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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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
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author van den Broek, Karina
Daniel, Mirco
Epple, Matthias
Kuhn, Hubert
Schaub, Jonas
Zielesny, Achim
author_facet van den Broek, Karina
Daniel, Mirco
Epple, Matthias
Kuhn, Hubert
Schaub, Jonas
Zielesny, Achim
author_sort van den Broek, Karina
collection PubMed
description 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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spelling pubmed-60852182018-08-24 SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation van den Broek, Karina Daniel, Mirco Epple, Matthias Kuhn, Hubert Schaub, Jonas Zielesny, Achim J Cheminform Software 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] Springer International Publishing 2018-08-09 /pmc/articles/PMC6085218/ /pubmed/30094683 http://dx.doi.org/10.1186/s13321-018-0294-7 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
van den Broek, Karina
Daniel, Mirco
Epple, Matthias
Kuhn, Hubert
Schaub, Jonas
Zielesny, Achim
SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
title SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
title_full SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
title_fullStr SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
title_full_unstemmed SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
title_short SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation
title_sort spices: a particle-based molecular structure line notation and support library for mesoscopic simulation
topic Software
url 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
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