5
$\begingroup$

When converting InCHI to canonical SMILES using Indigo, I will occasionally get an output SMILES string like this:

C[Si](C)C |^1:1|

What does the "|^1:1|" part mean? I can't find this explained anywhere in either SMILES grammar documentation, nor Indigo documentation, although other chemical software seem to accept it as a valid SMILES string. Any ideas on the meaning of this annotation?

Improve this question
$\endgroup$
1
  • 2
    $\begingroup$ This is part of an extended SMILES syntax used by ChemAxon. Please have a look at the docs $\endgroup$
    – Klaus-Dieter Warzecha
    Commented Mar 1, 2016 at 21:38

1 Answer 1

Reset to default
5
$\begingroup$

The SMILES syntax in question is neither mentioned in the Daylight Theory Manual, nor in the OpenSMILES specification.

It is not part of the canonical SMILES syntax, but an extension, developed by the ChemAxon company.

According to their documentation, extensions are tagged by leading and trailing | (pipe) symbols. ^1:, followed by an atom index, indicates a

monovalent radical center:

Improve this answer
$\endgroup$

Not the answer you're looking for? Browse other questions tagged or ask your own question.