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_geometry(self):
try:
import rdkit
geom = Geometry.from_string(
"(1R,2R)-1-Chloro-2-methylcyclohexane", form="iupac"
)
ref = TestFromString.chiral_geom
# really loose threshhold b/c rdkit can give a boat cyclohexane...
self.assertTrue(validate(geom, ref, thresh=0.35, heavy_only=True))
except (ImportError, ModuleNotFoundError):
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
geom = Geometry.from_string(
"(1R,2R)-1-Chloro-2-methylcyclohexane", form="iupac"
)
ref = TestFromString.chiral_geom
# really loose threshhold b/c rdkit can give a boat cyclohexane...
self.assertTrue(
validate(geom, ref, thresh=0.35, heavy_only=True)
)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
def test_ring(self):
try:
import rdkit
ring = Ring.from_string(
"benzene", end_length=1, end_atom="C", form="iupac"
)
ref = self.benzene
self.assertTrue(validate(ring, ref, thresh="loose"))
except ImportError:
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
ring = Ring.from_string(
"benzene", end_length=1, end_atom="C", form="iupac"
)
print(ring.comment)
ref = self.benzene
self.assertTrue(
validate(ring, ref, thresh="loose", debug=True)
)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
def test_fuseRing_copy(self):
ref1 = ResidueCollection(self.naphthalene)
ref2 = ResidueCollection(self.tetrahydronaphthalene)
run(self.session, "open %s" % self.benzene)
run(self.session, "fuseRing #1/a:1@H1 #1/a:1@H2 ring benzene modify false")
run(self.session, "fuseRing #1/a:1@H1 #1/a:1@H2 ring cyclohexane modify false")
mdl1 = self.session.models.list()[1]
rescol1 = ResidueCollection(mdl1)
mdl2 = self.session.models.list()[2]
rescol2 = ResidueCollection(mdl2)
self.assertTrue(validate(ref1, rescol1, thresh="loose"))
self.assertTrue(validate(ref2, rescol2, thresh="loose"))
def test_update_geometry(self):
test = Geometry(TestGeometry.benz_NO2_Cl)
# using coordinate matrix to update
ref = test.copy()
ref.coord_shift([-10, 0, 0])
tmp = test._stack_coords()
for t in tmp:
tmp = tmp - np.array([-10, 0, 0])
test.update_geometry(tmp)
self.assertTrue(validate(test, ref))
# using file
ref.coord_shift([10, 0, 0])
test.update_geometry(TestGeometry.benz_NO2_Cl)
self.assertTrue(validate(test, ref))
def test_substitute_copy(self):
ref1 = ResidueCollection(self.chlorobenzene)
ref2 = ResidueCollection(self.chlorobiphenyl)
run(self.session, "open %s" % self.benzene)
run(self.session,
"substitute #1/a:1@H5 substituent Cl minimize false modify false")
run(self.session,
"substitute #2/a:1@H6 substituent Ph minimize false modify false")
mdl1 = self.session.models.list()[1]
rescol1 = ResidueCollection(mdl1)
mdl2 = self.session.models.list()[2]
rescol2 = ResidueCollection(mdl2)
self.assertTrue(validate(ref1, rescol1))
self.assertTrue(validate(ref2, rescol2))
def test_sub_rotate(self):
geom = TestComponent.RQ_tBu.copy()
geom.sub_rotate("4", angle=60)
geom.sub_rotate("6", angle=60)
geom.sub_rotate("5", angle=60)
ref = Component(os.path.join(prefix, "ref_files", "sub_rotate.xyz"))
self.assertTrue(validate(geom, ref, heavy_only=True))
def test_substitute(self):
ref = Geometry(TestGeometry.benz_NO2_Cl)
mol = Geometry(TestGeometry.benzene)
mol.substitute(Substituent("NO2"), "12")
mol.substitute(Substituent("Cl"), "11")
self.assertTrue(validate(mol, 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))
self.assertTrue(validate(sub, ref))
return
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))
self.assertTrue(validate(sub, ref, thresh=1e-5))
return
def test_fuseRing_modify(self):
ref = ResidueCollection(self.naphthalene)
run(self.session, "open %s" % self.benzene)
run(self.session, "fuseRing #1/a:1@H1 #1/a:1@H2 ring benzene")
mdl = self.session.models.list()[0]
rescol = ResidueCollection(mdl)
self.assertTrue(validate(ref, rescol, thresh="loose"))
def test_substitute_modify(self):
ref = ResidueCollection(self.chlorobiphenyl)
run(self.session, "open %s" % self.benzene)
run(self.session, "substitute #1/a:1@H5 substituent Cl minimize false")
run(self.session, "substitute #1/a:1@H6 substituent Ph minimize false")
mdl = self.session.models.list()[0]
rescol = ResidueCollection(mdl)
self.assertTrue(validate(ref, rescol))
def test_minimize_torsion(self):
ref = Component(
os.path.join(prefix, "ref_files", "minimize_torsion.xyz")
)
geom = TestComponent.benz.copy()
geom.substitute(Substituent("tBu"), "12")
geom.substitute(Substituent("Ph"), "10")
geom.substitute(Substituent("OH"), "7")
geom.minimize_sub_torsion()
self.assertTrue(validate(geom, ref, heavy_only=True))
def test_substitution(self):
self.maxDiff = None
# substitute atom and fuse ring
config = Config(os.path.join(prefix, "test_files", "substitution.ini"),
quiet=True)
geom = Geometry.from_string(config["Geometry"]["structure"])
job = Job(geom, config, testing=True)
test = job.structure
ref = Geometry(
os.path.join(prefix, "ref_files", "substitution_with_rings.xyz"))
self.assertTrue(validate(test, ref, sort=True))
def test_add_sub_iter_len(self):
ref = Geometry(TestGeometry.benz_OH_Cl)
mol = Geometry(TestGeometry.benzene)
mol.debug = True
OH = ref.find(["12", "13"])
Cl = ref.find(["11"])
mol -= mol.find(["11", "12"])
mol += Cl
mol += OH
mol.refresh_connected()
mol.refresh_ranks()
self.assertTrue(validate(mol, ref, thresh="loose"))
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")
res = validate(mol, benz_Cl)
self.assertTrue(res)
mol.substitute(Substituent("NO2"), "12", "1")
res = validate(mol, benz_NO2_Cl, sort=True)
self.assertTrue(res)
mol.substitute(Substituent("OH"), "NO2")
res = validate(mol, benz_OH_Cl, sort=True)
self.assertTrue(res)
mol.substitute(Substituent("Ph"), ["12", "12.*"])
res = validate(mol, benz_Ph_Cl, sort=True, thresh="loose")
self.assertTrue(res)
def is_COCH3(self, sub, thresh=0.03):
ref = TestFromString.COCH3
ref.refresh_connected()
sub.refresh_connected()
ref.refresh_ranks()
ref.refresh_ranks()
ref.atoms = ref.reorder(start=ref.atoms[0])[0]
sub.atoms = sub.reorder(start=sub.atoms[0])[0]
self.assertTrue(
validate(
sub,
ref,
thresh=thresh,
heavy_only=True,
sort=False,
debug=False,
)
)
def test_substitute(self):
"""test substitute.py"""
ref = Geometry(TestCLS.benz_NO2_Cl)
args = [
sys.executable,
os.path.join(self.aarontools_bin, "substitute.py"),
TestCLS.benzene,
"-s",
"12=NO2",
"-s",
"11=Cl",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
# print(out.decode("utf-8"))
# print(err.decode("utf-8"))
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
self.assertTrue(validate(mol, ref))
def test_mapLigand(self):
"""test mapLigand.py"""
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_3.xyz"))
args = [
sys.executable,
os.path.join(self.aarontools_bin, "mapLigand.py"),
TestCLS.tm_simple,
"-l",
"35,36=S-tBu-BOX",
]
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)
self.assertTrue(validate(mol, ref, thresh="loose", debug=False))
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_changeElement(self):
"""test changeElement.py"""
ref = Geometry(TestCLS.pyridine)
args = [
sys.executable,
os.path.join(self.aarontools_bin, "changeElement.py"),
TestCLS.benzene,
"-e",
"1=N",
"-c",
]
proc = Popen(args, stdout=PIPE, stderr=PIPE)
out, err = proc.communicate()
if len(err) != 0:
print(out.decode("utf-8"))
print(err.decode("utf-8"))
raise RuntimeError(err.decode("utf-8"))
fr = FileReader(("out", "xyz", out.decode("utf-8")))
mol = Geometry(fr)
self.assertTrue(validate(ref, mol, thresh="loose"))
def is_NO2(self, sub):
ref = TestFromString.NO2
self.assertTrue(validate(sub, ref, thresh=2e-1))
def test_change_element(self):
mol = Geometry(TestGeometry.benzene)
ref = Geometry(TestGeometry.pyridine)
mol.change_element("1", "N", adjust_hydrogens=True)
self.assertTrue(validate(mol, ref, thresh="loose"))
def test_map_ligand(self):
monodentate = Component(TestGeometry.monodentate)
tridentate = Component(TestGeometry.tridentate)
debug = False
# import cProfile
#
# profile = cProfile.Profile()
# profile.enable()
"""
#TODO: get a reference file for this
# two monodentate -> bidentate
ptco4 = TestGeometry.ptco4.copy()
ptco4.map_ligand('EDA', ["3", "5"])
"""
# bidentate -> monodentate, none
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_1.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand(monodentate.copy(), ["35"])
self.assertTrue(
validate(tm_simple,
ref,
heavy_only=True,
thresh="loose",
debug=debug))
# bidentate -> two monodentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_2.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand([monodentate.copy(), "ACN"], ["35", "36"])
self.assertTrue(
validate(tm_simple,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# bidentate -> bidentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_3.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand("S-tBu-BOX", ["35", "36"])
self.assertTrue(
validate(tm_simple,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# tridentate -> tridentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_4.xyz"))
org_tri = Geometry(TestGeometry.org_tri)
org_tri.map_ligand(tridentate, ["30", "28", "58"])
self.assertTrue(
validate(org_tri,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# tridentate -> monodentate + bidentate -> tridentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_6.xyz"))
org_tri = Geometry(TestGeometry.org_tri)
org_tri.map_ligand(["EDA", "ACN"], ["30", "28", "58"])
self.assertTrue(
validate(org_tri,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_7.xyz"))
org_tri = Geometry(os.path.join(prefix, "ref_files", "lig_map_6.xyz"))
org_tri.map_ligand(tridentate, ["10", "11", "2"])
self.assertTrue(
validate(org_tri,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
# bidentate -> two bulky monodentate
ref = Geometry(os.path.join(prefix, "ref_files", "lig_map_5.xyz"))
tm_simple = Geometry(TestGeometry.tm_simple)
tm_simple.map_ligand(["iPr-NC3C"] * 2, ["35", "36"])
self.assertTrue(
validate(tm_simple,
ref,
thresh="loose",
heavy_only=True,
debug=debug))
