I am still curious why, this kind of dubious manipulation is how errors start propagating. Anyways I can only ask twice :-). These are not depiction options but you can achieve it by modifying the molecule.
1) I think what you're asking is to get the "parent" molecule. You should define a list of the salts (counter ions) you want to remove and just remove them from the IAtomContainer. A common hack is to remove everything but the largest component (OEChem has the amusingly name: OETheFunctionFormerlyKnownAsStripSalts <https://docs.eyesopen.com/toolkits/cpp/oechemtk/OEChemFunctions/OETheFunctionFormerlyKnownAsStripSalts.html#OEChem::OETheFunctionFormerlyKnownAsStripSalts>). In CDK you would use the ConnectivityChecker <http://cdk.github.io/cdk/latest/docs/api/index.html?org/openscience/cdk/graph/ConnectivityChecker.html> sort by size and take the largest one. Note you may end up with a non-neutral form if care is not taken and if there are two components of the same size you should decide what to do. 2) Remove the stereochemistry, *container.setStereoElements(Collections.emptyList())*; prior to generating coordinates. Or if you already have coordinates, iterate over the bonds and *setStereo(IBond.Stereo.NONE)*. Depending on what you're asking you may want to set the bond order to single (*setOrder(IBond.Order.SINGLE)*) too, note this will then mess up valence and so you'd have radicals, so you'd have to sort that out etc. Again removing information from the molecule is not a good.
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