G'day,
I'm migrating code from CDK 1.2 to 1.4. The code I wrote (several years
ago now) for structure diagram generation still compiles and runs
against CDK 1.4 but I'm wondering whether there are better techniques
available now.
The code I use is in a utility class (of static methods):
private static final StructureDiagramGenerator SDG = new
StructureDiagramGenerator();
/**
* Layout molecule structure diagram.
*
* @param mol the molecule to layout.
* @return Laid out molecule.
*/
public static IAtomContainer layoutMolecule(final IAtomContainer mol)
{
// Layout structure.
final IAtomContainer ac = makeHydrogensImplicit(mol);
// Aromaticity.
try
{
CDKHueckelAromaticityDetector.detectAromaticity(ac);
}
catch (final CDKException e)
{
LOG.log(Level.WARNING, "Failed to calculate aromaticity", e);
}
ac.setProperties(mol.getProperties());
return layout2D(ac);
}
/**
* Lays out a 2D structure diagram.
*
* @param ac the molecule to layout.
* @return A new molecule laid out in 2D. If the molecule already
has 2D
* coordinates then it is returned unchanged. If layout
fails then null is
* returned.
*/
public static IAtomContainer layout2D(final IAtomContainer ac)
{
LOG.fine("Layout structure");
// Generate 2D coordinates?
if (GeometryTools.has2DCoordinates(ac))
{
return ac;
}
else
{
// Generate 2D structure diagram (for each connected
component).
final IAtomContainer ac2d = new AtomContainer();
final IMoleculeSet som =
ConnectivityChecker.partitionIntoMolecules(ac);
for (int n = 0;
n < som.getMoleculeCount();
n++)
{
synchronized (SDG)
{
IMolecule mol = som.getMolecule(n);
SDG.setMolecule(mol, true);
try
{
// Generate 2D coordinates for this molecule.
SDG.generateCoordinates();
mol = SDG.getMolecule();
}
catch (final Exception e)
{
LOG.log(Level.WARNING,
"Failed to generate 2D structure for "
+ ac.getID() + " (" + n + ") - using projection",
e);
Projector.project2D(mol);
}
ac2d.add(mol); // add 2D molecule.
}
}
return GeometryTools.has2DCoordinates(ac2d) ? ac2d : null;
}
}
I'm also interested in checking the currency of makeHydrogensImplicit()
but I'll ask about that in a separate message.
Thanks,
Chris.
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Registered Office : Syngenta Limited, European Regional Centre, Priestley Road,
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