def test_set_angle_noadjust(four_particle_45_twist):
mol = four_particle_45_twist
assert mdt.angle(*mol.atoms[:3]) == 90.0 * u.degrees
final = 45 * u.degrees
origpos = mol.positions.copy()
mdt.set_angle(mol.atoms[0],
mol.atoms[1],
mol.atoms[2],
final,
adjustmol=False)
assert abs(mdt.angle(*mol.atoms[:3]) - final) < 0.1 * u.degrees
assert (mol.positions[-1] == origpos[-1]).all()
def _setup_angle_tools(self, atoms):
a1, a2, a3 = atoms
self.viewer.shapes = []
# creates a temp cylinder that will be overwritten in self.set_distance
angle_normal = np.cross(a1.position-a2.position,
a3.position-a2.position)
self._widgetshapes = {
'plane': self.viewer.draw_circle(a2.position, normal=angle_normal,
radius=max(a1.distance(a2), a3.distance(a2)),
opacity=0.55, color='blue'),
'origin': self.viewer.draw_sphere(a2.position,
radius=0.5, opacity=0.85, color='green'),
'b1': self.viewer.draw_cylinder(a1.position, a2.position, radius=0.3,
opacity=0.65, color='red'),
'b2': self.viewer.draw_cylinder(a3.position, a2.position, radius=0.3,
opacity=0.65, color='red')}
self.angle_slider.value = mdt.angle(a1, a2, a3).value_in(u.degrees)
self.angle_slider.description = ANGLEDESCRIPTION.format(
a1=a1, a2=a2, a3=a3,
c1=self.viewer.HIGHLIGHT_COLOR, c2=self.NBR2HIGHLIGHT)
b1 = mdt.Bond(a1, a2)
b2 = mdt.Bond(a3, a2)
if b1.is_cyclic:
b1, b2 = b2, b1 # try to find a b1 that is not cyclic
if b1.exists and b2.exists and not b1.is_cyclic:
self.tool_holder.children = (self.rigid_mol_selector, self.angle_slider,)
else:
self.tool_holder.children = (self.angle_slider,)
self.rigid_mol_selector.value = False
def _setup_angle_tools(self, atoms):
a1, a2, a3 = atoms
self.viewer.shapes = []
# creates a temp cylinder that will be overwritten in self.set_distance
angle_normal = np.cross(a1.position - a2.position,
a3.position - a2.position)
self._widgetshapes = {
'plane':
self.viewer.draw_circle(a2.position,
normal=angle_normal,
radius=max(a1.distance(a2),
a3.distance(a2)),
opacity=0.55,
color='blue'),
'origin':
self.viewer.draw_sphere(a2.position,
radius=0.5,
opacity=0.85,
color='green'),
'b1':
self.viewer.draw_cylinder(a1.position,
a2.position,
radius=0.3,
opacity=0.65,
color='red'),
'b2':
self.viewer.draw_cylinder(a3.position,
a2.position,
radius=0.3,
opacity=0.65,
color='red')
}
self.angle_slider.value = mdt.angle(a1, a2, a3).value_in(u.degrees)
self.angle_slider.description = ANGLEDESCRIPTION.format(
a1=a1,
a2=a2,
a3=a3,
c1=self.viewer.HIGHLIGHT_COLOR,
c2=self.NBR2HIGHLIGHT)
b1 = mdt.Bond(a1, a2)
b2 = mdt.Bond(a3, a2)
if b1.is_cyclic:
b1, b2 = b2, b1 # try to find a b1 that is not cyclic
if b1.exists and b2.exists and not b1.is_cyclic:
self.tool_holder.children = (
self.rigid_mol_selector,
self.angle_slider,
)
else:
self.tool_holder.children = (self.angle_slider, )
self.rigid_mol_selector.value = False
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_angle_measure(three_particle_right_angle):
mol = three_particle_right_angle
np.testing.assert_almost_equal(mdt.angle(*mol.atoms).value_in(u.degrees),
90.0,
decimal=8)
def angle(self, a1, a2, a3):
a1, a2, a3 = list(map(self._get_traj_atom, (a1, a2, a3)))
return mdt.angle(a1, a2, a3)
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_angle_with_monitor(three_particle_right_angle):
mol = three_particle_right_angle
ang = mdt.AngleMonitor(*mol.atoms)
ang.value = 45 * u.degrees
assert abs(mdt.angle(*mol.atoms) - (45 * u.degrees)) < 0.1 * u.degrees
def test_angle_measure(three_particle_right_angle):
mol = three_particle_right_angle
np.testing.assert_almost_equal(mdt.angle(*mol.atoms).value_in(u.degrees),
90.0,
decimal=8)