -1.4911567, -1.4858487, -1.4773947, -1.4673382, -1.4535547, -1.4120502, -1.3853478,
-1.3674825, -1.4858487]
self.assertAlmostEqualSeqs(_get_x_coord(), coords)
# Invalid key for slice
with self.assertRaises(TypeError):
del mol.frames[None]