
arXiv: 2207.08502
The most fundamental model of a molecule is a cloud of unordered atoms, even without chemical bonds that can depend on thresholds for distances and angles. The strongest equivalence between clouds of atoms is rigid motion, which is a composition of translations and rotations. The existing datasets of experimental and simulated molecules require a continuous quantification of similarity in terms of a distance metric. While clouds of m ordered points were continuously classified by Lagrange’s quadratic forms (distance matrices or Gram matrices), their extensions to m unordered points are impractical due to the exponential number of m! permutations. We propose new metrics that are continuous in general position and are computable in a polynomial time in the number m of unordered points in any Euclidean space of a fixed dimension n.
Computational Geometry (cs.CG), FOS: Computer and information sciences, Computer Science - Computational Geometry, 51F20, 51N20, 51K05, Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
Computational Geometry (cs.CG), FOS: Computer and information sciences, Computer Science - Computational Geometry, 51F20, 51N20, 51K05, Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
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