Question #238406 on Yade changed:
https://answers.launchpad.net/yade/+question/238406
Ricardo Pieralisi proposed the following answer:
If the spheres have different colors than the box, you can do something
like this:
C1=Vector(0,0,1) #color of the sphere
for b in O.bodies:
if b.shape.color==C1:
c=str(b.state.pos)
r=str(b.shape.radius)
f.write(c)
f.write(r)
f.write('\n')
u can use with more color too
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