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.
Highlights
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 28:31–36 22
In order to support the preparation step of a molecular simulation task cheminformatics methods allow for an effective interplay of different levels of molecular encoding that are constitutive for a comfortable and safe human–machine interface: The topological structural formula is a common way used by molecular scientists to represent a chemical compound
The compound may be represented by a textual line notation—where the interplay between structural formula and line notation may be realized by mutual conversion methods like an adequate structure diagram layout
Summary
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 28:31–36 22. Weininger D, Weininger A, Weininger JL (1989) SMILES. 2. The following transition from topological representations to 3D structures allows for the final mapping to their spatial positions within a simulation box which completes the preparation step.
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