/**
* Prepare a collection of molecules for rendering. If coordinates are not present they are
* generated, if coordinates exists they are scaled to be consistent (length=1.5).
*
* @param mols molecules
* @return coordinates
* @throws CDKException
*/
private List<Double> prepareCoords(Iterable<IAtomContainer> mols) throws CDKException {
List<Double> scaleFactors = new ArrayList<>();
for (IAtomContainer mol : mols) {
if (ensure2dLayout(mol)) {
scaleFactors.add(Double.NaN);
} else if (mol.getBondCount() > 0) {
final double factor = GeometryUtil.getScaleFactor(mol, 1.5);
GeometryUtil.scaleMolecule(mol, factor);
scaleFactors.add(factor);
} else {
scaleFactors.add(1d); // no bonds
}
}
return scaleFactors;
}
