def set_size(self, axis_length, axis_radius):
from chimerax.surface.shapes import cylinder_geometry, cone_geometry
vaz, naz, taz = cylinder_geometry(radius=axis_radius,
height=axis_length)
vcz, ncz, tcz = cone_geometry(radius=axis_radius * 2,
height=axis_length * 0.2,
caps=True)
from chimerax.geometry import Place
vct = Place(origin=(0, 0, axis_length / 2))
vcz = vct.transform_points(vcz)
nv = len(vaz)
tcz = tcz + nv
from numpy import concatenate
vaz = concatenate((vaz, vcz))
naz = concatenate((naz, ncz))
taz = concatenate((taz, tcz))
nv = len(vaz)
tx = Place(axes=[[0, 0, 1], [0, -1, 0], [1, 0, 0]])
vax, nax, tax = tx.transform_points(vaz), tx.transform_vectors(
naz), taz.copy() + nv
ty = Place(axes=[[1, 0, 0], [0, 0, -1], [0, 1, 0]])
vay, nay, tay = ty.transform_points(vaz), ty.transform_vectors(
naz), taz.copy() + 2 * nv
vc = self.vertex_colors
self.set_geometry(concatenate((vax, vay, vaz)),
concatenate((nax, nay, naz)),
concatenate((tax, tay, taz)))
self.vertex_colors = vc # Setting geometry clears vertex colors
def ellipsoid_geometry(center, axes, axis_lengths, num_triangles = 1000): from chimerax.surface import sphere_geometry varray, narray, tarray = sphere_geometry(num_triangles) narray = narray.copy() # Is same as varray for sphere. from chimerax.geometry import Place, scale, normalize_vectors ptf = Place(axes = axes, origin = center) * scale(axis_lengths) ptf.transform_points(varray, in_place = True) ntf = Place(axes = axes) * scale([1/l for l in axis_lengths]) ntf.transform_vectors(narray, in_place = True) normalize_vectors(narray) return varray, narray, tarray
