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A constrained molecular graph generation with imposed and forbidden fragments

In analytical chemistry, the molecular structure generation problem consists in finding all molecular structure that are consistent with a dataset derived from different kind of spectra. The automation of this task is an important research area which has been investigated in many systems known under the name of structure elucidation systems. In this paper, we encoded this real-world problem as a constraint satisfaction problem (CSP) in order to take advantage of the flurry of efficient solution algorithms available within the constraint programming (CP) framework. The CSP encoding allowed to take into account structural constraints like inter-atom distances, imposed and forbidden fragments.