CG-BigSMILES: Line Notation for Coarse-Grained Models of Polymers

The stochastic nature of polymers poses a challenge for developing machine-readable molecular representations, especially for coarse-grained computational models of materials. BigSMILES, a line notation that represents stochastic graphs, addresses this issue for atomistically resolved structures. Here, BigSMILES is extended to accommodate nonatomic particles, enabling it to represent coarse-grained models of polymers in a manner directly analogous to atomic structures. A new syntax, called coarse-grained BigSMILES (CG-BigSMILES), combines a layer-based annotation with linking to force field files to capture both chemical structures and interacting potentials, providing a complete description of coarse-grained models. The syntax allows optional definition of the mapping between the molecular structure and the coarse-grained “beads”, for both polymers and small molecules, in single- and multicomponent systems. CG-BigSMILES serves as a robust representation that allows researchers to unambiguously index coarse-grained systems in a manner analogous to that of atomistically resolved ones, enabling both types of systems to be integrated in single data structures and associated databases.