CG-BigSMILES: a line notation for coarse-grained polymers

The non-deterministic character of polymers imposes a challenge for researchers to have a machine-readable molecular representation, especially for computationally originated coarse-grained materials. Although a previous work from our lab introduces BigSMILES, an atomistic line notation that represents polymers, the problem is still open for coarse-grained polymers. Here, we propose a layer based annotation syntax, called CG-BigSMILES, as complement to the non-coarse-grained BigSMILES. This new syntax contains specific information about the type of coarse-grained model, such as Kremer-Grest, Slip Link and DPD. The detailed mapping between the group of atoms and the coarse-grained “beads”, is also allowed to indicate the molecular topology. Moreover, the syntax can represent mixtures of various solvents, small molecules and polymers as a list of components. By associating the forcefield file with the string of CG-BigSMILES, the proposed syntax allows the representation of computational materials on our recently developed data platform (CRIPT), greatly contributing to data integration and searchability in both the simulation and experimental fields for polymer science.