def test_RMSD(self):
ref = Geometry(TestGeometry.benz_NO2_Cl)
# RMSD of copied object should be 0
other = ref.copy()
self.assertTrue(ref.RMSD(other) < rmsd_tol(ref, superTight=True))
# if they are out of order, sorting should help
res = ref.RMSD(other, longsort=True)
self.assertTrue(res < rmsd_tol(other, superTight=True))
# RMSD of shifted copy should be 0
other = ref.copy()
other.coord_shift([1, 2, 3])
self.assertTrue(ref.RMSD(other) < rmsd_tol(ref, superTight=True))
# RMSD of rotated copy should be 0
other = ref.copy()
other.rotate([1, 2, 3], 2.8)
other.write("tmp")
self.assertTrue(ref.RMSD(other) < rmsd_tol(ref))
# RMSD of two different structures should not be 0
other = Geometry(TestGeometry.pent)
self.assertTrue(ref.RMSD(other) > 10**-2)
# RMSD of similar molecule
other = Geometry(TestGeometry.benzene)
res = ref.RMSD(other, targets="C", ref_targets="C")
self.assertTrue(res < rmsd_tol(ref))
res = ref.RMSD(other, sort=True)
def test_close_ring_approx(self):
mol = Geometry(TestGeometry.benzene)
ref1 = Geometry(TestGeometry.naphthalene)
mol1 = mol.copy()
mol1.ring_substitute(['7', '8'], RingFragment('benzene'))
rmsd = mol1.RMSD(ref1, align=True)
self.assertTrue(rmsd < rmsd_tol(ref1))
ref2 = Geometry(TestGeometry.tetrahydronaphthalene)
mol2 = mol.copy()
mol2.ring_substitute(['7', '8'], RingFragment('cyclohexane-chair.1'))
rmsd = mol2.RMSD(ref2, align=True)
self.assertTrue(rmsd < rmsd_tol(ref2))
def test_interpolate(self):
"""test interpolate.py
assumes current working directory is writable b/c interpolate doesn't
print structures to stdout"""
ref = Geometry(
os.path.join(prefix, "ref_files", "torsion_interpolation.xyz"))
args = [
sys.executable,
os.path.join(self.aarontools_bin, "interpolate.py"),
TestCLS.t60,
TestCLS.t90,
"-t",
"0.40",
"-u",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
mol = Geometry("traj-0.xyz")
os.remove("traj-0.xyz")
rmsd = mol.RMSD(ref, align=True, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref, superLoose=True))
def test_changeChirality(self):
"""test changeChirality.py"""
args = [
sys.executable,
os.path.join(self.aarontools_bin, "changeChirality.py"),
TestCLS.change_chir_1,
"--diastereomers",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")), get_all=True)
for step, ref in zip(fr.all_geom, self.change_chir_ref_1):
geom = None
for item in step:
if isinstance(item, list) and all(
isinstance(a, Atom) for a in item):
geom = Geometry(item)
if geom is None:
raise RuntimeError("an output is missing atoms")
ref_geom = Geometry(ref)
rmsd = ref_geom.RMSD(geom)
self.assertTrue(rmsd < rmsd_tol(ref_geom))
def test_RMSD(self):
ref = Geometry(TestGeometry.benz_NO2_Cl)
# RMSD of copied object should be 0
test = ref.copy()
self.assertTrue(validate(test, ref))
# RMSD of shifted copy should be 0
test = ref.copy()
test.coord_shift([1, 2, 3])
self.assertTrue(validate(test, ref))
# RMSD of rotated copy should be 0
test = ref.copy()
test.rotate([1, 2, 3], 2.8)
self.assertTrue(validate(test, ref))
# RMSD of two different structures should not be 0
test = Geometry(TestGeometry.pentane)
self.assertFalse(validate(test, ref))
# RMSD of similar molecule
test = Geometry(TestGeometry.benzene)
res = ref.RMSD(test, targets="C", ref_targets="C")
self.assertTrue(res < rmsd_tol(ref))
def test_interpolating_structure(self):
#test to see if interpolated geometry is correct
ref = Geometry(prefix + "ref_files/torsion_interpolation.xyz")
S = Pathway([self.t60, self.t90])
geom = S.Geom_func(0.4)
rmsd = geom.RMSD(ref, align=True)
self.assertTrue(rmsd < rmsd_tol(ref, superLoose=True))
def test_interpolating_structure(self):
# test to see if interpolated geometry is correct
ref = Geometry(
os.path.join(prefix, "ref_files", "torsion_interpolation.xyz"))
pathway = Pathway(self.t60, array([self.t60.coords, self.t90.coords]))
geom = pathway.geom_func(0.4)
rmsd = geom.RMSD(ref, align=True, sort=False)
self.assertTrue(rmsd < rmsd_tol(ref, superLoose=True))
def is_NO2(self, sub):
ref = TestSubstituent.NO2
self.assertEqual(sub.name, "NO2")
self.assertEqual(sub.comment, "CF:2,120")
self.assertEqual(sub.conf_num, 2)
self.assertEqual(sub.conf_angle, np.deg2rad(120))
rmsd = ref.RMSD(sub, sort=True, align=True)
self.assertTrue(rmsd < rmsd_tol(ref, superLoose=True))
return
def test_close_ring_rmsd(self):
mol = Geometry(TestGeometry.naphthalene)
ref = Geometry(TestGeometry.pyrene)
targets1 = mol.find(['9', '15'])
targets2 = mol.find(['10', '16'])
mol.ring_substitute(targets1, RingFragment('benzene'))
mol.ring_substitute(targets2, RingFragment('benzene'))
rmsd = mol.RMSD(ref, align=True)
self.assertTrue(rmsd < rmsd_tol(ref))
def is_COCH3(self, sub):
ref = TestSubstituent.COCH3
self.assertEqual(sub.name, "COCH3")
self.assertEqual(sub.comment, "CF:2,180")
self.assertEqual(sub.conf_num, 2)
self.assertEqual(sub.conf_angle, np.deg2rad(180))
rmsd = ref.RMSD(sub, longsort=True)
self.assertTrue(rmsd < rmsd_tol(ref))
return
def test_substitute(self):
ref = Geometry(TestGeometry.benz_NO2_Cl)
mol = Geometry(TestGeometry.benzene)
mol.substitute(Substituent("NO2"), "12")
mol.substitute(Substituent("Cl"), "11")
rmsd = mol.RMSD(ref, align=True)
self.assertTrue(rmsd < rmsd_tol(ref))
def test_close_ring(self):
mol = Geometry(TestGeometry.benzene)
ref1 = Geometry(TestGeometry.naphthalene)
mol1 = mol.copy()
mol1.ring_substitute(["7", "8"], Ring("benzene"))
self.assertTrue(validate(mol1, ref1, thresh="loose"))
ref2 = Geometry(TestGeometry.tetrahydronaphthalene)
mol2 = mol.copy()
mol2.ring_substitute(["7", "8"], Ring("cyclohexane"))
rmsd = mol2.RMSD(ref2, align=True, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref2, superLoose=True))
mol3 = Geometry(TestGeometry.naphthalene)
ref3 = Geometry(TestGeometry.pyrene)
targets1 = mol3.find(["9", "15"])
targets2 = mol3.find(["10", "16"])
mol3.ring_substitute(targets1, Ring("benzene"))
mol3.ring_substitute(targets2, Ring("benzene"))
rmsd = mol3.RMSD(ref3, align=True, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref3, superLoose=True))
def test_substitute(self):
mol = TestComponent.benz.copy()
benz_Cl = TestComponent.benz_Cl.copy()
benz_NO2_Cl = TestComponent.benz_NO2_Cl.copy()
benz_OH_Cl = TestComponent.benz_OH_Cl.copy()
benz_Ph_Cl = TestComponent.benz_Ph_Cl.copy()
mol.substitute(Substituent("Cl"), "11")
rmsd = mol.RMSD(benz_Cl, sort=True)
self.assertTrue(rmsd < rmsd_tol(benz_Cl))
mol.substitute(Substituent("NO2"), "12", "1")
rmsd = mol.RMSD(benz_NO2_Cl, sort=True)
self.assertTrue(rmsd < rmsd_tol(benz_NO2_Cl))
mol.substitute(Substituent("OH"), "NO2")
rmsd = mol.RMSD(benz_OH_Cl, sort=True)
self.assertTrue(rmsd < rmsd_tol(benz_OH_Cl))
mol.substitute(Substituent("Ph"), "12.*")
rmsd = mol.RMSD(benz_Ph_Cl)
self.assertTrue(rmsd < rmsd_tol(benz_Ph_Cl))
def validate(self, test, ref, thresh=None):
if thresh is None:
thresh = rmsd_tol(ref)
t_el = sorted([t.element for t in test.atoms])
r_el = sorted([r.element for r in ref.atoms])
if len(t_el) != len(r_el):
return False
for t, r in zip(t_el, r_el):
if t != r:
return False
rmsd = ref.RMSD(test, align=True)
return rmsd < thresh
def test_mirror(self):
"""test mirror.py"""
ref1 = Geometry(TestCLS.chiral_ring_mirror)
args = [
sys.executable,
os.path.join(self.aarontools_bin, "mirror.py"),
TestCLS.change_chir_1,
"-xy",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
rmsd = mol.RMSD(ref1, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref1, superLoose=True))
def test_closeRing(self):
"""test closeRing.py"""
ref1 = Geometry(TestCLS.naphthalene)
args = [
sys.executable,
os.path.join(self.aarontools_bin, "closeRing.py"),
TestCLS.benzene,
"-r",
"7",
"8",
"benzene",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
rmsd = mol.RMSD(ref1, sort=True)
self.assertTrue(rmsd < rmsd_tol(ref1, superLoose=True))
def test_rotate(self):
"""test rotate.py"""
ref = Geometry(TestCLS.chlorotoluene_ref)
# range of targets
args = [
sys.executable,
os.path.join(self.aarontools_bin, "rotate.py"),
TestCLS.chlorotoluene,
"-b",
"3",
"12",
"-c",
"3",
"-t",
"12-15",
"-a",
"180",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
rmsd = mol.RMSD(ref, align=True)
self.assertTrue(rmsd < rmsd_tol(ref))
# enumerate all targets
args = [
sys.executable,
os.path.join(self.aarontools_bin, "rotate.py"),
TestCLS.chlorotoluene,
"-b",
"3",
"12",
"-c",
"3",
"-t",
"12,13,14,15",
"-a",
"180",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
rmsd = mol.RMSD(ref, align=True)
self.assertTrue(rmsd < rmsd_tol(ref))
# rotate all atom by 180 - rmsd should be basically 0
ref2 = Geometry(TestCLS.chlorotoluene)
args = [
sys.executable,
os.path.join(self.aarontools_bin, "rotate.py"),
TestCLS.chlorotoluene,
"-x",
"x",
"-a",
"180",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
rmsd = mol.RMSD(ref2, align=True)
self.assertTrue(rmsd < rmsd_tol(ref2))
# rotate one fragment
ref3 = Geometry(TestCLS.benzene_dimer_ref)
args = [
sys.executable,
os.path.join(self.aarontools_bin, "rotate.py"),
TestCLS.benzene_dimer,
"-p",
"1-12",
"-c",
"1-12",
"-f",
"1",
"-a",
"10",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
raise RuntimeError(err)
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
rmsd = mol.RMSD(ref3, align=True)
self.assertTrue(rmsd < rmsd_tol(ref3))