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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-08-09

AUTHORS

Karina van den Broek, Mirco Daniel, Matthias Epple, Hubert Kuhn, Jonas Schaub, Achim Zielesny

ABSTRACT

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. More... »

PAGES

35

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13321-018-0294-7

DOI

http://dx.doi.org/10.1186/s13321-018-0294-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1106083226

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30094683


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