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Fig. 29 | Journal of Cheminformatics

Fig. 29

From: PubChem atom environments

Fig. 29

Aromaticity and connectivity in atom environment generation. a Influence of aromaticity perception annotation on atom and bond types using the example of aniline (CID 6115). If atom environments with radius r = 1 are generated around the highlighted atoms without aromaticity perception and annotation prior to atom environment generation, the resulting environments are not identical. Aromaticity perception and annotation and subsequent atom environment generation yields the intended result of two identical instances of the same environment. b Influence of encoding on connectivity information in atom types using the example of trimethylamine (CID 1146) and promazine (CID 4926). Dashed circles indicate atom environments of radius r = 1 that have identical element connectivity ‘N(C)(C)(C)’. b i If only the respective atomic number is considered as atom property, the three indicated atom environments cannot be distinguished. b ii Expanding the atom types to connectivity by including number of implicit hydrogen atom counts, explicit degree and valence allows to recognize all three fragments as being different. Light gray bonds for clarification of connectivity and valence.

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