def test_dihedral_two_atom_selection(four_particle_45_twist):
mol = four_particle_45_twist
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms[1:3]).value_in(u.degrees),
45.0,
decimal=8)
with pytest.raises(ValueError): # raises exception because it's not part of a dihedral
mdt.dihedral(mol.atoms[0], mol.atoms[1])
def test_dihedral_two_atom_selection(four_particle_45_twist):
mol = four_particle_45_twist
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms[1:3]).value_in(
u.degrees),
45.0,
decimal=8)
with pytest.raises(
ValueError
): # raises exception because it's not part of a dihedral
mdt.dihedral(mol.atoms[0], mol.atoms[1])
def test_dihedral_sign_convention(four_particle_45_twist):
mol = four_particle_45_twist
mol.atoms[-1].y += 0.4 * u.nm
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(
u.degrees),
315.0,
decimal=8)
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 _get_tool_state(self, selectedAtomIndices):
# start with everything disabled
for tool in self.atom_tools.children + self.bond_tools.children:
tool.disabled = True
if len(selectedAtomIndices) <= 0:
return (ipy.HTML('Please click on a bond or atom'), )
elif len(selectedAtomIndices) is 1:
atom = self.get_selected_atom(self.mol.atoms, selectedAtomIndices)
self.adjust_button.disabled = False
x, y, z = atom.position.value_in(u.angstrom)
self.x_slider.value = x
self.x_slider.disabled = False # for now
self.y_slider.value = y
self.y_slider.disabled = False # for now
self.z_slider.value = z
self.z_slider.disabled = False # for now
for tool in self.atom_tools.children:
tool.disabled = True
return (self.atom_tools, )
else:
bonds = self.viewer.get_selected_bonds()
bond = self.get_selected_bond(bonds)
self.adjust_button.disabled = False
# bond length
self.length_slider.value = bond.a1.distance(bond.a2).value_in(
u.angstrom)
self.length_slider.disabled = False
self.length_slider.description = '<b>Bond distance</b> <span style="color:{c1}">{a1.name}' \
' - {a2.name}</span>'.format(
a1=bond.a1, a2=bond.a2, c1=self.viewer.HIGHLIGHT_COLOR)
a1_neighbors = set(
[a for a in bond.a1.bond_graph if a is not bond.a2])
maxo = max(a1_neighbors, key=lambda x: x.mass)
bond_neighbors = self.get_bond_neighbors(bonds, bond)
# Bond angle
if bond_neighbors['a2']:
self.dihedral_slider.enable()
self.angle_slider.enable()
self.angle_slider.value = mdt.angle(
bond.a1, bond.a2, bond_neighbors['a2']).value_in(u.degrees)
# self.angle_slider.observe(self.set_angle, 'value')
self.angle_slider.description = '<b>Bond angle</b> <span style="color:{c1}">{a1.name}' \
' - {a2.name}</span> ' \
'- <span style="color:{c2}">{a3.name}</span>'.format(
a1=bond.a1, a2=bond.a2, a3=bond_neighbors['a2'],
c1=self.viewer.HIGHLIGHT_COLOR, c2=self.NBR2HIGHLIGHT)
else:
self.dihedral_slider.disable()
self.angle_slider.disable()
self.angle_slider.description = 'no angle associated with this bond'
# self.angle_slider.unobserve(self.set_angle)
# Dihedral twist
if bond_neighbors['a2'] and bond_neighbors['a1']:
self.dihedral_slider.value = mdt.dihedral(
bond_neighbors['a1'], bond.a1, bond.a2,
bond_neighbors['a2']).value_in(u.degrees)
# self.dihedral_slider.observe(self.set_dihedral, 'value')
self.dihedral_slider.description = '<b>Dihedral angle</b> <span style="color:{c0}">{a4.name}</span>' \
' - <span style="color:{c1}">{a1.name}' \
' - {a2.name}</span> ' \
'- <span style="color:{c2}">{a3.name}</span>'.format(
a4=bond_neighbors['a1'], a1=bond.a1, a2=bond.a2, a3=bond_neighbors['a2'],
c0=self.NBR1HIGHLIGHT, c1=self.viewer.HIGHLIGHT_COLOR,
c2=self.NBR2HIGHLIGHT)
else:
self.dihedral_slider.description = 'not a torsion bond'
# self.dihedral_slider.unobserve(self.set_dihedral)
self.dihedral_slider.disabled = True
return [self.bond_tools]
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)
def test_dihedral_measure(four_particle_45_twist):
mol = four_particle_45_twist
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(u.degrees),
45.0,
decimal=8)
def test_dihedral_sign_convention(four_particle_45_twist):
mol = four_particle_45_twist
mol.atoms[-1].y += 0.4 * u.nm
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(u.degrees),
315.0,
decimal=8)
def dihedral(self, a1, a2, a3=None, a4=None):
a1, a2, a3, a4 = list(map(self._get_traj_atom, (a1, a2, a3, a4)))
return mdt.dihedral(a1, a2, a3, a4)
def _get_tool_state(self, selectedAtomIndices):
# start with everything disabled
for tool in self.atom_tools.children + self.bond_tools.children: tool.disabled = True
if len(selectedAtomIndices) <= 0:
return (ipy.HTML('Please click on a bond or atom'),)
elif len(selectedAtomIndices) is 1:
atom = self.get_selected_atom(self.mol.atoms, selectedAtomIndices)
self.adjust_button.disabled = False
x, y, z = atom.position.value_in(u.angstrom)
self.x_slider.value = x
self.x_slider.disabled = False # for now
self.y_slider.value = y
self.y_slider.disabled = False # for now
self.z_slider.value = z
self.z_slider.disabled = False # for now
for tool in self.atom_tools.children: tool.disabled = True
return (self.atom_tools,)
else:
bonds = self.viewer.get_selected_bonds()
bond = self.get_selected_bond(bonds)
self.adjust_button.disabled = False
# bond length
self.length_slider.value = bond.a1.distance(bond.a2).value_in(u.angstrom)
self.length_slider.disabled = False
self.length_slider.description = '<b>Bond distance</b> <span style="color:{c1}">{a1.name}' \
' - {a2.name}</span>'.format(
a1=bond.a1, a2=bond.a2, c1=self.viewer.HIGHLIGHT_COLOR)
a1_neighbors = set([a for a in bond.a1.bond_graph if a is not bond.a2])
maxo = max(a1_neighbors, key=lambda x: x.mass)
bond_neighbors = self.get_bond_neighbors(bonds, bond)
# Bond angle
if bond_neighbors['a2']:
self.dihedral_slider.enable()
self.angle_slider.enable()
self.angle_slider.value = mdt.angle(bond.a1, bond.a2, bond_neighbors['a2']).value_in(u.degrees)
# self.angle_slider.observe(self.set_angle, 'value')
self.angle_slider.description = '<b>Bond angle</b> <span style="color:{c1}">{a1.name}' \
' - {a2.name}</span> ' \
'- <span style="color:{c2}">{a3.name}</span>'.format(
a1=bond.a1, a2=bond.a2, a3=bond_neighbors['a2'],
c1=self.viewer.HIGHLIGHT_COLOR, c2=self.NBR2HIGHLIGHT)
else:
self.dihedral_slider.disable()
self.angle_slider.disable()
self.angle_slider.description = 'no angle associated with this bond'
# self.angle_slider.unobserve(self.set_angle)
# Dihedral twist
if bond_neighbors['a2'] and bond_neighbors['a1']:
self.dihedral_slider.value = mdt.dihedral(bond_neighbors['a1'], bond.a1, bond.a2, bond_neighbors['a2']).value_in(u.degrees)
# self.dihedral_slider.observe(self.set_dihedral, 'value')
self.dihedral_slider.description = '<b>Dihedral angle</b> <span style="color:{c0}">{a4.name}</span>' \
' - <span style="color:{c1}">{a1.name}' \
' - {a2.name}</span> ' \
'- <span style="color:{c2}">{a3.name}</span>'.format(
a4=bond_neighbors['a1'], a1=bond.a1, a2=bond.a2, a3=bond_neighbors['a2'],
c0=self.NBR1HIGHLIGHT, c1=self.viewer.HIGHLIGHT_COLOR,
c2=self.NBR2HIGHLIGHT)
else:
self.dihedral_slider.description = 'not a torsion bond'
# self.dihedral_slider.unobserve(self.set_dihedral)
self.dihedral_slider.disabled = True
return [self.bond_tools]
def test_dihedral_measure(four_particle_45_twist):
mol = four_particle_45_twist
np.testing.assert_almost_equal(mdt.dihedral(*mol.atoms).value_in(
u.degrees),
45.0,
decimal=8)