def test_C1(self):
mol1 = Geometry(self.chiral_ring, refresh_ranks=False)
pg = PointGroup(mol1)
self.assertEqual(pg.name, "C1")
mol2 = Geometry(self.chiral_mol_1, refresh_ranks=False)
pg = PointGroup(mol2)
self.assertEqual(pg.name, "C1")
mol3 = Geometry(self.chiral_mol_2, refresh_ranks=False)
pg = PointGroup(mol3)
self.assertEqual(pg.name, "C1")
mol4 = Geometry(self.chiral_mol_3, refresh_ranks=False)
pg = PointGroup(mol4)
self.assertEqual(pg.name, "C1")
mol5 = Geometry(self.chiral_mol_4, refresh_ranks=False)
pg = PointGroup(mol5)
self.assertEqual(pg.name, "C1")
def test_Td(self):
mol = Geometry(self.adamantane, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "Td")
mol = Geometry(self.methane, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "Td")
def test_C2v(self):
mol = Geometry(self.h2o, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "C2v")
def test_D2d(self):
mol = Geometry(self.c3h4, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "D2d")
def test_Ih(self):
mol = Geometry(self.c60, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "Ih")
def test_S4(self):
# test to see if interpolated geometry is correct
mol = Geometry(self.Me_NO2_4, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "S4")
def test_Cs(self):
# test to see if interpolated geometry is correct
mol = Geometry(self.meoh, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "Cs")
def test_D6h(self):
# test to see if interpolated geometry is correct
mol = Geometry(self.benzene, refresh_ranks=False)
pg = PointGroup(mol)
self.assertEqual(pg.name, "D6h")
if args.input_format is not None:
infile = FileReader((f, args.input_format, None), just_geom=True)
else:
infile = FileReader(f, just_geom=True)
else:
if args.input_format is not None:
infile = FileReader(("from stdin", args.input_format[0], f),
just_geom=True)
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f), just_geom=True)
geom = Geometry(infile)
pg = PointGroup(
geom,
tolerance=args.tolerance,
rotation_tolerance=args.rotation_tolerance,
max_rotation=args.max_n,
)
if args.print_bild:
inv = ""
mirror = ""
prots = ""
irots = ""
for ele in sorted(pg.elements, reverse=True):
if isinstance(ele, InversionCenter):
inv += ".note %s\n" % repr(ele)
inv += ".sphere %.5f %.5f %.5f 0.1\n" % tuple(pg.center)
elif isinstance(ele, ProperRotation):
prots += ".note %s\n" % repr(ele)
prots += ".color red\n"
def pointGroup(
session,
selection,
printElements=False,
displayElements=True,
tolerance=0.1,
axisTolerance=0.5,
maxRotation=6,
):
for model in selection:
rescol = ResidueCollection(model, refresh_ranks=False)
pg = PointGroup(
rescol,
tolerance=tolerance,
rotation_tolerance=np.deg2rad(axisTolerance),
max_rotation=maxRotation,
)
session.logger.info("%s: %s" % (model.name, pg.name))
if printElements:
for ele in sorted(pg.elements, reverse=True):
session.logger.info(repr(ele))
if displayElements:
for ele in sorted(pg.elements, reverse=True):
if isinstance(ele, InversionCenter):
inv = ".note %s\n" % repr(ele)
inv += ".sphere %.5f %.5f %.5f 0.1\n" % tuple(
pg.center)
stream = BytesIO(bytes(inv, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
elif isinstance(ele, ProperRotation):
prots = ".note %s\n" % repr(ele)
prots += ".color red\n"
prots += ".arrow %.5f %.5f %.5f " % tuple(pg.center)
end = pg.center + ele.n * np.sqrt(ele.exp) * ele.axis
prots += "%.5f %.5f %.5f 0.05\n" % tuple(end)
stream = BytesIO(bytes(prots, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
elif isinstance(ele, ImproperRotation):
irots = ".note %s\n" % repr(ele)
irots += ".color blue\n"
irots += ".arrow %.5f %.5f %.5f " % tuple(pg.center)
end = pg.center + np.sqrt(ele.n) * np.sqrt(
ele.exp) * ele.axis
irots += "%.5f %.5f %.5f 0.05\n" % tuple(end)
irots += ".transparency 25\n"
z = ele.axis
x = perp_vector(z)
y = np.cross(x, z)
for angle in np.linspace(0, 2 * np.pi, num=250):
pt2 = ele.n**0.9 * x * np.cos(angle)
pt2 += ele.n**0.9 * y * np.sin(angle)
pt2 += pg.center
if angle > 0:
irots += ".polygon %6.3f %6.3f %6.3f" % tuple(
pt1)
irots += " %6.3f %6.3f %6.3f" % tuple(
pg.center)
irots += " %6.3f %6.3f %6.3f" % tuple(pt2)
irots += "\n"
pt1 = pt2
stream = BytesIO(bytes(irots, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)
elif isinstance(ele, MirrorPlane):
mirror = ".note %s\n" % repr(ele)
mirror += ".color purple\n"
mirror += ".transparency 25\n"
z = ele.axis
x = perp_vector(z)
y = np.cross(x, z)
for angle in np.linspace(0, 2 * np.pi, num=250):
pt2 = 5 * x * np.cos(angle)
pt2 += 5 * y * np.sin(angle)
pt2 += pg.center
if angle > 0:
mirror += ".polygon %6.3f %6.3f %6.3f" % tuple(
pt1)
mirror += " %6.3f %6.3f %6.3f" % tuple(
pg.center)
mirror += " %6.3f %6.3f %6.3f" % tuple(pt2)
mirror += "\n"
pt1 = pt2
stream = BytesIO(bytes(mirror, "utf-8"))
bild_obj, status = read_bild(session, stream, repr(ele))
session.models.add(bild_obj, parent=model)