A complete java program, using the api, is shown below.
import tailor.description.DescriptionFactory;
import tailor.engine.BasicEngine;
import tailor.engine.Engine;
import tailor.engine.Run;
public class SimpleExample {
public static void main(String[] args) {
String path = args[0];
DescriptionFactory factory = new DescriptionFactory();
factory.addResidues(4);
factory.addHBondCondition(3.5, 90.0, 90.0, 3, 0);
Run run = new Run(path);
run.addMeasure(factory.createPhiMeasure("psi2", 2));
run.addMeasure(factory.createPsiMeasure("phi2", 2));
run.addDescription(factory.getProduct());
Engine engine = new BasicEngine();
engine.run(run);
}
}
This code is making a very simple 4-residue description, with the condition that it have a backbone hydrogen bond from the CO of residue i + 4 to the NH of residue i. It then sets two torsion measures - phi and psi of residue 2 and runs against the file(s) represented by path
.
Most of these calls are to convenience methods, especially those to the DescriptionFactory
. For more complex descriptions, the relevant objects can be created directly. Or, for more advanced use, entirely new measures can be defined as classes that implement the Measure
interface.