How to define a graph using Cartesian coordinates

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For the first question, you can see the documentation of the Graph constructor by typing Graph?. You will see that it is possible to define a graph from its vertex set and a property defined by pairs of vertices that defines an edge if True:

  9. "Graph([V, f])" -- return a graph from a vertex set "V" and a *symmetric* function "f".
      The graph contains an edge u,v whenever "f(u,v)" is "True".. 
      Example: "Graph([ [1..10], lambda x,y: abs(x-y).is_square()])"

For your second question, you can use the .norm() method of vectors (since the distance between two vectors is the norm of the difference of the vectors): you can transform a tuple into a vector as follows:

sage: t=(3,4,1)
sage: v = vector(RDF, t)
sage: v.norm()
5.0990195135927845

So, you can combine everything into a one-liner as follows:

sage: d = 3
sage: L = [(0,0,0), (1,2,3), (1,1,1), (1,0,1)]
sage: G = Graph([L, lambda u,v: (vector(RDF, u)-vector(RDF, v)).norm() <= d])
sage: G
Looped graph on 4 vertices
sage: G.plot()