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Fig. 30 | Journal of Cheminformatics

Fig. 30

From: PubChem chemical structure standardization

Fig. 30

Functional group standardization I. If not mentioned otherwise, hydrogen atoms are as depicted and wildcard asterisks (*), representing connected any atoms, can be hydrogen atoms. Connected carbon atoms are shown without labels and should not be confused with ‘any’ connections. Parenthesis indicates terminal atom. Numbers above arrows are transformation indices for respective standardization rules (see the text for the description of transformation indices). a Oxygen and sulfur terminal; no implicit hydrogens on central atom. b Both oxygen atoms terminal, no implicit hydrogens on manipulated oxygen or center atom. c Center atom has one more explicit connection that is not further specified (with respect to bond order and adjacent atom). Oxygen is terminal, but carbon does not have to be terminal. Center atom and charged partner have no implicit hydrogen atoms. d Oxygen is terminal. Hydrogen atoms on uncharged carbon atoms are not checked. Center atom and charged partner cannot have implicit hydrogen atoms. e Ionic bond is set if situation is unambiguous, with A1 and A2 being the only matches of their kind. f No charges are assigned if A2 is di-valent oxygen or tri-valent nitrogen (after modification to ionic bond). Charge modification is incremental. Charge limit is + 1 on A1 and − 1 on A2. g No charges are assigned if A2 is di-valent oxygen or tri-valent nitrogen (after modification to ionic bond). Charge modification is incremental. Charge limit is + 2 on A1 and − 2 on A2. h Bond is annotated as dative bond. i M is a metal as defined in Fig. 28

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