The crucial issue is I need to preserve atom labels when importing into
Jmol. So even if I could generate SMILES, it wouldn't help.
On 14 September 2014 12:53, N David Brown <[email protected]> wrote:
> Hi all,
>
> I have a custom chemical file format, representing a chemical structure as
> a set of atom labels and an adjacency matrix i.e. connectivity
> representation.
>
> I need to load this into a Jmol viewer such that I’m able to call
> Viewer#getModelSet()#getMolecules() to retrieve the molecules as a
> JmolMolecule[].
>
> I could translate this custom format to an equivalent format Jmol
> supports, but apart from SMILES I don’t know of any format that represents
> connectivity alone, i.e. no atomic coordinates.
>
> It’s not possible for me to automatically translate the custom format to
> SMILES.
>
> Aside from CIF, is there a Jmol-supported format that’s fairly simple in
> syntax, and either contains only labels and connectivity information, or
> else these plus atomic coordinates but bonding is unaffected by positions?
>
> Cheers,
>
> Dave
>
>
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