If we follow these rules, will we ever have a situation where we will automatically create bonds when the end-user did not want one?
As long as an atom was mentioned in a CONECT record the Jmol will not touch it.
But, will people have molecules with single atoms floating around that could get auto-linked together?
(Sebastian, what do you think?)
For my application, the rules you mention would do what I want, because I don't see us producing atoms with no bonds at all. I'd still be happy for a CML variant I could use to explicitly ask for "chemical intelligence" like bonds calculcation to be turned off.
Sebastian
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