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We study a class of theories in which space-time is treated classically, while interacting with quantum fields. These circumvent various no-go theorems and the pathologies of semi-classical gravity, by being linear in the density matrix and phase-space density. The theory can either be considered fundamental or as an effective theory where the classical limit is taken of space-time. The theories have the dynamics of general relativity as their classical limit and provide a way to study the back-action of quantum fields on the space-time metric. The theory is invariant under spatial diffeomorphisms, and here, we provide a methodology to derive the constraint equations of such a theory by imposing invariance of the dynamics under time-reparametrization invariance. This leads to generalisations of the Hamiltonian and momentum constraints. We compute the constraint algebra for a wide class of realisations of the theory (the "discrete class") in the case of a quantum scalar field interacting with gravity. We find that the algebra doesn't close without additional constraints, although these do not necessarily reduce the number of local degrees of freedom.