def test_set_dihedral(four_particle_45_twist):
mol = four_particle_45_twist
mdt.set_dihedral(mol.atoms[0], mol.atoms[1], mol.atoms[2], mol.atoms[3],
10.0 * u.degrees)
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(
u.degrees),
10.0,
decimal=8)
def test_set_dihedral_bond_no_adjust(four_particle_45_twist):
mol = four_particle_45_twist
bond = mdt.Bond(mol.atoms[1], mol.atoms[2])
mdt.set_dihedral(bond, 10.0 * u.degrees, adjustmol=False)
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(
u.degrees),
10.0,
decimal=8)
def test_set_dihedral_two_atom_selection(four_particle_45_twist):
mol = four_particle_45_twist
mdt.set_dihedral(mol.atoms[1], mol.atoms[2], 10.0 * u.degrees)
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(u.degrees),
10.0,
decimal=8)
with pytest.raises(ValueError): # raises exception because it's not part of a dihedral
mdt.set_dihedral(mol.atoms[0], mol.atoms[1], 5.0 * u.degrees)
def set_dihedral(self, *args):
bonds = self.viewer.get_selected_bonds()
bond = self.get_selected_bond(bonds)
bond_neighbors = self.get_bond_neighbors(bonds, bond)
angle = self.dihedral_slider.value
mdt.set_dihedral(bond_neighbors['a1'], bond.a1, bond.a2, bond_neighbors['a2'], angle*u.pi/180.0,
adjustmol=self.adjust_button.value)
self.viewer.set_positions()
def test_set_dihedral_two_atom_selection(four_particle_45_twist):
mol = four_particle_45_twist
mdt.set_dihedral(mol.atoms[1], mol.atoms[2], 10.0 * u.degrees)
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(
u.degrees),
10.0,
decimal=8)
with pytest.raises(
ValueError
): # raises exception because it's not part of a dihedral
mdt.set_dihedral(mol.atoms[0], mol.atoms[1], 5.0 * u.degrees)
def set_dihedral(self, *args):
bonds = self.viewer.get_selected_bonds()
bond = self.get_selected_bond(bonds)
bond_neighbors = self.get_bond_neighbors(bonds, bond)
angle = self.dihedral_slider.value
mdt.set_dihedral(bond_neighbors['a1'],
bond.a1,
bond.a2,
bond_neighbors['a2'],
angle * u.pi / 180.0,
adjustmol=self.adjust_button.value)
self.viewer.set_positions()
def set_dihedral(self, *args):
a1, a2, a3, a4 = self.viewer.selected_atoms
mdt.set_dihedral(a1, a2, a3, a4,
self.dihedral_slider.value*u.pi/180.0,
adjustmol=self.rigid_mol_selector.value)
for endpoint, atom in ((self._widgetshapes['b1']['start'], a1),
(self._widgetshapes['b3']['end'], a4)):
endpoint['x'], endpoint['y'], endpoint['z'] = atom.position.value_in(u.angstrom)
with self.viewer.hold_trait_notifications():
self.viewer.send_state('shapes')
self.viewer.set_positions()
def set_dihedral(self, *args):
a1, a2, a3, a4 = self.viewer.selected_atoms
mdt.set_dihedral(a1,
a2,
a3,
a4,
self.dihedral_slider.value * u.pi / 180.0,
adjustmol=self.rigid_mol_selector.value)
for endpoint, atom in ((self._widgetshapes['b1']['start'], a1),
(self._widgetshapes['b3']['end'], a4)):
endpoint['x'], endpoint['y'], endpoint[
'z'] = atom.position.value_in(u.angstrom)
with self.viewer.hold_trait_notifications():
self.viewer.send_state('shapes')
self.viewer.set_positions()
def test_set_dihedral_sign_convention(four_particle_45_twist):
mol = four_particle_45_twist
mdt.set_dihedral(mol.atoms[0], mol.atoms[1], mol.atoms[2], mol.atoms[3], -23.0 * u.degrees)
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(u.degrees),
337.0,
decimal=8)