A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters
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 inv...
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| Veröffentlicht in: | Journal of chemical information and modeling 2023-02, Vol.63 (4), p.1157-1165 |
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| container_title | Journal of chemical information and modeling |
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| creator | Vásquez-Pérez, José Manuel Zárate-Hernández, Luis Ángel Gómez-Castro, Carlos Zepactonal Nolasco-Hernández, Uriel Alejandro |
| description | 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. |
| doi_str_mv | 10.1021/acs.jcim.2c01187 |
| format | Article |
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| language | eng |
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| source | ACS Publications |
| subjects | Algorithms Clusters Global optimization Local optimization Singular value decomposition |
| title | A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters |
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