[Kwant] Нow to set the coordinates of the atoms in the "2.5 Beyond square lattices: graphene"

Hi, I'm just starting to work with KWANT. I need to calculate conductivity of a graphene layer with defect (watch the picture). I have coordinates of atoms of this layer. As in an example "2.5 Beyond square lattices: graphene" to set the coordinates? -- Евгений Матусевич