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. 2023 Feb 20;15:24. doi: 10.1186/s13321-023-00694-z

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© The Author(s) 2023

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. 1 — scaffold-molecule pair dataset construction. (A) Each molecule in the dataset is decomposed hierarchically into a series of fragments with the BRICS algorithm. (B) Subsequently data pairs between input and output are created. Combinations of leaf fragments form the scaffold as input, while the whole molecule becomes the output. For clarity token colors alternate. (C) After conversion to an adjacency matrix, each molecule was represented as a graph matrix. The graph matrix contains five rows, standing for the atom type, bond type, connected atom index, atom index, and fragment index. Columns are divided in three parts to store the information of the fragment, the growing section and the linking section. (D) All tokens are collected to construct the vocabularies for SMILES-based and graph-based generators, respectively. (E) An example of the input and output matrices for the SMILES representation of scaffolds and molecules.