def plot(mol, save_as="null", show=True):
colors = np.zeros((mol.array_length(), 3))
colors[mol.element == "H"] = (0.8, 0.8, 0.8) # gray
colors[mol.element == "C"] = (0.0, 0.8, 0.0) # green
colors[mol.element == "N"] = (0.0, 0.0, 0.8) # blue
colors[mol.element == "O"] = (0.8, 0.0, 0.0) # red
fig = plt.figure(figsize=(8.0, 8.0))
ax = fig.add_subplot(1, 1, 1, projection="3d")
graphics.plot_atoms(ax, mol, colors, line_width=3, zoom=1.5)
ax.view_init(elev=165, azim=115)
fig.tight_layout()
if save_as != "null":
plt.savefig(save_as)
plt.close()
if show:
plt.show()
### Superimpose backbone onto first model for better visualization ###
rotamers, _ = struc.superimpose(rotamers[0],
rotamers,
atom_mask=struc.filter_backbone(rotamers))
### Visualize rotamers ###
colors = np.zeros((residue.array_length(), 3))
colors[residue.element == "H"] = (0.8, 0.8, 0.8) # gray
colors[residue.element == "C"] = (0.0, 0.8, 0.0) # green
colors[residue.element == "N"] = (0.0, 0.0, 0.8) # blue
colors[residue.element == "O"] = (0.8, 0.0, 0.0) # red
# For consistency, each subplot has the same box size
coord = rotamers.coord
size = np.array([
coord[:, :, 0].max() - coord[:, :, 0].min(), coord[:, :, 1].max() -
coord[:, :, 1].min(), coord[:, :, 2].max() - coord[:, :, 2].min()
]).max() * 0.5
fig = plt.figure(figsize=(8.0, 8.0))
fig.suptitle("Rotamers of tyrosine", fontsize=20, weight="bold")
for i, rotamer in enumerate(rotamers):
ax = fig.add_subplot(3, 3, i + 1, projection="3d")
graphics.plot_atoms(ax, rotamer, colors, line_width=3, size=size, zoom=0.9)
fig.tight_layout()
plt.show()
### Write rotamers to structure file ###
#strucio.save_structure("rotamers.pdb", rotamers)
) for base in (purine, pyrimidine)
]
pairs[i] = (purine, pyrimidine)
# Plot base pairs
# Merge bases into a single atom array
atoms = pairs[0][0] + pairs[0][1] + pairs[1][0] + pairs[1][1]
# Color by element
colors = np.zeros((atoms.array_length(), 3))
colors[atoms.element == "H"] = (0.8, 0.8, 0.8) # gray
colors[atoms.element == "C"] = (0.2, 0.2, 0.2) # darkgray
colors[atoms.element == "N"] = (0.0, 0.0, 0.8) # blue
colors[atoms.element == "O"] = (0.8, 0.0, 0.0) # red
colors[atoms.element == "P"] = (0.0, 0.6, 0.0) # green
graphics.plot_atoms(
ax, atoms, colors, line_width=3, background_color="white"
)
# Plot hydrogen bonds
for purine, pyrimidine in pairs:
pair = purine + pyrimidine
bonds = struc.hbond(pair)
for donor, hydrogen, acceptor in bonds:
hydrogen_coord = pair.coord[hydrogen]
acceptor_coord = pair.coord[acceptor]
x, y, z = zip(hydrogen_coord, acceptor_coord)
ax.plot(x, y, z, linestyle=":", color="gold", linewidth=2)
# Label bases
for pair in pairs:
for base in pair:
normal = np.cross(n1.coord - n3.coord, n1.coord - n7.coord)
# Align ring plane normal to z-axis
caffeine = struc.align_vectors(caffeine, normal, np.array([0, 0, 1]))
# Caffeine should be colored by element
colors = np.zeros((caffeine.array_length(), 3))
colors[caffeine.element == "H"] = (0.8, 0.8, 0.8) # gray
colors[caffeine.element == "C"] = (0.0, 0.8, 0.0) # green
colors[caffeine.element == "N"] = (0.0, 0.0, 0.8) # blue
colors[caffeine.element == "O"] = (0.8, 0.0, 0.0) # red
fig = plt.figure(figsize=(8.0, 8.0))
ax = fig.add_subplot(111, projection="3d")
graphics.plot_atoms(ax,
caffeine,
colors,
line_width=5,
background_color="white",
zoom=1.5)
fig.tight_layout()
# Create an animation that rotates the molecule about the x-axis
def update(angle):
ax.elev = angle
FPS = 50
DURATION = 4
angles = np.linspace(-180, 180, DURATION * FPS)
# Start at 90 degrees
angles = np.concatenate([