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Fig. 28 | Journal of Cheminformatics

Fig. 28

From: PubChem atom environments

Fig. 28

Bond inclusion in atom environment generation. Atom environments contain all bonds between included atoms. The effect is illustrated using the example of perhydrobenzimidazole (CID 21866348), the highlighted atom is the center atom in this example. i Atom environment with radius r = 1, ii.a Atom environment with radius r = 2 without including all connecting bonds, the five-membered ring remains open, ii.b atom environment with radius r = 2, including all connecting bonds closes the five-membered ring and enables distinguishing this case from branching scenarios.

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