def single_virus_gen():
"""
single_virus_gen()
Generates a virus object.
:return virus object
"""
object_texture = Texture(Pigment('color', [1, 1, 1], 'transmit', 0),
Finish('phong', 0.5, 'reflection', 0.9))
helix_test = 'f_helix1(x, y, z, 1, 1 * 4 * pi, 0.07, 0.8, 1, 0.3, 0)'
iso_spine = Isosurface(Function(helix_test), ContainedBy(Box(-5, 5)),
'translate', [0, 0, 0],
models.default_sphere_model) # spine helix
cyl = Cylinder([0, -5, 0], [0, 5, 0], 0.5,
object_texture) # spine cylinder
icosahedral = 'abs(x)+abs(y)+abs(z)-4.9'
ico_head = Isosurface(Function(icosahedral), ContainedBy(Box(-3.5, 3.5)),
'max_gradient', 5, 'translate', [0, 7, 0],
object_texture) # head object
ring = Torus(1.2, 0.3, 'translate', [0, -5, 0],
object_texture) # hip ring spine
# berelem radian, bijv: 1.05 * math.cos(radian * 3) 3 = step, 1.05 = straal
radian = (360 / 6) * (math.pi / 180)
x_tail_list = []
for coordinate_offset in range(1, 7, 2):
coordinate_offset += 0.05
x_tail_list.append(coordinate_offset) # [1.05, 3.05, 5.05]
x_axis_tail_list = []
z_axis_tail_list = []
for tail_nr in range(1, 7):
tail_steps = tail_nr
for coordinate in x_tail_list:
x_axis_tail_list.append(coordinate * math.cos(radian * tail_steps))
z_axis_tail_list.append(coordinate * math.sin(radian * tail_steps))
tails = []
for tail_coordinate in range(0, len(x_axis_tail_list), 3):
tails.append(
SphereSweep('linear_spline', 3, [
x_axis_tail_list[tail_coordinate], -5.00,
z_axis_tail_list[tail_coordinate]
], 0.1, [
x_axis_tail_list[tail_coordinate + 1], -1.00,
z_axis_tail_list[tail_coordinate + 1]
], 0.15, [
x_axis_tail_list[tail_coordinate + 2], -9.00,
z_axis_tail_list[tail_coordinate + 2]
], 0.1, object_texture))
# 6 tails
virus_object = Merge(iso_spine, ico_head, ring, cyl)
for tail in tails:
virus_object.args.append(tail)
return virus_object
def legend(start_position, axis_length):
"""
Returns the objects of a legend
:param start_position: the position where the legend is rendered
:param axis_length: the length of each line+arrow in the x, y and z direction
:return legend_objects: the objects of a legend
"""
# Reduce the AXIS_LENGTH by the length of the Cone (1) so that
# the total length is exactly the AXIS_LENGTH
axis_length -= 1
# Initialize the Cylinder END-position to a COPY of the start position
cylinder_coords_end = {
'x': list(start_position),
'y': list(start_position),
'z': list(start_position)
}
# Add the AXIS_LENGTHs to the corresponding coordinate
cylinder_coords_end['x'][0] += axis_length
cylinder_coords_end['y'][1] += axis_length
cylinder_coords_end['z'][2] += axis_length
''' CREATE THE CYLINDERS'''
cylinders = {
'x':
Cylinder(start_position, cylinder_coords_end['x'], 0.1,
Texture(Pigment('color', [1, 0, 0]), Finish('reflection',
1))),
'y':
Cylinder(start_position, cylinder_coords_end['y'], 0.1,
Texture(Pigment('color', [0, 0, 1]), Finish('reflection',
1))),
'z':
Cylinder(start_position, cylinder_coords_end['z'], 0.1,
Texture(Pigment('color', [0, 1, 0]), Finish('reflection', 1)))
}
# Cone START is the same as the Cylinder END, so we COPY these lists
cones_coords_start = {
'x': list(cylinder_coords_end['x']),
'y': list(cylinder_coords_end['y']),
'z': list(cylinder_coords_end['z'])
}
# Copy the START as END coordinate
cones_coords_end = {
'x': list(cones_coords_start['x']),
'y': list(cones_coords_start['y']),
'z': list(cones_coords_start['z'])
}
# Extend the tip of the cones with length 1
cones_coords_end['x'][0] += 1
cones_coords_end['y'][1] += 1
cones_coords_end['z'][2] += 1
''' CREATE THE CONES '''
cones = {
'x':
Cone(cones_coords_start['x'], 0.3, cones_coords_end['x'], 0,
Texture(Pigment('color', [1, 0, 0]), Finish('reflection', 1))),
'y':
Cone(cones_coords_start['y'], 0.3, cones_coords_end['y'], 0,
Texture(Pigment('color', [0, 0, 1]), Finish('reflection', 1))),
'z':
Cone(cones_coords_start['z'], 0.3, cones_coords_end['z'], 0,
Texture(Pigment('color', [0, 1, 0]), Finish('reflection', 1))),
}
# Add ALL objects to a LIST and return
legend_objects = list(cylinders.values()) + list(cones.values())
return legend_objects
def _render_structure(self, change=None):
"""Render the structure with POVRAY."""
if not isinstance(self.structure, Atoms):
return
self.render_btn.disabled = True
omat = np.array(self._viewer._camera_orientation).reshape(
4, 4).transpose()
zfactor = norm(omat[0, 0:3])
omat[0:3, 0:3] = omat[0:3, 0:3] / zfactor
bb = deepcopy(self.structure)
bb.pbc = (False, False, False)
for i in bb:
ixyz = omat[0:3, 0:3].dot(np.array([i.x, i.y, i.z]) + omat[0:3, 3])
i.x, i.y, i.z = -ixyz[0], ixyz[1], ixyz[2]
vertices = []
cell = bb.get_cell()
vertices.append(np.array([0, 0, 0]))
vertices.extend(cell)
vertices.extend([
cell[0] + cell[1],
cell[0] + cell[2],
cell[1] + cell[2],
cell[0] + cell[1] + cell[2],
])
for n, i in enumerate(vertices):
ixyz = omat[0:3, 0:3].dot(i + omat[0:3, 3])
vertices[n] = np.array([-ixyz[0], ixyz[1], ixyz[2]])
bonds = []
cutOff = neighborlist.natural_cutoffs(
bb) # Takes the cutoffs from the ASE database
neighborList = neighborlist.NeighborList(cutOff,
self_interaction=False,
bothways=False)
neighborList.update(bb)
matrix = neighborList.get_connectivity_matrix()
for k in matrix.keys():
i = bb[k[0]]
j = bb[k[1]]
v1 = np.array([i.x, i.y, i.z])
v2 = np.array([j.x, j.y, j.z])
midi = v1 + (v2 - v1) * Radius[i.symbol] / (Radius[i.symbol] +
Radius[j.symbol])
bond = Cylinder(
v1,
midi,
0.2,
Pigment("color", np.array(Colors[i.symbol])),
Finish("phong", 0.8, "reflection", 0.05),
)
bonds.append(bond)
bond = Cylinder(
v2,
midi,
0.2,
Pigment("color", np.array(Colors[j.symbol])),
Finish("phong", 0.8, "reflection", 0.05),
)
bonds.append(bond)
edges = []
for x, i in enumerate(vertices):
for j in vertices[x + 1:]:
if (norm(np.cross(i - j, vertices[1] - vertices[0])) < 0.001
or norm(np.cross(i - j,
vertices[2] - vertices[0])) < 0.001
or norm(np.cross(i - j,
vertices[3] - vertices[0])) < 0.001):
edge = Cylinder(
i,
j,
0.06,
Texture(
Pigment("color",
[212 / 255.0, 175 / 255.0, 55 / 255.0])),
Finish("phong", 0.9, "reflection", 0.01),
)
edges.append(edge)
camera = Camera(
"perspective",
"location",
[0, 0, -zfactor / 1.5],
"look_at",
[0.0, 0.0, 0.0],
)
light = LightSource([0, 0, -100.0], "color", [1.5, 1.5, 1.5])
spheres = [
Sphere(
[i.x, i.y, i.z],
Radius[i.symbol],
Texture(Pigment("color", np.array(Colors[i.symbol]))),
Finish("phong", 0.9, "reflection", 0.05),
) for i in bb
]
objects = (
[light] + spheres + edges + bonds +
[Background("color", np.array(to_rgb(self._viewer.background)))])
scene = Scene(camera, objects=objects)
fname = bb.get_chemical_formula() + ".png"
scene.render(
fname,
width=2560,
height=1440,
antialiasing=0.000,
quality=11,
remove_temp=False,
)
with open(fname, "rb") as raw:
payload = base64.b64encode(raw.read()).decode()
self._download(payload=payload, filename=fname)
self.render_btn.disabled = False