PerceiveStereo option for Bayesian class

[k-ujihara]

A flag whether to perceive stereo or not is added to Bayesian class.
Rolling back CircularFingerprinter.rubricTetrahedral(int) method is also included.

[johnmay]

What's the rollback for?

[k-ujihara]

A calculated relative x-position of implicit H of 'atom' should be stored in 'xp[3]' at the following of "// build an implicit H if necessary" line. 'x0' is just the absolute x-position of 'atom' here.
The previous code looks good.

[johnmay]

See #377, you get the wrong answer if you use that method. The better way is to use the XYZ of chiral atom.

[k-ujihara]

I understood using XYZ is better. Thanks.
But, I believe

        xp[3] = x0;
        yp[3] = y0;
        zp[3] = z0;

is corrected to

        xp[3] = 0;
        yp[3] = 0;
        zp[3] = 0;

because (xp, yp, zp) is relative position in this context .
In fact, it fails the following test.

@Test
public void testNonZZeroPlaner() throws Exception {
    IAtomContainer mol = new AtomContainer();
    Atom[] atoms = new Atom[] {
        new Atom("C"),
        new Atom("F"),
        new Atom("N"),
        new Atom("O"),
    };
    atoms[0].setPoint3d(new Point3d(0, 0, -10));
    atoms[1].setPoint3d(new Point3d(0, 1, -10));
    atoms[2].setPoint3d(new Point3d(-1, -1, -10));
    atoms[3].setPoint3d(new Point3d(1, -1, -10));
    mol.setAtoms(atoms);
    mol.addBond(0, 1, IBond.Order.SINGLE);
    mol.addBond(0, 2, IBond.Order.SINGLE);
    mol.addBond(0, 3, IBond.Order.SINGLE);
    mol.getBond(0).setStereo(IBond.Stereo.UP);
    
    CircularFingerprinter circ = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP6);
    circ.setPerceiveStereo(true);
    IBitFingerprint fp0 = circ.getBitFingerprint(mol);
    
    for (int i = 0; i < atoms.length; i++) {
        Point3d p = atoms[i].getPoint3d();
        atoms[i].setPoint3d(new Point3d(p.getX(), p.getY(), p.getZ() + 20));
    }

    IBitFingerprint fp1 = circ.getBitFingerprint(mol);
    
    Assert.assertThat(fp0, is(fp1));
}

[johnmay]

Yep you're right, could you make the patch for:

        xp[3] = 0;
        yp[3] = 0;
        zp[3] = 0;

and I'll pull that in.

[johnmay]

Perfect, thanks!