def draw_3D(
self,
atom_scale: float = 1,
background_color: str = "white",
point_color: str = "steelblue",
opacity: float = 0.25,
size: float = 1,
) -> None:
"""Draw a 3D representation.
Draws the molecule with the solvent accessible surface area.
Args:
atom_scale: Scaling factor for atom size
background_color: Background color for plot
point_color: Color of surface points
opacity: Point opacity
size: Point size
"""
# Set up plotter
p = BackgroundPlotter()
p.set_background(background_color)
# Draw molecule
for atom in self._atoms:
color = hex2color(jmol_colors[atom.element])
radius = atom.radius * atom_scale - self._probe_radius
sphere = pv.Sphere(center=list(atom.coordinates), radius=radius)
p.add_mesh(sphere, color=color, opacity=1, name=str(atom.index))
# Draw surface points
surface_points: Array2DFloat = np.vstack(
[atom.accessible_points for atom in self._atoms])
p.add_points(surface_points,
color=point_color,
opacity=opacity,
point_size=size)
def draw_3D(
self,
atom_scale: float = 0.5,
background_color: str = "white",
arrow_color: str = "steelblue",
) -> None:
"""Draw a 3D representation of the molecule with the Sterimol vectors.
Args:
atom_scale: Scaling factor for atom size
background_color: Background color for plot
arrow_color: Arrow color
"""
# Set up plotter
p = BackgroundPlotter()
p.set_background(background_color)
# Draw molecule
for atom in self._atoms:
color = hex2color(jmol_colors[atom.element])
if atom.element == 0:
radius = 0.5 * atom_scale
else:
radius = atom.radius * atom_scale
sphere = pv.Sphere(center=list(atom.coordinates), radius=radius)
if atom.index in self._excluded_atoms:
opacity = 0.25
else:
opacity = 1
p.add_mesh(sphere,
color=color,
opacity=opacity,
name=str(atom.index))
# Draw sphere for Buried Sterimol
if hasattr(self, "_sphere_radius"):
sphere = pv.Sphere(center=self._dummy_atom.coordinates,
radius=self._sphere_radius)
p.add_mesh(sphere, opacity=0.25)
if hasattr(self, "_points"):
p.add_points(self._points, color="gray")
# Get arrow starting points
start_L = self._dummy_atom.coordinates
start_B = self._attached_atom.coordinates
# Add L arrow with label
length = np.linalg.norm(self.L)
direction = self.L / length
stop_L = start_L + length * direction
L_arrow = get_drawing_arrow(start=start_L,
direction=direction,
length=length)
p.add_mesh(L_arrow, color=arrow_color)
# Add B_1 arrow
length = np.linalg.norm(self.B_1)
direction = self.B_1 / length
stop_B_1 = start_B + length * direction
B_1_arrow = get_drawing_arrow(start=start_B,
direction=direction,
length=length)
p.add_mesh(B_1_arrow, color=arrow_color)
# Add B_5 arrow
length = np.linalg.norm(self.B_5)
direction = self.B_5 / length
stop_B_5 = start_B + length * direction
B_5_arrow = get_drawing_arrow(start=start_B,
direction=direction,
length=length)
p.add_mesh(B_5_arrow, color=arrow_color)
# Add labels
points = np.vstack([stop_L, stop_B_1, stop_B_5])
labels = ["L", "B1", "B5"]
p.add_point_labels(
points,
labels,
text_color="black",
font_size=30,
bold=False,
show_points=False,
point_size=1,
)
self._plotter = p
