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. 2022 Jul 6;14:43. doi: 10.1186/s13321-022-00627-2

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Multiscale modeling framework in LigninGraphs. Lignin structures are modeled at multiple scales (atom, monomer, polymer, and population). The left column shows the atomic or molecular representations for a a C–O bond, b an H monomer with C and O atom indices, and c a lignin polymer of 12 monomers. The right column shows the corresponding structures as atomic graphs (d–f) and big (coarse-grained) graphs (g, h). d Building blocks in atomic graphs: each C or O atom is a node, and each bond is an edge in the graph with properties saved in a dictionary format. e Atomic graph for an H monomer with node index for each C or O atom (note that the node index starts from 0 and the atom index starts from 1, i.e., the node index is equal to the corresponding atom index minus 1). In this example, node 3 is the 4th C atom and node 9 is the 10th O atom in an H monomer. They are connected by a single bond (order = 1) edge (3, 9). f Atomic graph for the lignin polymer in (c). g Big graph for an H monomer. h Big graph for the lignin polymer in (c): each monomer is a node, and each linkage is an edge. H, G, and S monomers and the atoms belonging to each type are marked in red, green, and blue, respectively