/**
* Reset the coordinates to their position before rendering.
*
* @param mols molecules
* @param scales how molecules were scaled
*/
private static void resetCoords(Iterable<IAtomContainer> mols, List<Double> scales) {
Iterator<Double> it = scales.iterator();
for (IAtomContainer mol : mols) {
final double factor = it.next();
if (!Double.isNaN(factor)) {
GeometryUtil.scaleMolecule(mol, 1 / factor);
} else {
for (IAtom atom : mol.atoms()) atom.setPoint2d(null);
}
}
}
/**
* 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;
}