I'm trying to resolve a problem with the new Molecule[] functionality in Mathematica 12.
The "AtomDiagramCoordinates" property returns 2D coordinates of the molecular graph. These coordinates can be used to overlay graphics on the molecule. However, it appears that sometimes the coordinates need an extra minus sign to be consistent with the 2D-diagram created by MoleculePlot[]:
atomCoordinatesTest[m_Molecule, sign_: + 1] :=
Show[
MoleculePlot[m],
Graphics@Disk[
sign*m["AtomDiagramCoordinates"][[3]],
0.3]]
exampleMolecules = {Molecule["Azulene"], Molecule["Phenanthrene"]};
atomCoordinatesTest[#, +1] & /@ exampleMolecules (*no sign flip needed for phenanthrene*)
atomCoordinatesTest[#, -1] & /@ exampleMolecules (*azulene needs a sign flip*)
This is all in $Version "12.0.0 for Mac OS X x86 (64-bit) (April 7, 2019)"
Am I missing something here, or is this a bug?