Mathematica provides the Molecule function that can be visualized with MoleculePlot3D since version 12.0. Before, importing "XYZ" files would produce a Graphics3D object immediately. In this object, the coordinates of the atom were given in picometers, but not as Quantity. Changing the units here necessitated also fiddling with the Spheres and Cylinders used for the plot, which made it rather unfeasible.
Now, a Molecule has "AtomCoordinates" which are given as QuantityArray with the unit "Angstroms". Since ModifyMolecule with "TransformAtomCoordinates" allows applying any function receiving and returning a QuantityArray, I was hopeful that a UnitConvert would work. Sadly, that seems not to be the case.Firstly,
MoleculeModify[ Molecule["Benzene"], {"TransformAtomCoordinates", UnitConvert[#, "Picometers"] &}]["AtomCoordinates"]Out[]="QuantityArray[Dimensions:{12,3},Units:Angstroms]i.e. the units seem unchanged.Plotting the molecule as
Show[MoleculePlot3D[ MoleculeModify[ Molecule["Benzene"], {"TransformAtomCoordinates", UnitConvert[#, "Picometers"] &}], PlotTheme -> "BallAndStick"], Axes -> True]where the correct plot
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becomes
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reveals that the coordinates are indeed changed in some way, but the theme cannot keep up. I guess the data gets changed, but the unit information itself gets overwritten again after the transformation?
Can anything be done in this case? Different from the old XYZ plot, it seems even harder to access the internals of a Molecule to change how it is plotted, but maybe there is an option that is either undocumented or which I missed.
