SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation

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 mes...

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Detalles Bibliográficos
Autores principales: van den Broek, Karina, Daniel, Mirco, Epple, Matthias, Kuhn, Hubert, Schaub, Jonas, Zielesny, Achim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2018
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085218/
https://www.ncbi.nlm.nih.gov/pubmed/30094683
http://dx.doi.org/10.1186/s13321-018-0294-7
Descripción
Sumario: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. [Image: see text]

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