canonical isomeric SMILES

In OEChem TK, the name canonical isomeric SMILES is used for a unique SMILES string that also encodes isotopic and stereo information. Due to the unambiguity of canonical isomeric SMILES, they can be used as a universal identifier for a specific chemical structure. For generating an canonical isomeric SMILES, use the OEMolToSmiles function.


OEChem TK‘s canonical isomeric SMILES terminology corresponds to Daylight‘s ‘absolute‘ SMILES definition.

chiral atom

In OEChem TK, an atom is considered chiral, if it is connected to four different substituent groups i.e. its mirror image is non-superimposable.


In OEChem TK, an easily invertible nitrogen, i.e. a non-planar nitrogen with one attached hydrogen, is not considered to be chiral. This is due to the fact that trivalent nitrogen compound undergo rapid inversion that interconvert enantiomers.


Comma-separated-values file format.

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SMARTS is a language that allows specifying substructures by providing a number of primitive symbols describing atomic and bond properties. Atom and bond primitive specifications may be combined to form expressions by using logical operators.

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A SMILES string represents a molecule by describing only its molecular graph (i.e. atoms and bonds in the connection table, but no chiral or isotopic information). There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.

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SMIRKS is a reaction transform language.

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