def depthView(
figure,
atoms,
colormap='hot',
resolution=32,
vmax=3.5,
depth=4,
):
import numpy as np
from mayavi import mlab
input_atoms = atoms.copy()
vmin = vmax - depth
cell_center = cellCenter(input_atoms)
scale_factors = numpy.ones(len(input_atoms))*2
addDepthMap(
figure=figure,
input_atoms=input_atoms,
scale_factors=scale_factors,
colormap=colormap,
resolution=resolution,
vmin=vmin,
vmax=vmax,
)
def standardView(figure, atoms, resolution=32, scale=1):
from mayavi import mlab
input_atoms = atoms.copy()
del input_atoms.constraints
cell_center = cellCenter(input_atoms)
numbers = input_atoms.get_atomic_numbers()
u_numbers = np.unique(numbers)
vmin, vmax = input_atoms.positions[:,2].min(), input_atoms.positions[:,2].max()
vmin += (vmax - vmin)/2
for number in u_numbers:
take = np.array(numbers == number, bool)
atoms = input_atoms[take]
points = atoms.positions
points = points.transpose()
color = tuple(jmol_colors[number])
radius = my_radii[number]
if np.isnan(radius):
radius = 3.00
radius *= 2*scale
mlab.points3d(points[0], points[1], points[2], color=color,
scale_factor=radius,
resolution=resolution,
)
