def test_change_dihedral(self):
mol = Geometry(TestGeometry.benz_NO2_Cl)
atom_args = ("13", "12", "1", "6")
original_dihedral = mol.dihedral(*atom_args)
# adjust dihedral by 30 degrees
mol.change_dihedral(*atom_args, 30, radians=False, adjust=True)
self.assertTrue(
is_close(mol.dihedral(*atom_args),
original_dihedral + np.deg2rad(30)))
# set dihedral to 60 deg
mol.change_dihedral(*atom_args, 60, radians=False)
self.assertTrue(is_close(mol.dihedral(*atom_args), np.deg2rad(60)))
# adjust using just two atoms
mol.change_dihedral("12", "1", -30, radians=False, adjust=True)
self.assertTrue(is_close(mol.dihedral(*atom_args), np.deg2rad(30)))
else:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
# set dihedral to specified value
for dihedral in args.set_ang:
vals = four_atoms_and_a_float(dihedral)
a1 = geom.find(str(vals[0]))[0]
a2 = geom.find(str(vals[1]))[0]
a3 = geom.find(str(vals[2]))[0]
a4 = geom.find(str(vals[3]))[0]
geom.change_dihedral(a1,
a2,
a3,
a4,
vals[4],
radians=args.radians,
adjust=False,
as_group=True)
#change dihedral by specified amount
for dihedral in args.change:
vals = four_atoms_and_a_float(dihedral)
a1 = geom.find(str(vals[0]))[0]
a2 = geom.find(str(vals[1]))[0]
a3 = geom.find(str(vals[2]))[0]
a4 = geom.find(str(vals[3]))[0]
geom.change_dihedral(a1,
a2,
a3,
a4,
