Source code:
@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.*;
import org.openscience.cdk.config.*;
import javax.vecmath.Point3d;
methane = new AtomContainer();
methane.addAtom(new Atom("C", new Point3d(0.0, 0.0, 0.0)));
methane.addAtom(new Atom("H", new Point3d(0.6, 0.6, 0.6)));
methane.addAtom(new Atom("H", new Point3d(-0.6,-0.6,0.6)));
methane.addAtom(new Atom("H", new Point3d(0.6,-0.6,-0.6)));
methane.addAtom(new Atom("H", new Point3d(-0.6,0.6,-0.6)));
factory = AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt",
methane.getBuilder()
);
for (IAtom atom : methane.atoms()) {
factory.configure(atom);
println "$atom.symbol -> $atom.covalentRadius"
}
Output:
C -> 0.77
H -> 0.32
H -> 0.32
H -> 0.32
H -> 0.32