SPICES

SPICES encodes particle-based molecular structures derived from simplified adaptations of the atom-based SMILES line notation to support particle-based mesoscopic simulations such as Dissipative Particle Dynamics (DPD).

Key Features:

• SMILES-derived line notation: Encodes simplified adaptations of atom-based SMILES line notation into a particle-level line representation.
• Particle-Based Representation: Represents molecules as mesoscopic particles rather than atoms for particle-based simulations.
• Encoding-Level Interplay: Maps between topological line notations, particle-graph representations, and three-dimensional structural representations.
• Particle-Graph Visualizations: Produces particle-graph representations and visualizations of topological connectivity for particle-based models.
• 3D Spatial Mapping: Supports mapping of particle models into three-dimensional coordinates and placement into a simulation box.
• Standardized Structure Definitions: Automates and standardizes structure definitions to reduce errors in manual molecular specification.
• Open Java library: Provides a Java implementation for handling SPICES structures and supporting mesoscopic simulation workflows.

Scientific Applications:

• Mesoscopic simulations: Prepares particle-based models for mesoscopic simulation techniques such as Dissipative Particle Dynamics (DPD).
• Model preparation and standardization: Standardizes and automates molecular definition workflows to minimize specification errors prior to simulation.
• Topological and particle-graph analysis: Enables inspection and analysis of topological connectivity and particle-graph representations of molecular definitions.

Methodology:

An open Java library implements handling of SPICES structures and supports mapping between simplified SMILES-like line notations, particle-graph representations, and three-dimensional spatial mapping into a simulation box.