title: A hierarchical algorithm for molecular similarity (H-FORMS).
abstract: A new hierarchical method to determine molecular similarity is introduced. The goal of this method is to detect if a pair of molecules has the same structure by estimating a rigid transformation that aligns the molecules and a correspondence function that matches their atoms. The algorithm firstly detect similarity based on the global spatial structure. If this analysis is not sufficient, the algorithm computes novel local structural rotation-invariant descriptors for the atom neighborhood and uses this information to match atoms. Two strategies (deterministic and stochastic) on the matching based alignment computation are tested. As a result, the atom-matching based on local similarity indexes decreases the number of testing trials and significantly reduces the dimensionality of the Hungarian assignation problem. The experiments on well-known datasets show that our proposal outperforms state-of-the-art methods in terms of the required computational time and accuracy.
authors.affiliation: Computer Science Department, Centro de Investigación en Matemáticas, A.C. Callejón Jalisco S/N, Guanajuato, Gto, Mexico.
authors.forename: Alonso
authors.initials: A
authors.lastname: Ramirez-Manzanares
authors.affiliation: Computer Science Department, Centro de Investigación en Matemáticas, A.C. Callejón Jalisco S/N, Guanajuato, Gto, Mexico.
authors.forename: Joaquin
authors.initials: J
authors.lastname: Peña
authors.affiliation: Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Donostia International Physics Center (DIPC), P. K. 1072, 20080, Donostia, Euskadi, Spain.|Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), CNR-ISTM, Via Elce di Sotto 8, 06123, Perugia, Italy.
authors.forename: Jon M
authors.initials: JM
authors.lastname: Azpiroz
authors.affiliation: Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados Unidad Mérida. Km 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex, 97310, Mérida, Yuc, México.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Merino
keywords: global descriptors; local rotation-invariant features; molecular alignment; molecular similarity