testsa.java

    public void testSA() throws FileNotFoundException, CDKException {
        FileInputStream fis = new FileInputStream("/Users/guhar/tmp/after_alignment.sdf");
        MDLV2000Reader reader = new MDLV2000Reader(fis, Mode.STRICT);
        IAtomContainer after = reader.read(new AtomContainer());
        fis = new FileInputStream("/Users/guhar/tmp/before_alignment.sdf");
        reader = new MDLV2000Reader(fis, Mode.STRICT);
        IAtomContainer before = reader.read(new AtomContainer());

        System.out.println(before.getProperty(CDKConstants.TITLE));
        System.out.println(after.getProperty(CDKConstants.TITLE));
        NumericalSurface saAfter = new NumericalSurface(after);
        saAfter.calculateSurface();
        NumericalSurface saBefore = new NumericalSurface(before);
        saBefore.calculateSurface();
        System.out.println(saBefore.getTotalSurfaceArea()+" <-> "+saAfter.getTotalSurfaceArea());
    }