def test_change_distance(self):
def validate_distance(before, after, moved):
dist = np.linalg.norm(after.coords - before.coords)
return abs(dist - moved)
threshold = 10**(-8)
mol = Geometry(TestGeometry.benz_NO2_Cl)
a1 = mol.atoms[0] # C1
a3 = mol.atoms[5] # attached to C1
a2 = mol.atoms[11] # N12
a4 = mol.atoms[12] # attached to N12
# set distance and move fragments
a3_before = copy(a3)
a4_before = copy(a4)
dist_before = np.linalg.norm(a1.coords - a2.coords)
mol.change_distance(a1, a2, dist=2.00)
dist = np.linalg.norm(a1.coords - a2.coords)
self.assertTrue(is_close(dist, 2.00, threshold))
self.assertTrue(validate_distance(a3_before, a3, dist - dist_before))
self.assertTrue(validate_distance(a4_before, a4, dist - dist_before))
# adjust_distance and move fragments
a3_before = copy(a3)
a4_before = copy(a4)
dist_before = np.linalg.norm(a1.coords - a2.coords)
mol.change_distance(a1, a2, dist=-0.5, adjust=True)
self.assertTrue(is_close(a1.dist(a2), 1.5, threshold))
self.assertTrue(validate_distance(a3_before, a3, -0.5))
self.assertTrue(validate_distance(a4_before, a4, -0.5))
# set and fix atom 1
a1_before = copy(a1)
mol.change_distance(a1, a2, dist=2.00, fix=1)
self.assertTrue(is_close(a1.dist(a2), 2.00, threshold))
self.assertTrue(a1_before.dist(a1) < threshold)
# adjust and fix atom 2
a2_before = copy(a2)
mol.change_distance(a1, a2, dist=-0.5, adjust=True, fix=2)
self.assertTrue(is_close(a1.dist(a2), 1.5, threshold))
self.assertTrue(a2_before.dist(a2) < threshold)
# set and don't move fragments
a3_before = copy(a3)
a4_before = copy(a4)
dist_before = np.linalg.norm(a1.coords - a2.coords)
mol.change_distance(a1, a2, dist=2.00, as_group=False)
dist = np.linalg.norm(a1.coords - a2.coords)
self.assertTrue(is_close(a1.dist(a2), 2.00, threshold))
self.assertTrue(validate_distance(a3_before, a3, dist - dist_before))
self.assertTrue(validate_distance(a4_before, a4, dist - dist_before))
def test_compare_connectivity(self):
geom = Geometry(TestGeometry.cat)
ref = Geometry(TestGeometry.cat)
# no formed/broken
broken, formed = geom.compare_connectivity(ref)
self.assertTrue(len(broken) == 0)
self.assertTrue(len(formed) == 0)
# broken
geom.change_distance("10", "15", dist=1, adjust=True)
geom.refresh_connected()
broken, formed = geom.compare_connectivity(ref)
self.assertTrue(len(broken) == 1)
self.assertTrue(len(formed) == 0)
self.assertSetEqual(broken, set([("10", "15")]))
# formed
ref.change_distance("10", "15", dist=1, adjust=True)
ref.refresh_connected()
geom.change_distance("10", "15", dist=-1, adjust=True)
geom.refresh_connected()
broken, formed = geom.compare_connectivity(ref)
self.assertTrue(len(broken) == 0)
self.assertTrue(len(formed) == 1)
self.assertSetEqual(formed, set([("10", "15")]))
# broken and formed
geom.change_distance("20", "29", dist=1, adjust=True)
geom.refresh_connected()
broken, formed = geom.compare_connectivity(ref)
self.assertTrue(len(broken) == 1)
self.assertTrue(len(formed) == 1)
self.assertSetEqual(broken, set([("20", "29")]))
self.assertSetEqual(formed, set([("10", "15")]))
def test_examine_constraints(self):
cat = Geometry(TestGeometry.cat)
rv = cat.examine_constraints()
self.assertSequenceEqual(rv, [])
cat.change_distance(cat.atoms[0], cat.atoms[1], dist=0.5, adjust=True)
rv = cat.examine_constraints()
self.assertSequenceEqual(rv, [(0, 1, -1)])
cat.change_distance(cat.atoms[0], cat.atoms[1], dist=-1.0, adjust=True)
rv = cat.examine_constraints()
self.assertSequenceEqual(rv, [(0, 1, 1)])
cat.change_distance(cat.atoms[1], cat.atoms[2], dist=0.5, adjust=True)
rv = cat.examine_constraints()
self.assertSequenceEqual(rv, [(0, 1, 1), (1, 2, -1)])
else:
infile = FileReader(f)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format, f))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
#set bond to specified value
for bond in args.set_ang:
vals = two_atoms_and_a_float(bond)
a1 = geom.find(str(vals[0]))[0]
a2 = geom.find(str(vals[1]))[0]
geom.change_distance(a1, a2, dist=vals[2], adjust=False)
#change bond by specified amount
for bond in args.change:
vals = two_atoms_and_a_float(bond)
a1 = geom.find(str(vals[0]))[0]
a2 = geom.find(str(vals[1]))[0]
geom.change_distance(a1, a2, dist=vals[2], adjust=True)
#print specified bonds
out = ""
for bond in args.measure:
a1 = geom.find(str(bond[0]))[0]
a2 = geom.find(str(bond[1]))[0]
val = a1.dist(a2)
out += "%f\n" % val