cdkbook

TetrahedralIface.groovy

Source code:

@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.8')

import org.openscience.cdk.*;
import org.openscience.cdk.stereo.*;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;

isomer = new AtomContainer()
isomer.addAtom(new Atom("C"));
isomer.addAtom(new Atom("Cl"));
isomer.addAtom(new Atom("Br"));
isomer.addAtom(new Atom("F"));
isomer.addAtom(new Atom("I"));
isomer.addBond(0,1,Order.SINGLE)
isomer.addBond(0,2,Order.SINGLE)
isomer.addBond(0,3,Order.SINGLE)
isomer.addBond(0,4,Order.SINGLE)

ligands = new IAtom[4]
ligands[0] = isomer.getAtom(1)
ligands[1] = isomer.getAtom(2)
ligands[2] = isomer.getAtom(3)
ligands[3] = isomer.getAtom(4)
chirality = new TetrahedralChirality(
  isomer.getAtom(0), ligands,
  Stereo.CLOCKWISE
)

println "Central atom: " +
  chirality.chiralAtom.symbol
println "Ligand atoms: " +
  chirality.ligands[0].symbol + " " +
  chirality.ligands[1].symbol + " " +
  chirality.ligands[2].symbol + " " +
  chirality.ligands[3].symbol
println "Stereo: " +
  chirality.stereo

Output:

Central atom: C
Ligand atoms: Cl Br F I
Stereo: CLOCKWISE