def isHbond(d, h, a):
if norm(d-a) > 0.35*nanometer:
return False
deltaDH = h-d
deltaHA = a-h
deltaDH /= norm(deltaDH)
deltaHA /= norm(deltaHA)
return acos(dot(deltaDH, deltaHA)) < 50*degree
def isHbond(d, h, a):
if norm(d - a) > 0.35 * nanometer:
return False
deltaDH = h - d
deltaHA = a - h
deltaDH /= norm(deltaDH)
deltaHA /= norm(deltaHA)
return acos(dot(deltaDH, deltaHA)) < 50 * degree
def testUnitMathModule(self):
""" Tests the unit_math functions on Quantity objects """
self.assertEqual(u.sqrt(1.0*u.kilogram*u.joule),
1.0*u.kilogram*u.meter/u.second)
self.assertEqual(u.sqrt(1.0*u.kilogram*u.calorie),
math.sqrt(4.184)*u.kilogram*u.meter/u.second)
self.assertEqual(u.sqrt(9), 3) # Test on a scalar
self.assertEqual(u.sin(90*u.degrees), 1)
self.assertEqual(u.sin(math.pi/2*u.radians), 1)
self.assertEqual(u.sin(math.pi/2), 1)
self.assertEqual(u.cos(180*u.degrees), -1)
self.assertEqual(u.cos(math.pi*u.radians), -1)
self.assertEqual(u.cos(math.pi), -1)
self.assertAlmostEqual(u.tan(45*u.degrees), 1)
self.assertAlmostEqual(u.tan(math.pi/4*u.radians), 1)
self.assertAlmostEqual(u.tan(math.pi/4), 1)
acos = u.acos(1.0)
asin = u.asin(1.0)
atan = u.atan(1.0)
self.assertTrue(u.is_quantity(acos))
self.assertTrue(u.is_quantity(asin))
self.assertTrue(u.is_quantity(atan))
self.assertEqual(acos.unit, u.radians)
self.assertEqual(asin.unit, u.radians)
self.assertEqual(atan.unit, u.radians)
self.assertEqual(acos.value_in_unit(u.degrees), 0)
self.assertEqual(acos / u.radians, 0)
self.assertEqual(asin.value_in_unit(u.degrees), 90)
self.assertEqual(asin / u.radians, math.pi/2)
self.assertAlmostEqual(atan.value_in_unit(u.degrees), 45)
self.assertAlmostEqual(atan / u.radians, math.pi/4)
# Check some sequence maths
seq = [1, 2, 3, 4] * u.meters
self.assertEqual(u.sum(seq), 10*u.meters)
self.assertEqual(u.dot(seq, seq), (1+4+9+16)*u.meters**2)
self.assertEqual(u.norm(seq), math.sqrt(30)*u.meters)