文章基本信息

标题：SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
本地全文：下载
作者：Karina van den Broek ; Mirco Daniel ; Matthias Epple 等
期刊名称：Journal of Cheminformatics
印刷版ISSN：1758-2946
电子版ISSN：1758-2946
出版年度：2018
卷号：10
期号：1
页码：35
DOI：10.1186/s13321-018-0294-7
语种：English
出版社：BioMed Central
摘要：Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and mesoscopic simulation support in combination with an open Java Graphical User Interface viewer application for visual topological inspection of SPICES definitions are provided.