MolPainter is a novel GUI tool for constructing layered molecular systems represented using PDB files, it can be used to construct multilayer molecular systems.

MolPainter is a novel graphical tool that enables users to specifically define the location of molecules in multi-layered, planar molecular systems. MolPainter achieves this by treating each plane of a hypothetical molecular system, defined by a z-axial position, as a two dimensional grids which serve as canvases. By associating molecular structures (in PDB format) to colors, these canvases can be painted to precisely define molecular environments.

MolSolvator, the sister program of MolPainter, is a command line tool that can rapidly solvate such planar systems within the context of the lattices of the “solute” systems produced by MolPainter.

It can be installed using PIP

There is a comprehensive tutorial on GitHub

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