def testMultiEndGroups(self):
"""Test we can move correctly"""
# Try with no settings
f = ab_fragment.fragmentFactory('A', self.ch4_1Car)
m1 = Block(initFragment=f)
m2 = m1.copy()
eg1 = m1.freeEndGroups()[0]
eg2 = m2.freeEndGroups()[0]
m1.positionGrowBlock(eg1, eg2)
bond = Bond(eg1, eg2)
bond.engage()
self.assertEqual(6, len(m1.freeEndGroups()))
# Try with specifying bond
f = ab_fragment.fragmentFactory('A', self.ch4_1Car)
m1 = Block(initFragment=f)
f.setMaxBond("A:a", 1)
m2 = m1.copy()
eg1 = m1.freeEndGroups()[0]
eg2 = m2.freeEndGroups()[0]
m1.positionGrowBlock(eg1, eg2)
bond = Bond(eg1, eg2)
bond.engage()
self.assertEqual(4, len(m1.freeEndGroups()))
return
def testBodyConfigStr(self):
ch4ca = os.path.join(BLOCKS_DIR, "ch4Ca2.car")
ftype = "A"
f1 = ab_fragment.fragmentFactory(ftype, ch4ca)
for i, b in enumerate(f1.bodies()):
bstr = "{}{}{}".format(i, ftype, "0000")
self.assertEqual(bstr, b.rigidConfigStr)
def testConfig(self):
rigidParticleMgr = ab_rigidparticle.RigidParticleManager()
ch4ca = os.path.join(BLOCKS_DIR, "ch4Ca2.car")
ftype = "A"
f1 = ab_fragment.fragmentFactory(ftype, ch4ca)
rigidParticles = []
for body in f1.bodies():
rigidParticles.append(rigidParticleMgr.createParticle(body))
pfx = rigidParticleMgr.PREFIX_STR
configStr = {
"1A0000": pfx + "AB",
"2A0000": pfx + "AC",
"0A0000": pfx + "AA"
}
self.assertEqual(rigidParticleMgr._configStr, configStr)
self.assertEqual(len(rigidParticleMgr._configStr),
len(rigidParticleMgr._positions))
b1 = list(f1.bodies())[0]
quat_origin = np.array([1.0, 0.0, 0.0, 0.0])
self.assertEqual(rigidParticleMgr.configStr(b1), pfx + "AA")
# Rotate fragment and see if we get a different orientation
axis = np.array([1, 0, 0])
angle = math.pi / 3
rotationMatrix = xyz_core.rotation_matrix(axis, angle)
f1.rotate(rotationMatrix, f1._centerOfMass)
b1 = list(f1.bodies())[0]
ref_q = np.array([0.866, 0.5, 0.0, 0.0])
self.assertTrue(
np.allclose(rigidParticles[0].orientation,
quat_origin,
rtol=0.0001))
return
def testConfigStr(self):
ch4 = os.path.join(BLOCKS_DIR, "ch4.car")
ftype = 'A'
f1 = ab_fragment.fragmentFactory(ftype, ch4)
cstr = ftype + "0000"
self.assertEqual(cstr, f1.configStr)
for eg in f1.endGroups():
eg.bonded = True
f1.update()
cstr = ftype + "1111"
self.assertEqual(cstr, f1.configStr)
def testPickleRoundtrip(self):
ch4 = os.path.join(BLOCKS_DIR, "ch4.car")
ftype = 'A'
f1 = ab_fragment.fragmentFactory(ftype, ch4)
f2 = f1.copy()
labels = ['A', 'A', 'A', 'A', 'A']
f2._labels = labels
fname = 'f1.pkl.gz'
ab_util.pickleObj(f2, fname)
f3 = ab_util.unpickleObj(fname)
self.assertEqual(f3._labels, labels)
os.unlink(fname)
def testPrincipalMoments(self):
"""Test principal moments don't change with rotation"""
ch4 = os.path.join(BLOCKS_DIR, "ch4.car")
frag = ab_fragment.fragmentFactory('A', ch4)
body = list(frag.bodies())[0]
pi1 = body.principalMoments
axis = [1, 0, 1]
angle = math.pi / 3
rotationMatrix = xyz_core.rotation_matrix(axis, angle)
center = body.centreOfMass
frag.rotate(rotationMatrix, center)
pi2 = body.principalMoments
self.assertTrue(np.allclose(pi1, pi2))
def testBondingFunction(self):
carfile = os.path.join(BLOCKS_DIR, "benzene6.car")
f = ab_fragment.fragmentFactory('A', carfile)
def x(endGroup):
fragment = endGroup.fragment
egt = endGroup.type()
for eg in fragment.endGroups():
if egt == "A:a":
if not eg.bonded and eg.type() in ["A:c", "A:e"]:
eg.blocked = True
elif egt == "A:b":
if not eg.bonded and eg.type() in ["A:d", "A:f"]:
eg.blocked = True
elif egt == "A:c":
if not eg.bonded and eg.type() in ["A:a", "A:e"]:
eg.blocked = True
elif egt == "A:d":
if not eg.bonded and eg.type() in ["A:b", "A:f"]:
eg.blocked = True
elif egt == "A:e":
if not eg.bonded and eg.type() in ["A:a", "A:c"]:
eg.blocked = True
elif egt == "A:f":
if not eg.bonded and eg.type() in ["A:b", "A:d"]:
eg.blocked = True
return
f.onbondFunction = x
block1 = Block(initFragment=f)
block2 = Block(filePath=self.ch4Car, fragmentType="B")
# Check we have 6 free endGroups at the start
self.assertEqual(len(block1.freeEndGroups()), 6)
self.assertEqual(len(block2.freeEndGroups()), 4)
# Create a bond to the first endGroup
eg1 = block1.freeEndGroups(endGroupTypes="A:a")[0]
eg2 = block2.freeEndGroups()[0]
bond = Bond(eg1, eg2)
bond.engage()
# Now see if the other two are blocked - we need to include the three from the second block
self.assertEqual(len(block1.freeEndGroups()), 6)
return
def testMaxBond(self):
f = ab_fragment.fragmentFactory('A', self.ch4_1Car)
f.setMaxBond("A:b", 1)
block1 = Block(initFragment=f)
block2 = Block(filePath=self.ch4Car, fragmentType="B")
self.assertEqual(len(block1.freeEndGroups()), 4)
self.assertEqual(len(block2.freeEndGroups()), 4)
# Create a bond to the maxBonded type
eg1 = block1.freeEndGroups(endGroupTypes="A:b")[0]
eg2 = block2.freeEndGroups()[0]
bond = Bond(eg1, eg2)
bond.engage()
# Now see if the other three are blocked - we need to include the three from the second block
self.assertEqual(len(block1.freeEndGroups()), 5)
return
def testCoords(self):
ch4ca = os.path.join(BLOCKS_DIR, "ch4.car")
ftype = "A"
frag = ab_fragment.fragmentFactory(ftype, ch4ca)
body = list(frag.bodies())[0]
assert np.array_equal(body.coords, frag._coords)
def testMultipleCapAtoms(self):
h3car = os.path.join(BLOCKS_DIR, "H3.car")
with self.assertRaises(RuntimeError):
ab_fragment.fragmentFactory('A', h3car)
def testDisallowedFragmentType(self):
ch4 = os.path.join(BLOCKS_DIR, "ch4.car")
ftype = 'Fragment'
with self.assertRaises(AssertionError):
f1 = ab_fragment.fragmentFactory(ftype, ch4)
def testFragmentType(self):
ch4 = os.path.join(BLOCKS_DIR, "ch4.car")
ftype = 'A'
f1 = ab_fragment.fragmentFactory(ftype, ch4)
self.assertEqual(ftype, f1.fragmentType)