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Fig. 12 | Journal of Cheminformatics

Fig. 12

From: Development of an open-source software for isomer enumeration

Fig. 12

Illustration of a potential issue with generating cis/trans SMILES strings. The depicted molecule, described by the SMILES string BrC=CC=CBr, contains two true cis/trans stereocenters. The configuration vector is [1, 1], where 1 corresponds to a cis configuration. If the configuration is included in the SMILES string by adding a ‘/’ before the first visited half-stereocenters, and adding a ‘\’ before the first visited singly-bonded neighbors of the two second half-stereocenters, the SMILES string would become Br/C=C\/C=C\Br, which is not valid. Instead, the cis/trans half stereocenters are processed in the order in which they appear in the string. For each of the half-stereocenters, it is then checked whether the corresponding first visited half-stereocenter already possesses an encoding. In this example, the string would be built as Br/C=C, then before the singly-bonded neighbor of the second carbon atom, the encoding ‘\’ is added, leading to Br/C=C\ (i.e., cis). Then, the string continues to be processed until the next cis/trans half-stereocenter is encountered, leading to Br/C=C\C=C. Since the singly-bonded neighbor of the third carbon atom is already assigned the encoding ‘\’, the corresponding encoding before the singly-bonded neighbor of the fourth carbon atom is chosen accordingly, leading to the final string Br/C=C\C=C/Br (i.e., cis and cis)

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