A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters.

Autor:	Vásquez-Pérez JM; CONACyT Research Fellow, Universidad Autónoma del Estado de Hidalgo, Pachuca42184, México., Zárate-Hernández LÁ; Department of Chemistry, Universidad Autónoma del Estado de Hidalgo, Pachuca42184, México., Gómez-Castro CZ; CONACyT Research Fellow, Universidad Autónoma del Estado de Hidalgo, Pachuca42184, México., Nolasco-Hernández UA; Department of Mathematics, Universidad Autónoma del Estado de Hidalgo, Pachuca42184, México.
Jazyk:	angličtina
Zdroj:	Journal of chemical information and modeling [J Chem Inf Model] 2023 Feb 27; Vol. 63 (4), pp. 1157-1165. Date of Electronic Publication: 2023 Feb 07.
DOI:	10.1021/acs.jcim.2c01187
Abstrakt:	We present an improved algorithm to solve the near-congruence problem for rigid molecules and clusters based on the iterative application of assignment and alignment steps with biased Euclidean costs. The algorithm is formulated as a quasi-local optimization procedure with each optimization step involving a linear assignment (LAP) and a singular value decomposition (SVD). The efficiency of the algorithm is increased by up to 5 orders of magnitude with respect to the original unbiased noniterative method and can be applied to systems with hundreds or thousands of atoms, outperforming all state-of-the-art methods published so far in the literature. The Fortran implementation of the algorithm is available as an open source library (https://github.com/qcuaeh/molalignlib) and is suitable to be used in global optimization methods for the identification of local minima or basins.
Databáze:	MEDLINE
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