Atom Maps Semantics:


Tautomer bonds used in some systems. For example, carboxylate oxygens are chemcially equivalent, even though they are represented differently in SMILES.

CC(=[O:1])[OH:1].ClS(=O)Cl>>CC(=[O:1])Cl

  • Ambiguities in reaction mechanism.

  • Maps can be used to express the overall reactions in multi-step processes.

    [CH2:1]=[CH:2][CH2:1][CH2:3][C:4](C)[CH2:3]

  • Incomplete information.

    It is never acceptable to force a user to "make up" data in order to register a reaction.


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