### Identify rotatable bonds ###
rotatable_bonds = struc.find_rotatable_bonds(residue.bonds)
# Do not rotate about backbone bonds,
# as these are irrelevant for a amino rotamer library
for atom_name in BACKBONE:
index = np.where(residue.atom_name == atom_name)[0][0]
rotatable_bonds.remove_bonds_to(index)
print("Rotatable bonds in tyrosine:")
for atom_i, atom_j, _ in rotatable_bonds.as_array():
print(residue.atom_name[atom_i] + " <-> " + residue.atom_name[atom_j])
### VdW radii of each atom, required for the next step ###
vdw_radii = np.zeros(residue.array_length())
for i, element in enumerate(residue.element):
vdw_radii[i] = info.vdw_radius_single(element)
# The Minimum required distance between two atoms is mean of their
# VdW radii
vdw_radii_mean = (vdw_radii[:, np.newaxis] + vdw_radii[np.newaxis, :]) / 2
### Rotate randomly about bonds ###
np.random.seed(0)
rotamer_coord = np.zeros((LIBRARY_SIZE, residue.array_length(), 3))
for i in range(LIBRARY_SIZE):
# Coordinates for the current rotamer model
coord = residue.coord.copy()
for atom_i, atom_j, _ in rotatable_bonds.as_array():
# The bond axis
axis = coord[atom_j] - coord[atom_i]
# Position of one of the involved atoms
support = coord[atom_i]
normalized_charges = charges.copy()
# Show no partial charge for atoms
# that are not parametrized for the PEOE algorithm
normalized_charges[np.isnan(normalized_charges)] = 0
# Norm charge values to highest absolute value
max_charge = np.max(np.abs(normalized_charges))
normalized_charges /= max_charge
# Transform range (-1, 1) to range (0, 1)
normalized_charges = (normalized_charges + 1) / 2
# Calculate colors
color_map = plt.get_cmap(CMAP_NAME)
colors = color_map(normalized_charges)
# Ball size should be proportional to VdW radius of the respective atom
ball_sizes = np.array(
[info.vdw_radius_single(e) for e in molecule.element]
) * BALL_SCALE
# Gradient of ray strength
# The ray size is proportional to the absolute charge value
ray_full_sizes = ball_sizes + np.abs(charges) * RAY_SCALE
ray_sizes = np.array([
np.linspace(ray_full_sizes[i], ball_sizes[i], N_RAY_STEPS, endpoint=False)
for i in range(molecule.array_length())
]).T
# The plotting begins here
fig = plt.figure(figsize=(8.0, 6.0))
ax = fig.add_subplot(111, projection="3d")
def test_single_radii():
assert strucinfo.vdw_radius_single("N") == 1.55
# Later this variable stores values between 0 and 1 for use in color map
normalized_charges = charges.copy()
# Show no partial charge for atoms
# that are not parametrized for the PEOE algorithm
normalized_charges[np.isnan(normalized_charges)] = 0
# Norm charge values to highest absolute value
max_charge = np.max(np.abs(normalized_charges))
normalized_charges /= max_charge
# Transform range (-1, 1) to range (0, 1)
normalized_charges = (normalized_charges + 1) / 2
# Calculate colors
color_map = plt.get_cmap(CMAP_NAME)
colors = color_map(normalized_charges)
# Ball size should be proportional to VdW radius of the respective atom
ball_sizes = np.array([info.vdw_radius_single(e)
for e in molecule.element]) * BALL_SCALE
# Gradient of ray strength
# The ray size is proportional to the absolute charge value
ray_full_sizes = ball_sizes + np.abs(charges) * RAY_SCALE
ray_sizes = np.array([
np.linspace(ray_full_sizes[i], ball_sizes[i], N_RAY_STEPS, endpoint=False)
for i in range(molecule.array_length())
]).T
# The plotting begins here
fig = plt.figure(figsize=(8.0, 6.0))
ax = fig.add_subplot(111, projection="3d")
# Plot the atoms