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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