Abstract
Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https://bitbucket.org/sns-smartlab/proxima/src/master/.
Highlights
The goal of molecular perception algorithms is to build topological models of molecular systems starting from the minimal information conveyed by atomic symbols and coordinates, to be used for scientific visualization purposes, or for building initial guesses for quantum mechanics (QM) and/or molecular mechanics (MM) simulations
We are working on a virtual reality application, developed using the popular Unity game engine,[28] for the interactive visualization of three-dimensional
We have introduced a new molecular perception library called Proxima
Summary
The goal of molecular perception algorithms is to build topological models of molecular systems starting from the minimal information conveyed by atomic symbols and coordinates, to be used for scientific visualization purposes, or for building initial guesses for quantum mechanics (QM) and/or molecular mechanics (MM) simulations. We present Proxima, the molecular perception library under development at the SMART laboratory of Scuola Normale Superiore.[2] The purpose of Proxima is (i) to provide information about bonds, rings, atom types, and related data to imersive visualization software (e.g., Caffeine3), (ii) to compute molecular properties such as atomic charges, atomic hybridization, or hydrogen bonds, (iii) to be connected to workflow managers in order to exploit property calculations to prepare input files, and (iv) to allow user-friendly use by nonexperts. We tried to explore some innovative strategies for molecular perception like, e.g., the computation of continuous bond orders by setting sensible limits to atomic valence and taking into account uncertainty in the starting atom coordinates
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