Source code:
@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
import java.net.UnknownHostException;
import org.openscience.cdk.*
import org.openscience.cdk.io.*
import org.openscience.cdk.silent.*
import org.openscience.cdk.tools.manipulator.*
String bf3 = "4\n" +
"Bortrifluorid\n" +
"B 0.0000 0.0000 0.0000\n" +
"F 1.0000 0.0000 0.0000\n" +
"F -0.5000 -0.8660 0.0000\n" +
"F -0.5000 0.8660 0.0000\n";
reader = new XYZReader(
new StringReader(bf3)
)
chemfile = reader.read(new ChemFile())
mol = ChemFileManipulator.getAllAtomContainers(chemfile)
.get(0)
println "Atom count: $mol.atomCount"
assert mol.atomCount == 4
Output:
Atom count: 4