def testReadAmberPython(self):
# reimplemented the Amber trajectory reader in Python
# let's check we get the same data as the C++ reader
# (test for building a trajectory out of Snapshots from Python)
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data',
'water_coords2.trx')
traj = Trajectory(3, 3)
nCoords = traj.NumPoints() * 3
nSnapshots = 0
hnd = open(fName, 'r')
line = hnd.readline()
lineNum = 0
c = []
i = 0
while (line):
lineNum += 1
if (lineNum > 1):
tok = line.strip().split()
j = 0
while ((i < nCoords) and (j < len(tok))):
c.append(float(tok[j]))
j += 1
i += 1
if (i == nCoords):
nSnapshots += 1
traj.AddSnapshot(Snapshot(c))
c = []
i = 0
line = ' '.join(tok[j:]) + ' '
else:
line = ''
else:
line = ''
line += hnd.readline()
hnd.close()
self.assertEqual(i, 0)
self.assertEqual(nSnapshots, 2)
traj2 = Trajectory(3, 3)
ReadAmberTrajectory(fName, traj2)
self.assertEqual(len(traj), len(traj2))
self.assertEqual(traj.NumPoints(), traj2.NumPoints())
for snapshotNum in range(len(traj)):
for pointNum in range(traj.NumPoints()):
for i in range(3):
self.assertAlmostEqual(
traj.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i],
traj2.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i])
def testTrajectory3D(self):
dim = 3
np = 10
ns = 5
traj = Trajectory(dim, np)
self.assertEqual(traj.Dimension(), dim)
self.assertEqual(traj.NumPoints(), np)
c = []
for i in range(np * dim):
c.append(float(i))
for i in range(ns):
traj.AddSnapshot(Snapshot(c, float(i)))
self.assertEqual(len(traj), ns)
e = False
try:
traj.GetSnapshot(ns)
except Exception:
e = True
self.assertTrue(e)
e = False
try:
traj.GetSnapshot(0).GetPoint2D(np)
except Exception:
e = True
self.assertTrue(e)
for i in range(np):
self.assertAlmostEqual(
traj.GetSnapshot(0).GetPoint3D(i).x, float(i * dim))
self.assertAlmostEqual(
traj.GetSnapshot(0).GetPoint3D(i).y, float(i * dim + 1))
self.assertAlmostEqual(
traj.GetSnapshot(0).GetPoint3D(i).z, float(i * dim + 2))
if (not i):
e = False
try:
traj.GetSnapshot(0).GetPoint2D(i)
except Exception:
e = True
self.assertTrue(e)
for i in range(ns):
self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i))
traj.RemoveSnapshot(0)
self.assertEqual(len(traj), ns - 1)
for i in range(ns - 1):
self.assertAlmostEqual(
traj.GetSnapshot(i).GetEnergy(), float(i + 1))
traj.InsertSnapshot(0, Snapshot(c, 999.0))
self.assertEqual(len(traj), ns)
copySnapshot = Snapshot(traj.GetSnapshot(0))
traj.AddSnapshot(copySnapshot)
self.assertEqual(len(traj), ns + 1)
self.assertAlmostEqual(traj.GetSnapshot(0).GetEnergy(), 999.0)
self.assertAlmostEqual(traj.GetSnapshot(1).GetEnergy(), 1.0)
self.assertAlmostEqual(
traj.GetSnapshot(len(traj) - 1).GetEnergy(), 999.0)
traj2 = Trajectory(traj)
self.assertEqual(len(traj), len(traj2))