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Some misc cleanup. I was trying to debug the builder3d code for another patch and got annoyed with it's slowness. I still think we should deprecate it but anyways:
Currently
testModelBuilder3D_reserpine: ~27s
After Patch
testModelBuilder3D_reserpine: ~3s
Incidentally do you know where the 3D templates came from? I could get that 3 seconds down to under 1 second if I could convert to SMILES but the ringTemplateStructures.sdf.gz has some crazyness it in, lots of random isotopes and 5 valent carbons, aromatic query bonds etc. I can convert most of the structures but I worry at what the contents is, look here at these first entries, lots of Carbons with isotopes 2 or 4? Ehh?